Bug fix for observed in particles, getNth and naming for contact lists

update benchmarks file and romove the unused comments in rotatingDrumMedium

DEMSystems/DEMSystem/DEMSystem.hpp

@@ -183,4 +183,4 @@ public:
 
 } // pFlow
 
-#endif // __DEMSystem_hpp__
+#endif // __DEMSystem_hpp__

README.md

@@ -1,48 +1,66 @@
-<div align ="center">
-<img src="doc/phasicFlow_logo_github.png" style="width: 400px;">
+<div align="center">
+  <img src="doc/phasicFlow_logo_github.png" style="width: 400px;" alt="PhasicFlow Logo">
 </div>
 
+## **PhasicFlow: High-Performance Discrete Element Method Simulations**
 
-**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.
+PhasicFlow is a robust, open-source C++ framework designed for the efficient simulation of granular materials using the Discrete Element Method (DEM). Leveraging parallel computing paradigms, PhasicFlow is capable of executing simulations on shared-memory multi-core architectures, including CPUs and NVIDIA GPUs (CUDA-enabled). The core parallelization strategy focuses on loop-level parallelism, enabling significant performance gains on modern hardware. Users can seamlessly transition between serial execution on standard PCs, parallel execution on multi-core CPUs (OpenMP), and accelerated simulations on GPUs. Currently, PhasicFlow supports simulations involving up to 80 million particles on a single desktop workstation. Detailed performance benchmarks are available on the [PhasicFlow Wiki](https://github.com/PhasicFlow/phasicFlow/wiki/Performance-of-phasicFlow).
 
-**MPI** parallelization with dynamic load balancing is under development. With this level of parallelization, PhasicFlow can leverage the computational power of **multi-gpu** workstations or clusters with distributed memory CPUs. 
-In summary PhasicFlow can have 6 execution modes:
-1. Serial on a single CPU core,
-2. Parallel on a multi-core computer/node (using OpenMP),
-3. Parallel on an nvidia-GPU (using Cuda),
-4. Parallel on distributed memory workstation (Using MPI)
-5. Parallel on distributed memory workstations with multi-core nodes (using MPI+OpenMP)
-6. Parallel on workstations with multiple GPUs (using MPI+Cuda).
-## How to build?
-You can build PhasicFlow for CPU and GPU executions. The latest release of PhasicFlow is v-0.1. [Here is a complete step-by-step procedure for building phasicFlow-v-0.1.](https://github.com/PhasicFlow/phasicFlow/wiki/How-to-Build-PhasicFlow).
+**Scalable Parallelism: MPI Integration**
 
-## Online code documentation
-You can find a full documentation of the code, its features, and other related materials on [online documentation of the code](https://phasicflow.github.io/phasicFlow/)
+Ongoing development includes the integration of MPI-based parallelization with dynamic load balancing. This enhancement will extend PhasicFlow's capabilities to distributed memory environments, such as multi-GPU workstations and high-performance computing clusters. Upon completion, PhasicFlow will offer six distinct execution modes:
 
-## How to use PhasicFlow?
-You can navigate into [tutorials folder](./tutorials) in the phasicFlow folder to see some simulation case setups. If you need more detailed discription, visit our [wiki page tutorials](https://github.com/PhasicFlow/phasicFlow/wiki/Tutorials).  
+1.  **Serial Execution:** Single-core CPU.
+2.  **Shared-Memory Parallelism:** Multi-core CPU (OpenMP).
+3.  **GPU Acceleration:** NVIDIA GPU (CUDA).
+4.  **Distributed-Memory Parallelism:** MPI.
+5.  **Hybrid Parallelism:** MPI + OpenMP.
+6.  **Multi-GPU Parallelism:** MPI + CUDA.
 
-## [PhasicFlowPlus](https://github.com/PhasicFlow/PhasicFlowPlus)
-PhasicFlowPlus is and extension to PhasicFlow for simulating particle-fluid systems using resolved and unresolved CFD-DEM. [See the repository of this package.](https://github.com/PhasicFlow/PhasicFlowPlus)
+# **Build and Installation**
+
+PhasicFlow can be compiled for both CPU and GPU execution.
+
+* **Current Development (v-1.0):** Comprehensive build instructions are available [here](https://github.com/PhasicFlow/phasicFlow/wiki/How-to-build-PhasicFlow%E2%80%90v%E2%80%901.0).
+* **Latest Release (v-0.1):** Detailed build instructions are available [here](https://github.com/PhasicFlow/phasicFlow/wiki/How-to-Build-PhasicFlow).
+
+# **Comprehensive Documentation**
+
+In-depth documentation, including code structure, features, and usage guidelines, is accessible via the [online documentation portal](https://phasicflow.github.io/phasicFlow/).
+
+## **Tutorials and Examples**
+
+Practical examples and simulation setups are provided in the [tutorials directory](./tutorials). For detailed explanations and step-by-step guides, please refer to the [tutorial section on the PhasicFlow Wiki](https://github.com/PhasicFlow/phasicFlow/wiki/Tutorials).
+
+# **PhasicFlowPlus: Coupled CFD-DEM Simulations**
+
+PhasicFlowPlus is an extension of PhasicFlow that facilitates the simulation of particle-fluid systems using resolved and unresolved CFD-DEM methods. The repository for PhasicFlowPlus can be found [here](https://github.com/PhasicFlow/PhasicFlowPlus).
 
 
-## Supporting packages
-* [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?
 
-## 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}
+@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}
 }
 ```
+
+# **Dependencies**
+
+PhasicFlow relies on the following external libraries:
+
+* **Kokkos:** A performance portability ecosystem developed by National Technology & Engineering Solutions of Sandia, LLC (NTESS). ([https://github.com/kokkos/kokkos](https://github.com/kokkos/kokkos))
+* **CLI11 1.8:** A command-line interface parser developed by the University of Cincinnati. ([https://github.com/CLIUtils/CLI11](https://github.com/CLIUtils/CLI11))

benchmarks/rotatingDrum_4MParticles/caseSetup/interaction

@@ -3,57 +3,58 @@
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
 
-objectName interaction;
-objectType dicrionary;
+objectName     interaction;
+objectType     dictionary;
+fileFormat     ASCII;
+
+/*---------------------------------------------------------------------------*/
 
 materials   (glassMat wallMat); // a list of materials names
+
 densities   (2500.0 2500);      // density of materials [kg/m3]
 
 contactListType   sortedContactList;
 
-model
-{
-   contactForceModel nonLinearLimited;
-   rollingFrictionModel normal;
-
-   Yeff (1.0e6 1.0e6  // Young modulus [Pa]
-               1.0e6);
-   
-   Geff (0.8e6 0.8e6  // Shear modulus [Pa]
-               0.8e6);
-
-   nu    (0.25 0.25  // Poisson's ratio [-]
-               0.25);
-
-   en (0.97  0.85   // coefficient of normal restitution
-             1.00);
-
-   et (1.0   1.0    // coefficient of tangential restitution 
-             1.0);
-
-   mu (0.65  0.65   // dynamic friction 
-             0.65);
-
-   mur (0.1  0.1    // rolling friction 
-             0.1);
-        
-}
-
 contactSearch
 {
-   method         NBS;           
-   wallMapping    cellMapping;   
+    method         NBS;
 
-   NBSInfo
-   {
-      updateFrequency 10;        // each 20 timesteps, update neighbor list 
-      sizeRatio      1.05;       // bounding box size to particle diameter (max)
-   }
+    updateInterval   10;
 
-   cellMappingInfo
-   {
-      updateFrequency 10;        // each 20 timesteps, update neighbor list  
-      cellExtent     0.6;        // bounding box for particle-wall search (> 0.5)
-   }
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;
+}
+
+model
+{
+    contactForceModel    nonLinearLimited;
+
+    rollingFrictionModel normal;
+    
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
+
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);                                    // Young modulus [Pa]
+   
+    Geff (0.8e6  0.8e6  
+                 0.8e6);                                    // Shear modulus [Pa]
+
+    nu   (0.25   0.25  
+                 0.25);                                     // Poisson's ratio [-]
+
+    en   (0.97   0.85   
+                 1.00);                                     // coefficient of normal restitution
+
+    mu   (0.65   0.65   
+                 0.65);                                     // dynamic friction 
+
+    mur  (0.1    0.1    
+                 0.1);                                      // rolling friction 
+}
 
-}

benchmarks/rotatingDrum_4MParticles/caseSetup/particleInsertion

@@ -3,12 +3,10 @@
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
 
-objectName particleInsertion;
-objectType dicrionary;
-
-
-active  no;          // is insertion active?
-
-collisionCheck No;   // not implemented for yes
+objectName     particleInsertion;
+objectType     dicrionary;
+fileFormat     ASCII;
+
+active  No;          // is insertion active?
 
 

benchmarks/rotatingDrum_4MParticles/caseSetup/shapes

@@ -2,16 +2,14 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName 	sphereDict;
-objectType 	sphereShape;
-fileFormat  ASCII;
+
+objectName     shapes;
+objectType     dictionary;
+fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
 
-// name of shapes 
-names 		(sphere1); 	
+names          (glassBead);    // names of shapes 
 
-// diameter of shapes (m)
-diameters 	(0.005);
+diameters      (0.003);        // diameter of shapes 
 
-// material name for shapes 	
-materials	(solidProperty);	
+materials      (glassMat);     // material names for shapes 

benchmarks/rotatingDrum_4MParticles/caseSetup/sphereShape

@@ -1,11 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-
-objectName 	sphereDict;
-objectType 	sphereShape;
-
-names 		(glassBead); 	// names of shapes 
-diameters 	(0.003);		// diameter of shapes 
-materials	(glassMat);		// material names for shapes 

benchmarks/rotatingDrum_4MParticles/settings/domainDict

@@ -0,0 +1,46 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     domainDict;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+{
+    min (-0.2 -0.2 -0.0);
+    max ( 0.2  0.2  1.6);
+}
+
+boundaries
+{
+    left
+    {
+        type    exit;                            // other options: periodic, reflective 
+    }
+
+    right
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    bottom
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    top
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    rear
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    front
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+}

benchmarks/rotatingDrum_4MParticles/settings/geometryDict

@@ -3,61 +3,84 @@
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
 
-objectName 	geometryDict;
-objectType 	dictionary;
+objectName     geometryDict;
+objectType     dictionary;
+fileFormat     ASCII;
 
-motionModel rotatingAxisMotion; 
+motionModel rotatingAxis;         // motion model: rotating object around an axis
+
+rotatingAxisInfo                  // information for rotatingAxisMotion motion model 
+{
+    rotAxis 
+    {
+        p1    (0.0 0.0 0.0);      // first point for the axis of rotation    
+        
+        p2    (0.0 0.0 1.0);      // second point for the axis of rotation    
+        
+        omega 1.256;              // rotation speed (rad/s) => 12 rpm
+    }
+}
 
 surfaces
 {
-	
-	cylinder
-	{
-		type cylinderWall;  
-		p1 (0.0 0.0 0.0);   
-		p2 (0.0 0.0 1.6);  
-		radius1 0.2;		
-		radius2 0.2;		
-		resolution 24;      
-		material wallMat;   
-		motion rotAxis;
-	}
+    cylinder
+    {
+        type        cylinderWall;          // type of the wall
+        
+        p1          (0.0 0.0 0.0);         // begin point of cylinder axis
+           
+        p2          (0.0 0.0 1.6);         // end point of cylinder axis
+        
+        radius1     0.2;                   // radius at p1
+        
+        radius2     0.2;                   // radius at p2
+        
+        resolution  24;                    // number of divisions
+        
+        material    wallMat;               // material name of this wall
+        
+        motion      rotAxis;               // motion component name 
+    }
 
-	
-	wall1
-	{
-		type planeWall;			
-		p1 (-0.2 -0.2 0.0);	
-		p2 ( 0.2 -0.2 0.0);   
-		p3 ( 0.2  0.2 0.0);   
-		p4 (-0.2  0.2 0.0);   
-		material wallMat;     
-		motion rotAxis;		
-	}
+    /*
+        This is a plane wall at the rear end of cylinder
+    */
+    
+    wall1
+    {
+        type      planeWall;               // type of the wall  
+        
+        p1        (-0.2 -0.2 0.0);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.0);         // second point
+        
+        p3        ( 0.2  0.2 0.0);         // third point
+        
+        p4        (-0.2  0.2 0.0);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
 
-	/*
-	This is a plane wall at the front end of cylinder
-	*/
-	wall2
-	{
-		type planeWall;
-		p1 (-0.2 -0.2 1.6);
-		p2 ( 0.2 -0.2 1.6);
-		p3 ( 0.2  0.2 1.6);
-		p4 (-0.2  0.2 1.6);
-		material wallMat;
-		motion rotAxis;
-	}
-		
+    /*
+        This is a plane wall at the front end of cylinder
+    */
+    
+    wall2
+    {
+        type      planeWall;               // type of the wall
+        
+        p1        (-0.2 -0.2 1.6);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 1.6);         // second point
+        
+        p3        ( 0.2  0.2 1.6);         // third point
+        
+        p4        (-0.2  0.2 1.6);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
 }
-
-// information for rotatingAxisMotion motion model 
-rotatingAxisMotionInfo
-{
-	rotAxis 
-	{
-		p1 (0.0 0.0 0.0);	
-		p2 (0.0 0.0 1.0);	
-		omega 1.256; 		// rotation speed (rad/s) => 12 rpm
-	}
-}

benchmarks/rotatingDrum_4MParticles/settings/particlesDict

@@ -3,42 +3,45 @@
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
 
-objectName 	particlesDict;
-objectType 	dictionary;
+objectName     particlesDict;
+objectType     dictionary;
+fileFormat     ASCII;
 
 setFields
 {
-	
-	defaultValue 
-	{
-		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)
-		shapeName 		word	glassBead; // name of the particle shape 
-	}
+    defaultValue 
+    {
+        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)
+        shapeName        word       glassBead;   // name of the particle shape 
+    }
 
-	selectors
-	{}
+    selectors
+    {}
 }
 
 positionParticles
 {
-	method positionOrdered;     		
+    method ordered;
 
-	maxNumberOfParticles 	4000001; 
-	mortonSorting 			Yes;    
+    orderedInfo
+    {
+        diameter   0.003;           // minimum space between centers of particles
+        
+        numPoints  4000000;         // number of particles in the simulation 
+        
+        axisOrder  (z x y);         // axis order for filling the space with particles
+    }
 
-	cylinder  // box for positioning particles 
-	{
-		p1 ( 0.0  0.0 0.01);    // lower corner point of the box 
-		p2 ( 0.0  0.0 1.59);	// upper corner point of the box 
-		radius 0.195;
-	}
-	
-	positionOrderedInfo
-	{
-		diameter 0.003; 	// minimum space between centers of particles
-		numPoints 4000000; 	// number of particles in the simulation 
-		axisOrder (z x y);  // axis order for filling the space with particles
-	}
+    regionType cylinder;            // other options: box and sphere    
+
+    cylinderInfo                    // cylinder for positioning particles 
+    {
+        p1     (0.0  0.0  0.01);    // lower corner point of the box 
+        
+        p2     (0.0  0.0  1.59);    // upper corner point of the box 
+        
+        radius 0.195;               // radius of cylinder 
+    }
 }

benchmarks/rotatingDrum_4MParticles/settings/settingsDict

@@ -2,31 +2,33 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
-objectName 	settingsDict;
-objectType 	dictionary;;
+objectName    settingsDict;
+objectType    dictionary;
+fileFormat    ASCII;
+/*---------------------------------------------------------------------------*/
+run             rotatingDrum_4MParticles;
 
-run 			rotatingDrum_1;
+dt              0.00001;      // time step for integration (s)
 
-dt 				0.00001; 	// time step for integration (s)
+startTime       0;            // start time for simulation 
 
-startTime 		0; 			// start time for simulation 
+endTime         10;           // end time for simulation 
 
-endTime 		10; 		// end time for simulation 
+saveInterval    0.2;          // time interval for saving the simulation
 
-saveInterval 	0.2; 		// time interval for saving the simulation
+timePrecision   5;            // maximum number of digits for time folder 
 
-timePrecision   5;			// maximum number of digits for time folder 
+g               (0 -9.8 0);   // gravity vector (m/s2) 
 
-g 				(0 -9.8 0); // gravity vector (m/s2) 
+includeObjects (diameter);                     // save necessary (i.e., required) data on disk
 
-domain 
-{
-	min (-0.2 -0.2 -0.0);
-	max ( 0.2  0.2  1.6);
-}
+// exclude unnecessary data from saving on disk
+excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
-integrationMethod 		AdamsBashforth3; 	// integration method 
+integrationMethod         AdamsBashforth2;     // integration method 
 
-timersReport 			Yes;  	
+writeFormat               binary;              // data writting format (ascii or binary)
 
-timersReportInterval   	0.01;	
+timersReport              Yes;      
+
+timersReportInterval      0.05;    

cmake/preReq.cmake

@@ -36,12 +36,12 @@ if(NOT EXISTS "${Kokkos_Source_DIR}/CMakeLists.txt")
     FetchContent_Declare(
         kokkos
         GIT_REPOSITORY https://github.com/kokkos/kokkos.git
-        GIT_TAG 4.3.01
+        GIT_TAG 4.4.01
     )
     
     FetchContent_GetProperties(kokkos)
     if(NOT kokkos_POPULATED)
-        message(STATUS "Kokkos source directory not found. Downloading Kokkos version 4.3.01 ...")
+        message(STATUS "Kokkos source directory not found. Downloading Kokkos version 4.4.1 ...")
         FetchContent_Populate(kokkos)
         set(Kokkos_Source_DIR ${kokkos_SOURCE_DIR})
     endif()

src/Interaction/contactLists/sortedContactList.hpp

@@ -80,13 +80,17 @@ public:
 
 	TypeInfoNV("sortedContactList");
 
-
-	explicit sortedContactList(uint32 initialSize =1)
+	sortedContactList(uint32 initialSize =1)
 	:
-		SortedPairs(initialSize),
-		values_("values", SortedPairs::capacity()),
-		sortedPairs0_("sortedPairs0", SortedPairs::capacity()),
-		values0_("values0", SortedPairs::capacity())
+		sortedContactList("sortedContactList", initialSize)
+	{}
+	
+	sortedContactList(const word& name, uint32 initialSize =1)
+	:
+		SortedPairs(name, initialSize),
+		values_(groupNames(name, "values"), SortedPairs::capacity()),
+		sortedPairs0_(groupNames(name, "sortedPairs0"), SortedPairs::capacity()),
+		values0_(groupNames(name, "values0"), SortedPairs::capacity())
 	{}
 
 	bool beforeBroadSearch()

src/Interaction/contactLists/sortedPairs.hpp

@@ -110,11 +110,11 @@ public:
 
 
 	// constructors
-	explicit sortedPairs(uint32 initialSize =1)
+	explicit sortedPairs(const word& name, uint32 initialSize =1)
 	:
 		UnsortedPairs(initialSize),
-		flags_("flags_",UnsortedPairs::capacity()+1),
-		sortedPairs_("sortedPairs_",UnsortedPairs::capacity())
+		flags_( groupNames(name, "flags_"), UnsortedPairs::capacity()+1),
+		sortedPairs_(groupNames(name, "sortedPairs_"), UnsortedPairs::capacity())
 	{}
 
 	

src/Interaction/contactLists/unsortedContactList.hpp

@@ -82,11 +82,16 @@ public:
 	TypeInfoNV("unsortedContactList");
 
 	explicit unsortedContactList(uint32 capacity=1)
+	:
+	unsortedContactList("unsortedContactList", capacity)
+	{}
+	
+	unsortedContactList(const word& name, uint32 capacity=1)
 	:
 		UnsortedPairs(capacity),
-		values_("values", UnsortedPairs::capacity()),
+		values_(groupNames(name, "values"), UnsortedPairs::capacity()),
 		container0_(capacity),
-		values0_("values0",container0_.capacity())
+		values0_(groupNames(name, "values0"),container0_.capacity())
 	{}
 
 

src/Interaction/contactLists/unsortedPairs.hpp

@@ -194,7 +194,9 @@ public:
 	{
 		uint newCap = container_.capacity()+len;
 		this->clear();
+		//output<<"----------------before "<<capacity()<< " " << size()<<endl;
 		container_.rehash(newCap);
+		//output<<"----------------after "<<capacity()<< " " << size()<<endl;
 	}
 
 	INLINE_FUNCTION_H

src/Interaction/contactSearch/methods/cellBased/NBS/mapperNBSKernels.cpp

@@ -21,6 +21,7 @@ Licence:
 -----------------------------------------------------------------------------*/
 
 #include "mapperNBSKernels.hpp"
+#include "streams.hpp"
 
 void pFlow::mapperNBSKernels::findPointExtends
 (
@@ -152,7 +153,9 @@ bool pFlow::mapperNBSKernels::buildLists
     const pFlagTypeDevice &flags
 )
 {
+    
     auto aRange = flags.activeRange();
+    
     auto pp = points;
     if(flags.isAllActive() )
     { 
@@ -162,7 +165,7 @@ bool pFlow::mapperNBSKernels::buildLists
             deviceRPolicyStatic(aRange.start(), aRange.end()),
             LAMBDA_HD(uint32 i)
             {               
-                auto ind = searchCell.pointIndex(pp[i]);	
+                auto ind = searchCell.pointIndex(pp[i]);
                 uint32 old = Kokkos::atomic_exchange(&head(ind.x(), ind.y(), ind.z()), i);
                 next[i] = old;
             }

src/Interaction/grainInteraction/grainInteraction/grainInteraction.cpp

@@ -41,9 +41,9 @@ bool pFlow::grainInteraction<cFM,gMM, cLT>::createGrainInteraction()
 	geometryMotion_,
 	timers());
 
-	ppContactList_ = makeUnique<ContactListType>(nPrtcl+1);
+	ppContactList_ = makeUnique<ContactListType>("Grain-Grain",nPrtcl+1);
 	
-	pwContactList_ = makeUnique<ContactListType>(nPrtcl/5+1);
+	pwContactList_ = makeUnique<ContactListType>("Grain-wall",nPrtcl/5+1);
 
 	return true;
 }

src/Interaction/sphereInteraction/sphereInteraction/sphereInteraction.cpp

@@ -41,9 +41,9 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::createSphereInteraction()
 	geometryMotion_,
 	timers());
 
-	ppContactList_ = makeUnique<ContactListType>(nPrtcl+1);
+	ppContactList_ = makeUnique<ContactListType>("sphere-sphere",nPrtcl+1);
 	
-	pwContactList_ = makeUnique<ContactListType>(nPrtcl/5+1);
+	pwContactList_ = makeUnique<ContactListType>("sphere-wall",nPrtcl/5+1);
 
 	return true;
 }

src/Particles/particles/particles.cpp

@@ -62,6 +62,12 @@ pFlow::particles::particles(systemControl& control, const shape& shapes)
 	//idHandler_().initialIdCheck();
 }
 
+pFlow::particles::~particles()
+{
+  // invalidates / unsobscribe from subscriber before its actual destruction
+  addToSubscriber(nullptr, message::Empty());
+}
+
 bool
 pFlow::particles::beforeIteration()
 {

src/Particles/particles/particles.hpp

@@ -98,6 +98,8 @@ public:
 
 	explicit particles(systemControl& control, const shape& shapes);
 
+	~particles() override; 
+
 	inline const auto& dynPointStruct() const
 	{
 		return dynPointStruct_;

src/phasicFlow/Kokkos/ViewAlgorithms.hpp

@@ -269,11 +269,19 @@ template<typename Type, typename... sProperties>
 INLINE_FUNCTION_H void
 getNth(Type& dst, const ViewType1D<Type, sProperties...>& src, const uint32 n)
 {
-	auto subV = Kokkos::subview(src, Kokkos::make_pair(n, n + 1));
-	hostViewType1D<Type> dstView("getNth", 1);
-	// hostViewTypeScalar
-	Kokkos::deep_copy(dstView, subV);
-	dst = *dstView.data();
+	using exeSpace = ViewType1D<Type, sProperties...>::execution_space;
+	if constexpr(isHostAccessible<exeSpace>())
+	{
+		dst = src[n];
+	}
+	else
+	{
+		auto subV = Kokkos::subview(src, Kokkos::make_pair(n, n + 1));
+		hostViewType1D<Type> dstView("getNth", 1);
+		// hostViewTypeScalar
+		Kokkos::deep_copy(dstView, subV);
+		dst = *dstView.data();
+	}
 }
 
 template<typename T, typename... properties>

src/phasicFlow/algorithms/algorithmFunctions.hpp

@@ -62,4 +62,4 @@ struct minimum
 
 } 
 
-#endif // __algorithmFunctions_hpp__
+#endif // __algorithmFunctions_hpp__

src/phasicFlow/algorithms/stdAlgorithms.hpp

@@ -240,4 +240,4 @@ void inclusiveScan(Type* first, DestType* dFirst, int32 numElems)
 }
 
 
-#endif //__stdAlgorithms_hpp__
+#endif //__stdAlgorithms_hpp__

src/phasicFlow/containers/List/List/ListI.hpp

@@ -270,4 +270,4 @@ inline pFlow::iIstream& pFlow::operator >>(iIstream& is, List<T>& lst)
 		fatalExit;
 	}
 	return is;
-}
+}

src/phasicFlow/containers/List/ListPtr/ListPtrI.hpp

@@ -320,4 +320,4 @@ void pFlow::ListPtr<T>::clear
 		delete p;
 		list_.erase(pos(i));
 	}
-}
+}

src/phasicFlow/containers/Map/Map/MapI.hpp

@@ -131,4 +131,4 @@ inline iOstream& printKeys(iOstream& os, const int64Map<T> & m)
 	}
 
 	return os;
-}
+}

src/phasicFlow/containers/span/span.hpp

@@ -185,4 +185,4 @@ span<const char> charSpan(span<const T> s)
 
 } // pFlow
 
-#endif //__span_hpp__
+#endif //__span_hpp__

src/phasicFlow/dictionary/fileDictionary.hpp

@@ -60,4 +60,4 @@ public:
 
 }
 
-#endif //__fileDictionary_hpp__
+#endif //__fileDictionary_hpp__

src/phasicFlow/eventManagement/subscriber.hpp

@@ -20,9 +20,8 @@ Licence:
 #ifndef __subscriber_hpp__
 #define __subscriber_hpp__
 
-
-
-#include <array>
+// from std
+#include <vector>
 
 #include "List.hpp"
 #include "message.hpp"

src/phasicFlow/processors/localProcessors.hpp

@@ -20,10 +20,13 @@ Licence:
 #ifndef __pFlowProcessors_hpp__
 #define __pFlowProcessors_hpp__
 
+// from std
+#include <vector>
 
 #include "processors.hpp"
 #include "types.hpp"
 
+// from mpi
 #ifdef pFlow_Build_MPI
     #include "mpi.h"
 #endif
@@ -158,4 +161,4 @@ public:
 
 }
 
-#endif
+#endif

src/phasicFlow/repository/IOobject/IOPattern.cpp

@@ -32,4 +32,4 @@ pFlow::IOPattern::IOPattern( IOType iotype)
 pFlow::word pFlow::IOPattern::exeMode()
 {
     return processors::globalRunTypeName();
-}
+}

src/phasicFlow/repository/Time/timeInfo.hpp

@@ -115,4 +115,4 @@ public:
 
 } // namespace pFlow
 
-#endif //__timeInfo__hpp_
+#endif //__timeInfo__hpp_

src/phasicFlow/repository/repository/repositoryTemplates.cpp

@@ -93,4 +93,4 @@ const T& pFlow::repository::lookupObject(const word& name)const
 		fatalExit;
 		return static_cast<T&>(*iter->second);
 	}
-}
+}

src/phasicFlow/streams/streams.hpp

@@ -46,4 +46,4 @@ namespace pFlow
 #define ERR pFlow::errReport<<boldChar<<redColor<<"> ERROR\n"<<defaultColor<<redColor<<"  " 
 #define END_ERR defaultColor<<pFlow::endl
 
-#endif
+#endif

src/phasicFlow/types/quadruple/quadrupleFwd.hpp

@@ -84,4 +84,4 @@ operator>>(iIstream& str, quadruple<T>& iv);
 
 template<typename T>
 INLINE_FUNCTION_H void
-readIstream(iIstream& str, quadruple<T>& iv);
+readIstream(iIstream& str, quadruple<T>& iv);

src/phasicFlow/types/quadruple/quadrupleMath.hpp

@@ -91,4 +91,4 @@ pFlow::max(const quadruple<T>& q4)
 }
 
 #undef Q4Func
-#undef Q4Func2
+#undef Q4Func2

src/phasicFlow/types/triple/tripleFwd.hpp

@@ -112,4 +112,4 @@ operator>>(iIstream& str, triple<T>& iv);
 
 template<typename T>
 inline void
-readIstream(iIstream& str, triple<T>& iv);
+readIstream(iIstream& str, triple<T>& iv);

src/phasicFlow/types/triple/tripleI.hpp

@@ -342,4 +342,4 @@ pFlow::equal(const triple<T>& opr1, const triple<T>& opr2)
 {
 	return equal(opr1.x(), opr2.x()) && equal(opr1.y(), opr2.y()) &&
 	       equal(opr1.z(), opr2.z());
-}
+}

src/phasicFlow/types/types.hpp

@@ -50,90 +50,6 @@ using realx4 = quadruple<real>;
 
 using realx4x3 = quadruple<realx3>;
 
-/*template<>
-inline word
-triple<int8>::TYPENAME()
-{
-	return "int8x3";
-}
-
-template<>
-inline word
-triple<int32>::TYPENAME()
-{
-	return "int32x3";
-}
-
-template<>
-inline word
-basicTypeName<int64x3>()
-{
-	return "int64x3";
-}
-
-template<>
-inline word
-basicTypeName<uint8x3>()
-{
-	return "uint8x3";
-}
-
-template<>
-inline word
-basicTypeName<uint32x3>()
-{
-	return "uint32x3";
-}
-
-template<>
-inline word
-basicTypeName<uint64x3>()
-{
-	return "unit64x3";
-}
-
-template<>
-inline word
-basicTypeName<realx3>()
-{
-	return "realx3";
-}
-
-template<>
-inline word
-basicTypeName<int32x3x3>()
-{
-	return "int32x3x3";
-}
-
-template<>
-inline word
-basicTypeName<uint32x3x3>()
-{
-	return "uint32x3x3";
-}
-
-template<>
-inline word
-basicTypeName<realx3x3>()
-{
-	return "realx3x3";
-}
-
-template<>
-inline word
-basicTypeName<realx4>()
-{
-	return "realx4";
-}
-
-template<>
-inline word
-basicTypeName<realx4x3>()
-{
-	return "realx4x3";
-}*/
-
 extern const realx3   zero3;
 extern const realx3   one3;
 
@@ -144,4 +60,4 @@ extern const realx4   zero4;
 
 } // pFlow
 
-#endif //__types_hpp__
+#endif //__types_hpp__

tutorials/sphereGranFlow/RotatingDrumWithBaffles/ReadMe.md

@@ -1,5 +1,5 @@
-# Problem Definition 
-The problem is to simulate a rotating drum with the diameter **0.24 m**, the length **0.1 m** and **6** Baffles, rotating at **15 rpm**. This drum is filled with **20000** Particles.The timestep for integration is **0.00001 s**. There are 2 types of Particles in this drum each are being inserted during simulation to fill the drum.
+# Problem Definition (v-1.0)
+The problem is to simulate a rotating drum with a diameter of 0.24 m, a length of 0.1 m and 6 baffles rotating at 15 rpm. This drum is filled with 20000 particles, the integration time step is 0.00001 s. There are 2 types of particles in this drum, each of which is inserted during the simulation to fill the drum.
 * **12500** Particles with **4 mm** diameter, at the rate of 12500 particles/s for 1 sec. 
 * **7500** Particles with **5mm** diameter, at the rate of 7500 particles/s for 1 sec.   
 
@@ -15,10 +15,10 @@ The problem is to simulate a rotating drum with the diameter **0.24 m**, the len
 </html>
 
 # Setting up the Case
-As it has been explained in the previous cases, the simulation case setup is based on text-based scripts. Here, the simulation case setup are sotred in three folders: `caseSetup`, `setting` and `stl` (see the above folders). 
+As it has been explained in the previous cases, the simulation case setup is based on text-based scripts. Here, the simulation case setup are sorted in three folders: `caseSetup`, `setting` and `stl`. 
 
 ## Defining small and large particles 
-Then in the `caseSetup/sphereShape` the diameter and the material name of the particles are defined.  Two sizes are defined: 4 and 5 mm. 
+Then in the `caseSetup/shapes` the diameter and the material name of the particles are defined.  Two sizes are defined: 4 and 5 mm. 
 ```C++
 // names of shapes 
 names 		(smallSphere largeSphere);
@@ -30,7 +30,7 @@ materials	(lightMat heavyMat);
 
 
 ## Particle Insertion
-In this case we have two region for inserting our particles. In the both region we define rate of insertion, start and end time of insertion, information for the volume of the space throught which particles are being inserted. The insertion phase in the simulation is performed between times 0 and 1 seconds.   
+In this case we have two regions for inserting the particles. In both regions we define the insertion rate, the start and end time of the insertion, information about the volume of space through which the particles are inserted. The insertion phase in the simulation is performed between times 0 and 1 second.   
 For example, for the insertion region for inserting light particles is shown below.
 
 <div align="center"> 
@@ -43,7 +43,8 @@ in <b>caseSetup/particleInsertion</b> file
 layerrightregion 
 {
 // type of insertion region
-   type	          cylinderRegion;
+   timeControl           simulationTime;
+   regionType	           cylinder;
 // insertion rate (particles/s)    
    rate 	  12500;
 // Start time of LightParticles insertion (s)
@@ -51,9 +52,9 @@ layerrightregion
 // End time of LightParticles insertion (s)      
    endTime   	  1;
 // Time Interval of LightParticles insertion (s)
-   interval       0.025; 
+   insertionInterval       0.025; 
 
-   cylinderRegionInfo 
+   cylinderInfo 
    {
 // Coordinates of cylinderRegion (m,m,m)
    	p2 (-0.15 0.25 0.05);
@@ -64,7 +65,7 @@ layerrightregion
 }
 ```
 ## Interaction between particles and walls
-In `caseSetup/interaction` file, material names and properties and interaction parameters are defined: interaction between the particles and the shell of rotating drum. Since we are defining 3 materials for simulation, the interaction matrix is 3x3, while we are only required to enter upper-triangle elements (interactions are symetric). 
+The `caseSetup/interaction` file defines the material names and properties as well as the interaction parameters: the interaction between the particles and the shell of the rotating drum. Since we define 3 materials for simulation, the interaction matrix is 3x3, while we only need to enter upper triangle elements (interactions are symmetric). 
 
 ```C++
 // a list of materials names
@@ -93,10 +94,6 @@ densities   (1000 1500 2500);
    en (0.97  0.97    0.85   
              0.97    0.85
                      1.00);
-// coefficient of tangential restitution
-   et (1.0   1.0  1.0    
-             1.0  1.0
-                  1.0);
 // dynamic friction 
    mu (0.65   0.65 0.35   
               0.65 0.35
@@ -166,7 +163,8 @@ surfaces
 In this part of `geometryDict` the information of rotating axis and speed of rotation are defined. The start of rotation is at 2 s. The first 2 seconds of simulation is for allowing particles to settle donw in the drum. 
 
 ```C++
-rotatingAxisMotionInfo
+motionModel rotatingAxis;   
+rotatingAxisInfo
 {
     rotAxis 
     {
@@ -184,9 +182,9 @@ rotatingAxisMotionInfo
 }
 ```
 ## Performing Simulation
-To perform simulations, enter the following commands one after another in the terminal. 
+To run simulations, type the following commands in the terminal one at a time.
 
-Enter `$ particlesPhasicFlow` command to create the initial fields for particles.  
-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 storred in ./VTK folder. 
+Enter `particlesPhasicFlow` command to create the initial fields for particles.  
+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/RotatingDrumWithBaffles/caseSetup/interaction

@@ -6,62 +6,58 @@ objectName interaction;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-materials   (lightMat heavyMat wallMat);         // a list of materials names
+materials           (lightMat heavyMat wallMat); // a list of materials names
 
-densities              (1000 1500 2500);         // density of materials [kg/m3]  
+densities           (1000 1500 2500);            // density of materials [kg/m3]  
 
-contactListType       sortedContactList;
+contactListType     sortedContactList;
 
 contactSearch
 {
-    method         NBS;                          // method for broad search 
+    method             NBS;                       // method for broad search 
     
-   updateInterval   10;
+    updateInterval     10;
 
-   sizeRatio       1.1;
+    sizeRatio          1.1;
 
-   cellExtent     0.55;
+    cellExtent         0.55;
 
-   adjustableBox   Yes;     
+    adjustableBox      Yes;     
 }
 
 model
 {
-   contactForceModel  nonLinearLimited;
+    contactForceModel        nonLinearLimited;
 
-   rollingFrictionModel         normal;
+    rollingFrictionModel     normal;
 
-   /*
-      Property (lightMat-lightMat   lightMat-heavyMat    lightMat-wallMat
-                                    heavyMat-heavyMat    heavyMat-wallMat
-                                                         wallMat-wallMat);
-   */
+    /*
+       Property (lightMat-lightMat   lightMat-heavyMat    lightMat-wallMat
+                                     heavyMat-heavyMat    heavyMat-wallMat
+                                                          wallMat-wallMat);
+    */
 
-   Yeff (1.0e6 1.0e6 1.0e6  
-               1.0e6 1.0e6
-                     1.0e6);                     // Young modulus [Pa]
+    Yeff (1.0e6 1.0e6 1.0e6  
+                1.0e6 1.0e6
+                      1.0e6);                    // Young modulus [Pa]
 
-   Geff (0.8e6 0.8e6 0.8e6  
-               0.8e6 0.8e6
-                     0.8e6);                     // Shear modulus [Pa]   
+    Geff (0.8e6 0.8e6 0.8e6  
+                0.8e6 0.8e6
+                      0.8e6);                    // Shear modulus [Pa]   
 
-   nu      (0.25 0.25 0.25  
-                 0.25 0.25
-                      0.25);                     // Poisson's ratio [-]
+    nu (0.25 0.25 0.25  
+             0.25 0.25
+                  0.25);                         // Poisson's ratio [-]
 
-   en (0.97   0.97    0.85   
-              0.97    0.85
-                      1.00);                     // coefficient of normal restitution
-
-   et         (1.0 1.0 1.0    
-                   1.0 1.0
-                       1.0);                     // coefficient of tangential restitution
+    en (0.97 0.97 0.85   
+             0.97 0.85
+                  1.00);                         // coefficient of normal restitution
  
-   mu      (0.65 0.65 0.35   
-                 0.65 0.35
-                      0.35);                     // dynamic friction
+    mu (0.65 0.65 0.35   
+             0.65 0.35
+                  0.35);                         // dynamic friction
 
-   mur        (0.1 0.1 0.1    
-                   0.1 0.1
-                       0.1);                     // rolling friction     
+    mur (0.1 0.1 0.1    
+             0.1 0.1
+                 0.1);                           // rolling friction     
 }

tutorials/sphereGranFlow/RotatingDrumWithBaffles/caseSetup/particleInsertion

@@ -6,9 +6,7 @@ objectName particleInsertion;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-active           Yes;                            // is insertion active -> Yes or No
-
-checkForCollision No;                            // is checked          -> Yes or No
+active     Yes;                                  // is insertion active -> Yes or No
 
 /*
       Two layers of particles are packed one-by-one using 1 insertion steps 
@@ -17,70 +15,69 @@ checkForCollision No;                            // is checked          -> Yes o
 
 layerrightregion                                 // Right Layer Region
 {
-   timeControl     simulationTime;
+    timeControl           simulationTime;
 
-   regionType	    cylinder;               // type of insertion region
+    regionType	          cylinder;              // type of insertion region
  
-   rate 	                   12500;               // Right Region Particles Insertion Rate (particles/s)
+    rate 	              12500;                 // Right Region Particles Insertion Rate (particles/s)
 
-   startTime 	                 0;               // Start time of LightParticles insertion (s)
+    startTime 	          0;                     // Start time of LightParticles insertion (s)
     
-   endTime   	                 1;               // End time of LightParticles insertion (s) 
+    endTime   	          1;                     // End time of LightParticles insertion (s) 
 
-   insertionInterval        0.025;               // Time Interval of LightParticles insertion (s)
+    insertionInterval     0.025;                 // Time Interval of LightParticles insertion (s)
 
-   cylinderInfo 
-   {
+    cylinderInfo 
+    {
+        p2         (-0.15 0.25 0.05);            // Top of cylinderRegion (m,m,m)
 
-   	p2 (-0.15 0.25 0.05);                      // 
+   	    p1         (-0.15 0.24 0.05);            // Bottom of cylinderRegion (m,m,m)
 
-   	p1 (-0.15 0.24	0.05);                      // Bottom of cylinderRegion (m,m,m)
-
-   	radius         0.035;                      // radius of cylinder (m)
-   }
+   	    radius     0.035;                        // radius of cylinder (m)
+    }
    
-   setFields
-   {
-      velocity   realx3 (0.0 -0.6 0.0);          // initial velocity of inserted particles
-   }
+    setFields
+    {
+        velocity   realx3 (0.0 -0.6 0.0);        // initial velocity of inserted particles
+    }
    
-   mixture
-   {
-      smallSphere 1;                             // mixture composition of inserted particles
-   }
+    mixture
+    {
+        smallSphere     1;                       // mixture composition of inserted particles
+    }
 }
 
 layerleftregion                                  // Left Layer Region
 {
-   timeControl     simulationTime;
+    timeControl           simulationTime;
 
-   regionType      cylinder;               // type of insertion region
+    regionType            cylinder;               // type of insertion region
 
-   rate                      7500;               // Left Region Particles Insertion Rate (particles/s)
+    rate                  7500;                   // Left Region Particles Insertion Rate (particles/s)
 
-   startTime                    0;               // Start time of LightParticles insertion (s)
+    startTime             0;                      // Start time of LightParticles insertion (s)
   
-   endTime                      1;               // End time of LightParticles insertion (s)
+    endTime               1;                      // End time of LightParticles insertion (s)
 
-   insertionInterval        0.025;               // Time Interval of LightParticles insertion (s)
+    insertionInterval     0.025;                  // Time Interval of LightParticles insertion (s)
 
-   cylinderInfo 
-   {
-      p2 (-0.23 0.25	0.05);                      // Top of cylinderRegion (m,m,m)
+    cylinderInfo 
+    {
+        p2         (-0.23 0.25 0.05);             // Top of cylinderRegion (m,m,m)
 
-      p1 (-0.23 0.24	0.05);                      // Bottom of cylinderRegion (m,m,m)
+        p1         (-0.23 0.24 0.05);             // Bottom of cylinderRegion (m,m,m)
    
-      radius         0.035;                      // radius of cylinder (m)   
-   }
+        radius     0.035;                         // radius of cylinder (m)   
+    }
    
-   setFields
-   {
-     velocity    realx3 (0.0 -0.6 0.0);          // initial velocity of inserted particles
-   }
+    setFields
+    {
+        velocity    realx3 (0.0 -0.6 0.0);       // initial velocity of inserted particles
+    }
    
-   mixture
-   {
-      largeSphere 1;                             // only heavySphere
-   }
+    mixture
+    {
+        largeSphere     1;                       // only heavySphere
+    }
 }
 

tutorials/sphereGranFlow/RotatingDrumWithBaffles/caseSetup/shapes

@@ -6,8 +6,8 @@ objectName 	sphereDict;
 objectType 	sphereShape;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-names 		(smallSphere largeSphere);           // names of shapes 
+names 		  (smallSphere largeSphere);         // names of shapes 
 	
-diameters 	            (0.004 0.005);           // diameter of shapes (m) 
+diameters 	  (0.004 0.005);                     // diameter of shapes (m) 
 			
-materials	      (lightMat heavyMat);           // material names for shapes 		
+materials     (lightMat heavyMat);               // material names for shapes 		

tutorials/sphereGranFlow/RotatingDrumWithBaffles/caseSetup/sphereShape

@@ -1,15 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName 	sphereDict;
-objectType 	sphereShape;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-
-// names of shapes 
-names 		(smallSphere largeSphere);
-// diameter of shapes (m) 	
-diameters 	(0.004 0.005);
-// material names for shapes 			
-materials	(lightMat heavyMat);		

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/domainDict

@@ -8,33 +8,16 @@ fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
 {
-		min (-0.328 0.095 -0.025);               // lower corner point of the box 
+    min (-0.328 0.095 -0.025);                   // lower corner point of the box 
 
-	    max (-0.068  0.355 0.125);               // upper corner point of the box 
-}
-
-decomposition
-{
-	direction z;
+	max (-0.068  0.355 0.125);                   // upper corner point of the box 
 }
 
 boundaries
 {
-	
-
-	neighborListUpdateInterval     50;           /* Determines how often (how many iterations) do you want to 
-
-	                                                rebuild the list of particles in the neighbor list 
-
-	                                                of all boundaries in the simulation domain        */
-
-	updateInterval                 10;           // Determines how often do you want to update the new changes in the boundary
-
-	neighborLength              0.004;           // The distance from the boundary plane within which particles are marked to be in the boundary list
-
-	left
+    left
 	{
-		type     exit;	                         // other options: periodic, reflective 
+	    type     exit;	                         // other options: periodic, reflective 
 	}
 
 	right

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/geometryDict

@@ -10,17 +10,17 @@ motionModel rotatingAxis;
 
 rotatingAxisInfo
 {
-	rotAxis 
+    rotAxis 
 	{
-		p1   (-0.1974  0.2269  0);               // first point for the axis of rotation
+		p1            (-0.1974 0.2269 0);        // first point for the axis of rotation
 			 
-		p2 (-0.1974  0.2269  0.1);               // second point for the axis of rotation
+		p2            (-0.1974 0.2269 0.1);      // second point for the axis of rotation
 		
-		omega             2.38733;               // rotation speed (rad/s) => 15 rpm	
+		omega         2.38733;                   // rotation speed (rad/s) => 15 rpm	
 				
-		startTime               2;               // Start time of Geometry Rotating 
+		startTime     2;                         // Start time of Geometry Rotating 
 		
-		endTime               9.5;               // End time of Geometry Rotating
+		endTime       9.5;                       // End time of Geometry Rotating
 	}
 }
 
@@ -28,13 +28,13 @@ surfaces
 {
 	body
 	{
-		type 	  stlWall;                       // type of the wall
+		type 	     stlWall;                    // type of the wall
 			
-		file 	 Body.stl;                       // file name in stl folder  
+		file 	     Body.stl;                   // file name in stl folder  
 			
-		material  wallMat;                       // material name of this wall	
+		material     wallMat;                    // material name of this wall	
 		 
-		motion 	  rotAxis;	                     // motion component name  	 
+		motion 	     rotAxis;	                 // motion component name  	 
 	}
 
 	/*	
@@ -43,19 +43,19 @@ surfaces
 
 	rearEnd
 	{
-		type            cylinderWall;            // type of the wall
+		type         cylinderWall;               // type of the wall
 				
-		p1 (-0.1974 0.2269 -0.001);              // first point for the axis of rotation	
-		 
-		p2    (-0.1974 0.2269 0.0);              // second point for the axis of rotation	
+		p1           (-0.1974 0.2269 -0.001);    // first point for the axis of rotation	
+		  
+		p2           (-0.1974 0.2269 0.0);       // second point for the axis of rotation	
 		
-		radius1 0.0001;                          // Radius of p1	
+		radius1      0.0001;                     // Radius of p1	
 		
-		radius2 0.12;                            // Radius of p2
+		radius2      0.12;                       // Radius of p2
 		
-		material wallMat;                        // material name of the wall
+		material     wallMat;                    // material name of the wall
 		         
-		motion rotAxis;	                         // motion component name 		 
+		motion       rotAxis;	                 // motion component name 		 
 	}
 
 	/*	
@@ -64,19 +64,18 @@ surfaces
 
 	frontEnd
 	{
-		type          cylinderWall;              // type of the wall
+		type         cylinderWall;               // type of the wall
 				
-		p1 (-0.1974 0.2269 0.0989);              // first point for the axis of rotation	
+		p1           (-0.1974 0.2269 0.0989);    // first point for the axis of rotation	
 			 
-		p2 (-0.1974 0.2269 0.0990);	             // second point for the axis of rotation
+		p2           (-0.1974 0.2269 0.0990);	 // second point for the axis of rotation
 	
-		radius1             0.0001;	             // Radius of p1
+		radius1      0.0001;	                 // Radius of p1
 		
-		radius2               0.12;              // Radius of p2
+		radius2      0.12;                       // Radius of p2
 		
-		material           wallMat;              // material name of the wall
+		material     wallMat;                    // material name of the wall
 		      
-		motion             rotAxis;	             // motion component name    		 
+		motion       rotAxis;	                 // motion component name    		 
 	}
 }
-

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/particlesDict

@@ -16,13 +16,13 @@ setFields
 		spherical particles.
 	*/
 
-	defaultValue 
+    defaultValue 
 	{
-		velocity 	      realx3 	(0 0 0);     // linear velocity (m/s)
+		velocity 	     realx3 	(0 0 0);     // linear velocity (m/s)
 			
-		acceleration 	  realx3 	(0 0 0);	 // linear acceleration (m/s2) 
+		acceleration     realx3 	(0 0 0);	 // linear acceleration (m/s2) 
 			
-		rVelocity 		  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  
 	}
@@ -31,15 +31,15 @@ setFields
 	{
 		shapeAssigne
 		{
-			selector 	stridedRange; 	         // other options: box, cylinder, sphere, randomPoints 
+			selector     stridedRange; 	         // other options: box, cylinder, sphere, randomPoints 
  
 			stridedRangeInfo
 			{
-				begin 	    0;			         // begin index of points
+				begin 	   0;			         // begin index of points
 
-				end 	20000;		 			 // end index of points 
+				end 	   20000;		 		 // end index of points 
 
-				stride      3;			 		 // stride for selector 
+				stride     3;			 		 // stride for selector 
 			}
 
 			fieldValue  					     // fields that the selector is applied to 
@@ -52,27 +52,7 @@ setFields
 
 positionParticles                                // positions particles 
 {
-	method ordered;     		                 // other options: random and empty
-
-	mortonSorting 			   Yes;              // perform initial sorting based on morton code?   
-
-	orderedInfo
-	{
-		diameter  0.005; 						 // minimum space between centers of particles
-
-		numPoints 20000; 	                     // number of particles in the simulation 
-
-		axisOrder (z y x);                       // axis order for filling the space with particles
-	}
-
-	regionType box;                              // other options: cylinder and sphere  
-
-	boxInfo  				                     // box information for positioning particles 
-	{
-		min (-0.08 -0.08 0.015);                 // lower corner point of the box 
-
-		max ( 0.08  0.08 0.2);	                 // upper corner point of the box 
-	}
+	method empty;     		                     // other options: random and ordered
 }
 
 

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/settingsDict

@@ -6,29 +6,30 @@ objectName 	settingsDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-run 	RotatingDrumwithBaffles;
+run 	          RotatingDrumwithBaffles;
 
-dt 			            0.00001;                 // time step for integration (s)
+dt 			      0.00001;                       // time step for integration (s)
 
-startTime 	   	              0;                 // start time for simulation 
+startTime 	   	  0;                             // start time for simulation 
 
-endTime 		             10;	 	         // end time for simulation 	
+endTime 		  10;	 	                     // end time for simulation 	
 
-saveInterval 	           0.05; 		         // time interval for saving the simulation
+saveInterval 	  0.05; 		                 // time interval for saving the simulation
 
-timePrecision                 6;		         // maximum number of digits for time folder 	
+timePrecision     6;		                     // maximum number of digits for time folder 	
 
-g 		  (0 -9.8 0);                            // gravity vector (m/s2) 
+g 		         (0 -9.8 0);                     // gravity vector (m/s2) 
 
-includeObjects (diameter);                       // save necessary (i.e., required) data on disk
+// save necessary (i.e., required) data on disk
+includeObjects (diameter);                       
 
 // exclude unnecessary data from saving on disk
 excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
-integrationMethod 		AdamsBashforth2;         // integration method 
+integrationMethod 		 AdamsBashforth2;        // integration method 
 
-writeFormat				          ascii;         // data writting format (ascii or binary)
+writeFormat				 ascii;                  // data writting format (ascii or binary)
 
-timersReport 			            Yes;  	     // report timers (Yes or No)
+timersReport 			 Yes;  	                 // report timers (Yes or No)
 
-timersReportInterval   	           0.01;	     // time interval for reporting timers
+timersReportInterval     0.1;	                 // time interval for reporting timers

tutorials/sphereGranFlow/rotatingDrumMedium/caseSetup/interaction

@@ -6,56 +6,52 @@ objectName interaction;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-materials        (glassMat wallMat);                       // a list of materials names
+materials         (glassMat wallMat);                       // a list of materials names
 
-densities             (2500.0 2500);                       // density of materials [kg/m3]
+densities         (2500.0 2500);                            // density of materials [kg/m3]
 
 contactListType   sortedContactList;
 
 contactSearch
 {
-  
-   method          NBS;                                    // method for broad search 
+    method          NBS;                                    // method for broad search 
     
-   updateInterval   10;
+    updateInterval   10;
 
-   sizeRatio       1.1;
+    sizeRatio       1.1;
 
-   cellExtent     0.55;
+    cellExtent     0.55;
 
-   adjustableBox   Yes;
+    adjustableBox   Yes;
 } 
 
 model
 {
-   contactForceModel    nonLinearLimited;
+    contactForceModel    nonLinearLimited;
 
-   rollingFrictionModel           normal;
+    rollingFrictionModel           normal;
 
-   /*
-      Property (glassMat-glassMat      glassMat-wallMat
-                                       wallMat-wallMat);
-   */
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
 
-   Yeff (1.0e6 1.0e6  
-               1.0e6);                                     // Young modulus [Pa]
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);                                    // Young modulus [Pa]
    
-   Geff (0.8e6 0.8e6  
-               0.8e6);                                     // Shear modulus [Pa]
+    Geff (0.8e6  0.8e6  
+                 0.8e6);                                    // Shear modulus [Pa]
 
-   nu    (0.25  0.25  
-                0.25);                                     // Poisson's ratio [-]
+    nu   (0.25   0.25  
+                 0.25);                                     // Poisson's ratio [-]
 
-   en (0.97     0.85   
-                1.00);                                     // coefficient of normal restitution
+    en   (0.97   0.85   
+                 1.00);                                     // coefficient of normal restitution
 
-   et (1.0       1.0    
-                 1.0);                                     // coefficient of tangential restitution 
+    mu   (0.65   0.65   
+                 0.65);                                     // dynamic friction 
 
-   mu (0.65     0.65   
-                0.65);                                     // dynamic friction 
-
-   mur (0.1      0.1    
-                 0.1);                                     // rolling friction        
+    mur  (0.1    0.1    
+                 0.1);                                      // rolling friction        
 }
 

tutorials/sphereGranFlow/rotatingDrumMedium/caseSetup/particleInsertion

@@ -8,5 +8,3 @@ fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 active         No;                                      // is checked          -> Yes or No
 
-collisionCheck No;                                      // is insertion active -> Yes or No
-

tutorials/sphereGranFlow/rotatingDrumMedium/caseSetup/shapes

@@ -2,12 +2,12 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName 	sphereDict;
-objectType 	sphereShape;
+objectName  shapes;
+objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-names 		(glassBead); 	                               // names of shapes 
+names       (glassBead);                                   // names of shapes 
 
-diameters 	    (0.003);		                           // diameter of shapes 
+diameters       (0.003);                                   // diameter of shapes 
 
-materials	 (glassMat);		                           // material names for shapes 
+materials    (glassMat);                                   // material names for shapes 

tutorials/sphereGranFlow/rotatingDrumMedium/caseSetup/sphereShape

@@ -1,12 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName 	sphereDict;
-objectType 	sphereShape;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-
-names 		(glassBead); 	// names of shapes 
-diameters 	(0.003);		// diameter of shapes 
-materials	(glassMat);		// material names for shapes 

tutorials/sphereGranFlow/rotatingDrumMedium/settings/domainDict

@@ -2,63 +2,46 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
-objectName 	domainDict;
-objectType 	dictionary;
-fileFormat  ASCII;
+objectName     domainDict;
+objectType     dictionary;
+fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
 globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
 {
-		min (-0.12 -0.12 0);
+    min (-0.12 -0.12 0);
 
-	    max (0.12   0.12 0.36);                  // upper corner point of the box 
-}
-
-decomposition
-{
-	direction z;
+    max (0.12   0.12 0.36);                      // upper corner point of the box 
 }
 
 boundaries
 {
-	
+    left
+    {
+        type    exit;                            // other options: periodic, reflective 
+    }
 
-	neighborListUpdateInterval     50;           /* Determines how often (how many iterations) do you want to 
+    right
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
 
-	                                                rebuild the list of particles in the neighbor list 
+    bottom
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
 
-	                                                of all boundaries in the simulation domain        */
+    top
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
 
-	updateInterval                 10;           // Determines how often do you want to update the new changes in the boundary
+    rear
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
 
-	neighborLength              0.004;           // The distance from the boundary plane within which particles are marked to be in the boundary list
-
-	left
-	{
-		type     exit;	                         // other options: periodict, reflective 
-	}
-
-	right
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-
-	bottom
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-
-	top
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-
-	rear
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-
-	front
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
+    front
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
 }

tutorials/sphereGranFlow/rotatingDrumMedium/settings/geometryDict

@@ -2,91 +2,90 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
-objectName 	geometryDict;
-objectType 	dictionary;
-fileFormat  ASCII;
+objectName     geometryDict;
+objectType     dictionary;
+fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
-motionModel rotatingAxis;                  // motion model: rotating object around an axis
+motionModel rotatingAxis;                         // motion model: rotating object around an axis
 
 
-rotatingAxisInfo                           // information for rotatingAxisMotion motion model 
+rotatingAxisInfo                                  // information for rotatingAxisMotion motion model 
 {
-	rotAxis 
-	{
-		p1 (0.0 0.0 0.0);	                     // first point for the axis of rotation 
+    rotAxis 
+    {
+        p1 (0.0 0.0 0.0);                         // first point for the axis of rotation 
 
-		p2 (0.0 0.0 1.0);	                     // second point for the axis of rotation
+        p2 (0.0 0.0 1.0);                         // second point for the axis of rotation
 
-		omega      1.214; 		                 // rotation speed (rad/s) => 11.6 rpm
-	}
+        omega      1.214;                         // rotation speed (rad/s) => 11.6 rpm
+    }
 }
 
 surfaces
 {
-	/*
-	    A cylinder with begin and end radii 0.12 m and axis points at (0 0 0) and (0 0 0.36)
-	*/
+    /*
+        A cylinder with begin and end radii 0.12 m and axis points at (0 0 0) and (0 0 0.36)
+    */
 
-	cylinder
-	{
-		type cylinderWall;                       // type of the wall
+    cylinder
+    {
+        type cylinderWall;                       // type of the wall
 
-		p1  (0.0 0.0 0.0);                       // begin point of cylinder axis
+        p1  (0.0 0.0 0.0);                       // begin point of cylinder axis
 
-		p2 (0.0 0.0 0.36);                       // end point of cylinder axis
+        p2 (0.0 0.0 0.36);                       // end point of cylinder axis
 
-		radius1      0.12;		                 // radius at p1
+        radius1      0.12;                       // radius at p1
 
-		radius2      0.12;		                 // radius at p2
+        radius2      0.12;                       // radius at p2
 
-		resolution     24;                       // number of divisions
+        resolution     24;                       // number of divisions
 
-		material  wallMat;                       // material name of this wall
+        material  wallMat;                       // material name of this wall
 
-		motion    rotAxis;		                 // motion component name 
-	}
+        motion    rotAxis;                       // motion component name 
+    }
 
-	/*
-		This is a plane wall at the rear end of cylinder
-	*/
+    /*
+        This is a plane wall at the rear end of cylinder
+    */
 
-	wall1
-	{
-		type       planeWall;			         // type of the wall
+    wall1
+    {
+        type       planeWall;                    // type of the wall
 
-		p1 (-0.12 -0.12 0.0);	                 // first point of the wall
+        p1 (-0.12 -0.12 0.0);                    // first point of the wall
 
-		p2 ( 0.12 -0.12 0.0);                    // second point
+        p2 ( 0.12 -0.12 0.0);                    // second point
 
-		p3 ( 0.12  0.12 0.0);                    // third point
+        p3 ( 0.12  0.12 0.0);                    // third point
 
-		p4 (-0.12  0.12 0.0);                    // fourth point 
+        p4 (-0.12  0.12 0.0);                    // fourth point 
 
-		material     wallMat;                    // material name of the wall  
+        material     wallMat;                    // material name of the wall  
 
-		motion       rotAxis;			         // motion component name 
-	}
+        motion       rotAxis;                    // motion component name 
+    }
 
-	/*
-		This is a plane wall at the front end of cylinder
-	*/
+    /*
+        This is a plane wall at the front end of cylinder
+    */
 
-	wall2
-	{
-		type        planeWall;                   // type of the wall
+    wall2
+    {
+        type        planeWall;                   // type of the wall
 
-		p1 (-0.12 -0.12 0.36);                   // first point of the wall
+        p1 (-0.12 -0.12 0.36);                   // first point of the wall
 
-		p2 ( 0.12 -0.12 0.36);                   // second point
+        p2 ( 0.12 -0.12 0.36);                   // second point
 
-		p3 ( 0.12  0.12 0.36);                   // third point
+        p3 ( 0.12  0.12 0.36);                   // third point
 
-		p4 (-0.12  0.12 0.36);                   // fourth point 
+        p4 (-0.12  0.12 0.36);                   // fourth point 
 
-		material      wallMat;                   // material name of the wall  
+        material      wallMat;                   // material name of the wall  
 
-		motion        rotAxis;                   // motion component name 
-	}
-		
+        motion        rotAxis;                   // motion component name 
+    }
 }
 

tutorials/sphereGranFlow/rotatingDrumMedium/settings/particlesDict

@@ -2,79 +2,55 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
-objectName 	particlesDict;
-objectType 	dictionary;
-fileFormat  ASCII;
+objectName     particlesDict;
+objectType     dictionary;
+fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
 setFields
 {
-	/*
-	    Default value for fields defined for particles
-		These fields should always be defined for simulations with 
-		spherical particles
-	*/
+    /*
+        Default value for fields defined for particles
+        These fields should always be defined for simulations with 
+        spherical particles
+    */
 
-	defaultValue 
-	{
-		velocity 		realx3 	  (0 0 0);       // linear velocity (m/s)
+    defaultValue 
+    {
+        velocity          realx3       (0 0 0);      // linear velocity (m/s)
 
-		acceleration 	realx3 	  (0 0 0);       // linear acceleration (m/s2)
+        acceleration      realx3       (0 0 0);      // linear acceleration (m/s2)
 
-		rVelocity 		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 
-	}
+        shapeName         word         glassBead;    // name of the particle shape 
+    }
 
-	selectors
-	{
-		shapeAssigne
-		{
-			selector 	stridedRange; 	         // other options: box, cylinder, sphere, randomPoints 
- 
-			stridedRangeInfo
-			{
-				begin 	    0;			         // begin index of points
-
-				end 	250000;		 			 // end index of points 
-
-				stride      3;			 		 // stride for selector 
-			}
-
-			fieldValue  					     // fields that the selector is applied to 
-			{
-				shapeName 	word    glassBead; // sets shapeName of the selected points to largeSphere
-			}
-		}
-	}
+    selectors
+    {
+    }
 }
 
-positionParticles                                // positions particles 
+positionParticles                                    // positions particles 
 {
-	method ordered;     		                 // other options: random and empty
+    method ordered;                                  // other options: random and empty
 
-	//maxNumberOfParticles 	250001;              // maximum number of particles in the simulation
+    orderedInfo
+    {
+        diameter   0.003;                            // minimum space between centers of particles
 
-	//mortonSorting 			   Yes;              // perform initial sorting based on morton code?   
+        numPoints  250000;                           // number of particles in the simulation 
 
-	orderedInfo
-	{
-		diameter 0.003; 						 // minimum space between centers of particles
+        axisOrder  (z y x);                          // axis order for filling the space with particles
+    }
 
-		numPoints 250000; 	                     // number of particles in the simulation 
+    regionType cylinder;                             // other options: box and sphere  
 
-		axisOrder (z y x);                       // axis order for filling the space with particles
-	}
-
-	regionType cylinder;                         // other options: box and sphere  
-
-	cylinderInfo  				                 // cylinder information for positioning particles 
-	{
-		p1 (0.0 0.003 0.0); 	                 // begin point of cylinder axis
-
-		p2 (0.0 0.22 0.0);		                 // end point of cylinder axis
-
-		radius 		0.117;		                 // radius of cylinder 
-	}
+    cylinderInfo                                     // cylinder information for positioning particles 
+    {
+        p1 (0.0 0.0 0.003);                          // begin point of cylinder axis
 
+        p2 (0.0 0.0 0.357);                          // end point of cylinder axis
 
+        radius     0.117;                            // radius of cylinder 
+    }
 }

tutorials/sphereGranFlow/rotatingDrumMedium/settings/settingsDict

@@ -2,38 +2,33 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
-objectName 	settingsDict;
-objectType 	dictionary;;
+objectName  settingsDict;
+objectType  dictionary;;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-run 			rotatingDrumMedium;
+run             rotatingDrumMedium;
 
-dt 				           0.00001; 	         // time step for integration (s)
+dt                         0.00001;              // time step for integration (s)
 
-startTime 		                 0; 			 // start time for simulation 
+startTime                        0;              // start time for simulation 
 
-endTime 		                10; 		     // end time for simulation 
+endTime                         10;              // end time for simulation 
 
-saveInterval 	               0.1; 		     // time interval for saving the simulation
+saveInterval                   0.1;              // time interval for saving the simulation
 
-timePrecision                    6;			     // maximum number of digits for time folder 
+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.
-*/
+g                       (0 -9.8 0);              // gravity vector (m/s2) 
 
 includeObjects (diameter);                       // save necessary (i.e., required) data on disk
 
 // exclude unnecessary data from saving on disk
 excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
-integrationMethod 		AdamsBashforth2; 	     // integration method 
+integrationMethod       AdamsBashforth2;         // integration method 
 
-writeFormat				binary;                  // data writting format (ascii or binary)
+writeFormat             binary;                  // data writting format (ascii or binary)
 
-timersReport 			Yes;  	                 // report timers?
+timersReport            Yes;                     // report timers?
 
-timersReportInterval   	0.01;	                 // time interval for reporting timers
+timersReportInterval    0.05;                    // time interval for reporting timers

tutorials/sphereGranFlow/toteBlender/ReadMe.md

@@ -0,0 +1,304 @@
+# Tote Blender simulation (v-1.0)
+
+## Problem Definition
+The problem is to simulate a double pedestal tote blender (mixer) with the diameter **0.03 m** and **0.1 m** respectively, the length **0.3 m**, rotating at **28 rpm**. This blender is filled with **24000** particles. The timestep for integration is **0.00002 s**. There is one type of particle in this blender. Particles are positioned before the start of simulation to fill the blender.
+* **24000** particles with **5 mm** diameter are positioned, in order, and let to be settled under gravity. After settling particles, this blender starts to rotate at t=**1s**. 
+
+<html>
+<body>
+<div align="center"><b>
+    a view of the tote-blender while rotating 
+</div></b>
+<div align="center">
+<img src="https://github.com/PhasicFlow/phasicFlow/blob/media/media/Tote-blender.gif", width=700px>
+</div>
+<div align="center"><i>
+    particles are colored according to their velocity
+</div></i>
+</body>
+</html>
+
+# Setting up the Case
+As it has been explained in the previous cases, the simulation case setup is based on text-based scripts. Here, the simulation case setup files are stored into two folders: `caseSetup`, `setting` (see the above folders). Unlike the previous cases, this case does not have the `stl` file and the surfaces are defined based on the built-in utilities in phasicFlow. 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 and speed of rotation are defined. The rotation of this blender starts at time=**0.5 s** and ends at time=**9.5 s**.
+
+```C++
+// information for rotatingAxis motion model 
+rotatingAxis
+{
+    axisOfRotation 
+    {
+        p1 (-0.1 0.0 0.15);    // first point for the axis of rotation 
+        p2 ( 0.1 0.0 0.15);    // second point for the axis of rotation
+        
+        omega 1.5708;         // rotation speed ==> 15 rad/s
+        
+        // Start time of Geometry Rotating (s)         
+        startTime 0.5;
+        
+        // End time of Geometry Rotating (s)
+        endTime 9.5;
+    }
+}
+```
+
+### Surfaces 
+In `settings/geometryDict` file, the surfaces and motion component of each surface are defined to form a rotating tote-blender. The geometry is composed of top and bottom cylinders, top and bottom cones, a cylindrical shell and top and bottom Gates.
+
+```C++
+surfaces
+{
+    
+    topGate
+    {
+        // type of wall
+        type cylinderWall;
+        
+        // begin point of cylinder axis 
+        p1 (0.0    0.0   0.3);
+        
+        // end point of cylinder axis 
+        p2 (0.0    0.0   0.301);
+        
+        // radius at p1  
+        radius1  0.03;
+        
+        // radius at p2        
+        radius2     0.0001;
+        
+        // material of wall
+        material solidProperty;
+        
+        // motion component name
+        motion axisOfRotation;    
+    }
+
+    topCylinder
+    {
+        type         cylinderWall;
+        
+        p1             (0.0 0.0 0.28);
+        
+        p2             (0.0 0.0 0.3);
+        
+        radius1     0.03;
+        
+        radius2     0.03;
+        
+        resolution     36;
+        
+        material     solidProperty;
+        
+        motion axisOfRotation;        
+    }
+
+    coneShelltop
+    {    
+        type         cylinderWall;
+        
+        p1             (0.0 0.0 0.2);
+        
+        p2             (0.0 0.0 0.28);
+        
+        radius1     0.1;
+        
+        radius2     0.03;
+        
+        resolution     36;
+        
+        material     solidProperty;
+        
+        motion axisOfRotation;        
+    }
+
+    cylinderShell
+    {
+        type         cylinderWall;
+        
+        p1             (0.0 0.0 0.1);
+        
+        p2             (0.0 0.0 0.2);
+        
+        radius1     0.1;
+        
+        radius2     0.1;
+        
+        resolution     36;
+        
+        material     solidProperty; 
+        
+        motion axisOfRotation;        
+    }
+
+    coneShelldown
+    {
+        type         cylinderWall;
+        
+        p1             (0.0 0.0 0.02);
+        
+        p2             (0.0 0.0 0.1);
+
+        radius1     0.03;
+        
+        radius2     0.1;
+        
+        resolution     36;
+        
+        material     solidProperty;
+        
+        motion axisOfRotation;        
+    }
+
+    bottomCylinder
+    {
+        type         cylinderWall;      
+        
+        p1             (0.0 0.0 0.0);
+        
+        p2             (0.0 0.0 0.02);
+        
+        radius1     0.03;
+        
+        radius2     0.03;
+        
+        resolution     36;
+        
+        material     solidProperty;
+        
+        motion axisOfRotation;        
+    }
+
+    exitGate
+    {
+        
+        type         cylinderWall;      
+        
+        p1             (0.0 0.0 -0.001);
+        
+        p2             (0.0 0.0 0.0);
+        
+        radius1     0.03;
+        
+        radius2     0.0001;
+        
+        resolution     36;
+        
+        material     solidProperty;
+        
+        motion axisOfRotation;            
+    }
+        
+}
+```
+
+## Defining particles 
+### Diameter and material of spheres 
+In the `caseSetup/shapes` the diameter and the material name of the particles are defined.
+
+<div align="center"> 
+in <b>caseSetup/shapes</b> file
+</div>
+
+```C++
+// name of shapes 
+names         (sphere1);     
+
+// diameter of shapes (m)
+diameters     (0.005);
+
+// material name for shapes     
+materials    (solidProperty);
+```
+### Particle positioning before start of simulation 
+Particles are positioned before the start of simulation. The positioning can be ordered or random. Here we use ordered positioning. 24000 particles are positioned in a cylinderical region inside the tote-blender.
+
+<div align="center"> 
+in <b>settings/particlesDict</b> file
+</div>
+
+```C++
+// positions particles 
+positionParticles
+{
+    // ordered positioning
+    method     positionOrdered;     
+
+    // maximum number of particles in the simulation
+    maxNumberOfParticles 25001;
+    
+    // perform initial sorting based on morton code? 
+    mortonSorting     Yes;             
+    
+    // cylinderical region for positioning particles 
+    cylinder
+    {
+        p1 (0.0 0.0 0.09);    
+        p2 (0.0 0.0 0.21);
+        radius 0.09;
+    }
+
+    positionOrderedInfo
+    {
+        // minimum space between centers of particles
+        diameter 0.005;
+        
+        // number of particles in the simulation          
+        numPoints 24000;
+    
+        // axis order for filling the space with particles             
+        axisOrder (x y z);  
+    }
+}
+```
+
+ ## 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 1x1 (interactions are symmetric). 
+```C++
+ // a list of materials names
+materials      (solidProperty);
+
+// density of materials [kg/m3]
+densities      (1000.0);   
+
+contactListType   sortedContactList; 
+
+model
+{
+   contactForceModel       nonLinearNonLimited;
+    
+   rollingFrictionModel    normal;
+   
+   /*
+   Property (solidProperty-solidProperty);
+   */
+   // Young modulus [Pa]
+   Yeff  (1.0e6);       
+
+   // Shear modulus [Pa]
+   Geff  (0.8e6);       
+    
+   // Poisson's ratio [-]
+   nu    (0.25);        
+    
+   // coefficient of normal restitution
+   en    (0.7);                  
+
+   // dynamic friction
+   mu    (0.3);          
+
+   // rolling friction
+   mur   (0.1);                  
+}
+```
+
+# Performing Simulation and previewing 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.  
+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/toteBlender/caseSetup/interaction

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+materials       (solidProperty);  // a list of materials names
+
+densities       (1000.0);         // density of materials [kg/m3]
+
+contactListType  sortedContactList; 
+
+model
+{
+   contactForceModel     nonLinearNonLimited;
+    
+   rollingFrictionModel  normal;
+   
+   /*
+      Property (solidProperty-solidProperty)
+   */   
+   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             
+   
+   mu      (0.3);        // dynamic friction    
+
+   mur     (0.1);        // rolling friction               
+}
+
+contactSearch
+{
+    method         NBS;   
+    
+   updateInterval   10;
+
+   sizeRatio       1.1;
+
+   cellExtent     0.55;
+
+   adjustableBox   Yes;     
+}

tutorials/sphereGranFlow/toteBlender/caseSetup/shapes

@@ -2,12 +2,13 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
-objectType dicrionary;
-fileFormat  ASCII;
+objectName     sphereDict;
+objectType     sphereShape;
+fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
-active         No;                               // is insertion active -> Yes or No
 
-collisionCheck No;                               // is checked          -> Yes or No
+names               (sphere1);  // name of shapes 
 
+diameters             (0.005);  // diameter of shapes (m)
 
+materials    (solidProperty);  // material name for shapes 

tutorials/sphereGranFlow/toteBlender/settings/domainDict

@@ -0,0 +1,50 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     domainDict;
+objectType     dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                                        
+{
+    min        (-0.3 -0.3 -0.3);   // lower corner point of the box 
+
+    max        ( 0.5  0.5  0.5);   // upper corner point of the box 
+}
+
+boundaries
+{
+
+    left
+    {
+        type     exit;
+    }
+
+    right
+    {
+        type     exit;
+    }
+
+    bottom
+    {
+        type     exit;
+    }
+
+    top
+    {
+        type     exit;
+    }
+
+    rear
+    {
+        type     exit;
+    }
+
+    front
+    {
+        type     exit;
+    }
+}

tutorials/sphereGranFlow/toteBlender/settings/geometryDict

@@ -0,0 +1,160 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     geometryDict;
+objectType     dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+motionModel rotatingAxis;                       
+
+rotatingAxisInfo                                
+{
+    axisOfRotation 
+    {
+        p1 (-0.1 0.0 0.15);
+
+        p2 ( 0.1 0.0 0.15);
+        
+        omega       1.5708;
+            
+        startTime      0.5;
+        
+        endTime        9.5;
+    }
+}
+
+surfaces
+{
+    topGate
+    {
+        type       cylinderWall;     // type of wall
+        
+        p1         (0.0 0.0 0.3);    // begin point of cylinder axis 
+        
+        p2         (0.0 0.0 0.301);  // end point of cylinder axis
+        
+        radius1    0.03;             // radius at p1  
+        
+        radius2    0.0001;           // radius at p2    
+        
+        material   solidProperty;    // material of wall
+        
+        motion     axisOfRotation;                    
+    }
+
+    topCylinder
+    {
+        type       cylinderWall;
+            
+        p1         (0.0 0.0 0.28);
+        
+        p2         (0.0 0.0 0.3);
+          
+        radius1     0.03;
+            
+        radius2     0.03;
+                
+        resolution  36;
+        
+        material    solidProperty;
+        
+        motion      axisOfRotation;                 
+    }
+
+    coneShelltop
+    {    
+        type        cylinderWall;
+        
+        p1          (0.0 0.0 0.2);
+        
+        p2          (0.0 0.0 0.28);
+        
+        radius1      0.1;
+        
+        radius2      0.03;
+            
+        resolution   36;
+            
+        material     solidProperty;
+             
+        motion       axisOfRotation;                    
+    }
+
+    cylinderShell
+    {
+        type        cylinderWall;
+            
+        p1          (0.0 0.0 0.1);
+        
+        p2          (0.0 0.0 0.2);
+         
+        radius1     0.1;
+            
+        radius2     0.1;
+            
+        resolution  36;
+                      
+        material    solidProperty;
+            
+        motion      axisOfRotation;        
+    }
+
+    coneShelldown
+    {
+        type         cylinderWall;
+        
+        p1           (0.0 0.0 0.02);
+         
+        p2           (0.0 0.0 0.1);
+        
+        radius1      0.03;
+        
+        radius2      0.1;
+            
+        resolution   36;
+                 
+        material     solidProperty;
+            
+        motion       axisOfRotation;            
+    }
+
+    bottomCylinder
+    {
+        type        cylinderWall;
+        
+        p1          (0.0 0.0 0.0);
+          
+        p2          (0.0 0.0 0.02);
+        
+        radius1     0.03;
+            
+        radius2     0.03;
+                
+        resolution  36;
+                      
+        material    solidProperty;
+                   
+        motion      axisOfRotation;            
+    }
+
+    exitGate
+    {
+        type       cylinderWall;
+        
+        p1         (0.0 0.0 -0.001);
+          
+        p2         (0.0 0.0 0.0);
+        
+        radius1    0.03;
+                
+        radius2    0.0001;
+            
+        resolution 36;
+                      
+        material   solidProperty;
+        
+        motion     axisOfRotation;                       
+    }    
+}

tutorials/sphereGranFlow/toteBlender/settings/particlesDict

@@ -0,0 +1,58 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     particlesDict;
+objectType     dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+setFields
+{
+    /*
+        Default value for fields defined for particles
+        These fields should always be defined for simulations with 
+        spherical particles.
+    */
+    defaultValue 
+    {    
+        velocity         realx3     (0 0 0);  // linear velocity (m/s) 
+            
+        acceleration     realx3     (0 0 0);  // linear acceleration (m/s2)
+         
+        rVelocity         realx3     (0 0 0); // rotational velocity (rad/s)    
+             
+        shapeName         word    sphere1;    // name of the particle shape     
+    }
+
+    selectors
+    {}
+}
+
+positionParticles 
+{
+    
+    method           ordered; // ordered positioning
+
+    mortonSorting     Yes;    // perform initial sorting based on morton code?  
+
+    orderedInfo
+    {
+        diameter    0.005;   // minimum space between centers of particles
+                 
+        numPoints   24000;   // number of particles in the simulation 
+             
+        axisOrder (x y z);   // axis order for filling the space with particles    
+    }  
+
+    regionType cylinder;     // other options: cylinder and sphere               
+    
+    cylinderInfo              
+    {
+        p1 (0.0 0.0 0.09);   
+        
+        p2 (0.0 0.0 0.21);   
+        
+        radius       0.09;   // radius of cylinder
+    }
+}

tutorials/sphereGranFlow/toteBlender/settings/settingsDict

@@ -0,0 +1,35 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     settingsDict;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+
+run             toteBlender;
+
+dt              0.00002;         // time step for integration (s)
+
+startTime       0;               // start time for simulation 
+
+endTime         10;              // end time for simulation 
+
+saveInterval    0.05;            // time interval for saving the simulation
+
+timePrecision   4;               // maximum number of digits for time folder 
+
+g               (0 0 -9.8);      // gravity vector (m/s2) 
+
+// include/exclude fields for saving on disk 
+includeObjects  (diameter);                       
+
+excludeObjects  (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+
+integrationMethod        AdamsBashforth2;
+
+writeFormat              ascii;
+
+timersReport             Yes;
+
+timersReportInterval     0.05;

tutorials/sphereGranFlow/toteblender/ReadMe.md

@@ -1,356 +0,0 @@
-# Problem Definition
-The problem is to simulate a double pedestal tote blender (mixer) with the diameter **0.03 m** and **0.1 m** respectively, the length **0.3 m**, rotating at **28 rpm**. This blender is filled with **24000** particles. The timestep for integration is **0.00001 s**. There is one type of particle in this blender. Particles are positioned before start of simulation to fill the blender.
-* **24000** particles with **5 mm** diameter are positioned, in order, and let to be settled under gravity. After settling particles, this blender starts to rotate at t=**1s**. 
-
-<html>
-<body>
-<div align="center"><b>
-	a view of the tote-blender while rotating 
-</div></b>
-<div align="center">
-<img src="https://github.com/PhasicFlow/phasicFlow/blob/media/media/Tote-blender.gif", width=700px>
-</div>
-<div align="center"><i>
-	particles are colored according to their velocity
-</div></i>
-</body>
-</html>
-
-# Setting up the Case
-As it has been explained in the previous cases, the simulation case setup is based on text-based scripts. Here, the simulation case setup files are stored into two folders: `caseSetup`, `setting` (see the above folders). Unlike the previous cases, this case does not have the `stl` file and the surfaces are defined based on the built-in utilities in phasicFlow. 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 and speed of rotation are defined. The rotation of this blender starts at time=**0.5 s** and ends at time=**9.5 s**.
-
-```C++
-// information for rotatingAxisMotion motion model 
-rotatingAxisMotionInfo
-{
-	axisOfRotation 
-	{
-		p1 (-0.1 0.0 0.15);	// first point for the axis of rotation 
-		p2 ( 0.1 0.0 0.15);	// second point for the axis of rotation
-		
-		omega 1.5708; 		// rotation speed ==> 15 rad/s
-		
-		// Start time of Geometry Rotating (s) 		
-		startTime 0.5;
-		
-		// End time of Geometry Rotating (s)
-		endTime 9.5;
-	}
-}
-```
-
-
-### Surfaces 
-In `settings/geometryDict` file, the surfaces and motion component of each surface are defined to form a rotating tote-blender. The geometry is composed of top and bottom cylinders, top and bottom cones, a cylindrical shell and top and bottom Gates.
-
-```C++
-surfaces
-{
-	
-	topGate
-	{
-		// type of wall
-		type cylinderWall;
-		
-		// begin point of cylinder axis 
-		p1 (0.0    0.0   0.3);
-		
-		// end point of cylinder axis 
-		p2 (0.0    0.0   0.301);
-		
-		// radius at p1  
-		radius1  0.03;
-		
-		// radius at p2		
-		radius2	 0.0001;
-		
-		// material of wall
-		material solidProperty;
-		
-		// motion component name
-		motion axisOfRotation;	
-	}
-
-    topCylinder
-	{
-		// type of the wall
-		type 		cylinderWall;
-		
-		// begin point of cylinder axis 	
-		p1 			(0.0 0.0 0.28);
-		
-		// end point of cylinder axis  
-		p2 			(0.0 0.0 0.3);
-		
-		// radius at p1  
-		radius1 	0.03;
-		
-		// radius at p2		
-		radius2 	0.03;
-		
-		// number of divisions		
-		resolution 	36;
-		
-		// material name of this wall
-		material 	solidProperty;
-		
-		// motion component name   	
-		motion axisOfRotation;		
-	}
-
-	coneShelltop
-	{	
-		// type of the wall	
-		type 		cylinderWall;
-		
-		// begin point of cylinder axis  	
-		p1 			(0.0 0.0 0.2);
-		
-		// end point of cylinder axis  
-		p2 			(0.0 0.0 0.28);
-		
-		// radius at p1  
-		radius1 	0.1;
-		
-		// radius at p2		
-		radius2 	0.03;
-		
-		// number of divisions		
-		resolution 	36;
-		
-		// material name of this wall      	
-		material 	solidProperty;
-		
-		// motion component name   	
-		motion axisOfRotation;		
-	}
-
-	cylinderShell
-	{
-		// type of the wall
-		type 		cylinderWall;
-		
-		// begin point of cylinder axis  	
-		p1 			(0.0 0.0 0.1);
-		
-		// end point of cylinder axis
-		p2 			(0.0 0.0 0.2);
-		
-		// radius at p1	  
-		radius1 	0.1;
-		
-		// radius at p2			
-		radius2 	0.1;
-		
-		// number of divisions		
-		resolution 	36;
-		
-		// material name of this wall	      	
-		material 	solidProperty; 
-		
-		// motion component name  	
-		motion axisOfRotation;		
-	}
-
-	coneShelldown
-	{
-		
-		// type of the wall
-		type 		cylinderWall;
-		
-		// begin point of cylinder axis  	
-		p1 			(0.0 0.0 0.02);
-		
-		// end point of cylinder axis  
-		p2 			(0.0 0.0 0.1);
-		
-		// radius at p1  
-		radius1 	0.03;
-		
-		// radius at p2		
-		radius2 	0.1;
-		
-		// number of divisions		
-		resolution 	36;
-		
-		// material name of this wall	      	
-		material 	solidProperty;
-		
-		// motion component name   	
-		motion axisOfRotation;		
-	}
-
-	bottomCylinder
-	{
-		// type of the wall
-		type 		cylinderWall;  	
-		
-		// begin point of cylinder axis	
-		p1 			(0.0 0.0 0.0);
-		
-		// end point of cylinder axis	  
-		p2 			(0.0 0.0 0.02);
-		
-		// radius at p1  
-		radius1 	0.03;
-		
-		// radius at p2			
-		radius2 	0.03;
-		
-		// number of divisions			
-		resolution 	36;
-		
-		// material name of this wall	      	
-		material 	solidProperty;
-		
-		// motion component name	   	
-		motion axisOfRotation;		
-	}
-
-	exitGate
-	{
-		
-		// type of the wall
-		type 		cylinderWall;  	
-		
-		// begin point of cylinder axis	
-		p1 			(0.0 0.0 -0.001);
-		
-		// end point of cylinder axis	  
-		p2 			(0.0 0.0 0.0);
-		
-		// radius at p1  
-		radius1 	0.03;
-		
-		// radius at p2			
-		radius2 	0.0001;
-		
-		// number of divisions			
-		resolution 	36;
-		
-		// material name of this wall	      	
-		material 	solidProperty;
-		
-		// motion component name	   	
-		motion axisOfRotation;			
-	}
-		
-}
-```
-
-## 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++
-// name of shapes 
-names 		(sphere1); 	
-
-// diameter of shapes (m)
-diameters 	(0.005);
-
-// material name for shapes 	
-materials	(solidProperty);
-```
-### Particle positioning before start of simulation 
-Particles are positioned before the start of simulation. The positioning can be ordered or random. Here we use ordered positioning. 24000 particles are positioned in a cylinderical region inside the tote-blender.
-
-<div align="center"> 
-in <b>settings/particlesDict</b> file
-</div>
-
-```C++
-// positions particles 
-positionParticles
-{
-	// ordered positioning
-	method 	positionOrdered;     
-
-	// maximum number of particles in the simulation
-	maxNumberOfParticles 25001;
-	
-	// perform initial sorting based on morton code? 
-	mortonSorting 	Yes;             
-	
-	// cylinderical region for positioning particles 
-	cylinder
-	{
-		p1 (0.0 0.0 0.09);	
-		p2 (0.0 0.0 0.21);
-		radius 0.09;
-	}
-
-	positionOrderedInfo
-	{
-		// minimum space between centers of particles
-		diameter 0.005;
-		
-		// number of particles in the simulation 	 	
-		numPoints 24000;
-	
-		// axis order for filling the space with particles		 	
-		axisOrder (x y z);  
-	}
-}
-```
-
- ## 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 1x1 (interactions are symmetric). 
-```C++
- // a list of materials names
-materials      (solidProperty);
-
-// density of materials [kg/m3]
-densities      (1000.0);   
-
-contactListType   sortedContactList; 
-
-model
-{
-   contactForceModel       nonLinearNonLimited;
-    
-   rollingFrictionModel    normal;
-   
-   /*
-   Property (solidProperty-solidProperty);
-   */
-    
-   // Young modulus [Pa]
-   Yeff  (1.0e6);       
-
-   // Shear modulus [Pa]
-   Geff  (0.8e6);       
-    
-   // Poisson's ratio [-]
-   nu    (0.25);        
-    
-   // coefficient of normal restitution
-   en    (0.7);         
-
-   // coefficient of tangential restitution
-   et    (1.0);          
-
-   // dynamic friction
-   mu    (0.3);          
-
-   // rolling friction
-   mur   (0.1);                  
-}
-```
-
-# Performing Simulation and previewing 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.  
-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/toteblender/caseSetup/interaction

@@ -1,52 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName interaction;
-objectType dicrionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-materials    (solidProperty);                    // a list of materials names
-
-densities           (1000.0);                    // density of materials [kg/m3]
-
-contactListType   sortedContactList; 
-
-contactSearch
-{
-    method         NBS;                          // method for broad search 
-    
-   updateInterval   10;
-
-   sizeRatio       1.1;
-
-   cellExtent     0.55;
-
-   adjustableBox   Yes;     
-}
-
-model
-{
-   contactForceModel     nonLinearNonLimited;
-    
-   rollingFrictionModel               normal;
-   
-   /*
-      Property (solidProperty-solidProperty)
-   */
-    
-   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               
-}
-

tutorials/sphereGranFlow/toteblender/caseSetup/shapes

@@ -1,13 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName 	sphereDict;
-objectType 	sphereShape;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-names 		      (sphere1); 	                 // name of shapes 
-
-diameters 	        (0.005);                     // diameter of shapes (m)
-
-materials	(solidProperty);	                 // material name for shapes 

tutorials/sphereGranFlow/toteblender/settings/domainDict

@@ -1,64 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-objectName 	domainDict;
-objectType 	dictionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
-{
-	min (-0.3 -0.3 -0.3);                        // lower corner point of the box 
-
-	max    (0.5 0.5 0.5);                        // upper corner point of the box 
-}
-
-decomposition
-{
-	direction z;
-}
-
-boundaries
-{
-	
-
-	neighborListUpdateInterval     50;           /* Determines how often (how many iterations) do you want to 
-
-	                                                rebuild the list of particles in the neighbor list 
-
-	                                                of all boundaries in the simulation domain        */
-
-	updateInterval                 10;           // Determines how often do you want to update the new changes in the boundary
-
-	neighborLength              0.004;           // The distance from the boundary plane within which particles are marked to be in the boundary list
-
-	left
-	{
-		type     exit;	                         // other options: periodic, reflective 
-	}
-
-	right
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-
-	bottom
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-
-	top
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-
-	rear
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-
-	front
-	{
-		type     exit;                           // other options: periodict, reflective 
-	}
-}

tutorials/sphereGranFlow/toteblender/settings/geometryDict

@@ -1,159 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-objectName 	geometryDict;
-objectType 	dictionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-motionModel rotatingAxis;                        // motion model: rotating object around an axis
-
-rotatingAxisInfo                                 // information for rotatingAxisMotion motion model 
-{
-	axisOfRotation 
-	{
-		p1 (-0.1 0.0 0.15);	                     // first point for the axis of rotation 
-
-		p2 ( 0.1 0.0 0.15);	                     // second point for the axis of rotation
-		
-		omega       1.5708; 		             // rotation speed ==> 15 rad/s
-			
-		startTime      0.5;                      // Start time of Geometry Rotating (s) 
-		
-		endTime        9.5;                      // End time of Geometry Rotating (s)
-	}
-}
-
-surfaces
-{
-	topGate
-	{
-		type      cylinderWall;                  // type of wall
-		
-		p1       (0.0 0.0 0.3);                  // begin point of cylinder axis 
-		
-		p2     (0.0 0.0 0.301);                  // end point of cylinder axis
-		
-		radius1           0.03;                  // radius at p1  
-		
-		radius2	        0.0001;                  // radius at p2	
-		
-		material solidProperty;                  // material of wall
-		
-		motion  axisOfRotation;	                 // motion component name
-	}
-
-    topCylinder
-	{
-		type 	  cylinderWall;                  // type of the wall
-			
-		p1 	    (0.0 0.0 0.28);                  // begin point of cylinder axis 
-		
-		p2 		 (0.0 0.0 0.3);                  // end point of cylinder axis 
-		  
-		radius1 	      0.03;                  // radius at p1 
-			
-		radius2 	      0.03;                  // radius at p2	
-				
-		resolution 	        36;                  // number of divisions
-		
-		material solidProperty;                  // material name of this wall
-		
-		motion  axisOfRotation;                  // motion component name 		
-	}
-
-	coneShelltop
-	{	
-		type 	  cylinderWall;                  // type of the wall	
-		
-		p1 		 (0.0 0.0 0.2);                  // begin point of cylinder axis  
-		
-		p2 		(0.0 0.0 0.28);                  // end point of cylinder axis 
-		
-		radius1 	       0.1;	                 // radius at p1  
-			
-		radius2 	      0.03;                  // radius at p2	
-			
-		resolution 	        36;                  // number of divisions	
-			
-		material solidProperty;                  // material name of this wall    
-		 	
-		motion  axisOfRotation;	                 // motion component name 	
-	}
-
-	cylinderShell
-	{
-		type 	  cylinderWall;                  // type of the wall
-			
-		p1 		 (0.0 0.0 0.1);                  // begin point of cylinder axis 
-		
-		p2 		 (0.0 0.0 0.2);                  // end point of cylinder axis
-		 
-		radius1 	       0.1;                  // radius at p1	
-			
-		radius2 	       0.1;	                 // radius at p2	
-			
-		resolution 	        36;                  // number of divisions	
-			      	
-		material solidProperty;                  // material name of this wall
-			
-		motion  axisOfRotation;                  // motion component name 		
-	}
-
-	coneShelldown
-	{
-		type 	  cylinderWall;                  // type of the wall
-		
-		p1 		(0.0 0.0 0.02);                  // begin point of cylinder axis
-		 
-		p2 		 (0.0 0.0 0.1);                  // end point of cylinder axis 
-		
-		radius1 	      0.03;                  // radius at p1 
-		
-		radius2 	       0.1;                  // radius at p2	
-			
-		resolution 	        36;                  // number of divisions	
-		     	
-		material solidProperty;                  // material name of this wall	
-			
-		motion  axisOfRotation;	                 // motion component name  	
-	}
-
-	bottomCylinder
-	{
-		type 	  cylinderWall;  	             // type of the wall
-		
-		p1 		 (0.0 0.0 0.0);                  // begin point of cylinder axis	
-		  
-		p2 		(0.0 0.0 0.02);                  // end point of cylinder axis	
-		
-		radius1 	      0.03;		             // radius at p1  
-			
-		radius2 	      0.03;	                 // radius at p2	
-				
-		resolution 	        36;                  // number of divisions	
-			      	
-		material solidProperty;                  // material name of this wall
-			   	
-		motion  axisOfRotation;	                 // motion component name	
-	}
-
-	exitGate
-	{
-		type 	  cylinderWall;  	             // type of the wall	
-		
-		p1 	  (0.0 0.0 -0.001);                  // begin point of cylinder axis	
-		  
-		p2 		 (0.0 0.0 0.0);                  // end point of cylinder axis
-		
-		radius1 	      0.03;                  // radius at p1 
-				
-		radius2 	    0.0001;                  // radius at p2	
-			
-		resolution 	        36;	                 // number of divisions	
-			      	
-		material solidProperty;                  // material name of this wall
-		
-		motion  axisOfRotation;		             // motion component name			
-	}	
-}

tutorials/sphereGranFlow/toteblender/settings/particlesDict

@@ -1,79 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-objectName 	particlesDict;
-objectType 	dictionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-setFields
-{
-	/*
-	    Default value for fields defined for particles
-
-		These fields should always be defined for simulations with 
-
-		spherical particles.
-	*/
-
-	defaultValue 
-	{	
-		velocity 		realx3 	(0 0 0);         // linear velocity (m/s) 
-			
-		acceleration 	realx3 	(0 0 0);         // linear acceleration (m/s2)
-		 
-		rVelocity 		realx3 	(0 0 0);         // rotational velocity (rad/s)	
-			 
-		shapeName 		word	sphere1;         // name of the particle shape 	
-	}
-
-	selectors
-	{
-		shapeAssigne
-		{
-			selector 	stridedRange; 	         // other options: box, cylinder, sphere, randomPoints 
- 
-			stridedRangeInfo
-			{
-				begin 	    0;			         // begin index of points
-
-				end 	24000;		 			 // end index of points 
-
-				stride      3;			 		 // stride for selector 
-			}
-
-			fieldValue  					     // fields that the selector is applied to 
-			{
-				shapeName 	word    sphere1;     // sets shapeName of the selected points to largeSphere
-			}
-		}
-	}
-}
-
-positionParticles                                // positions particles 
-{
-	
-	method 	      ordered;                       // ordered positioning
-
-	mortonSorting     Yes;                       // perform initial sorting based on morton code?  
-
-	orderedInfo
-	{
-		diameter    0.005;                       // minimum space between centers of particles
-			 	
-		numPoints   24000;                       // number of particles in the simulation 
-		 	
-		axisOrder (x y z);                       // axis order for filling the space with particles	
-	}  
-
-	regionType cylinder;                         // other options: cylinder and sphere               
-	
-	cylinderInfo                                 // cylinder for positioning particles 
-	{
-		p1 (0.0 0.0 0.09);                       // Coordinates of bottom cylinderRegion (m,m,m)
-		
-		p2 (0.0 0.0 0.21);                       // Coordinates of top cylinderRegion (m,m,m)
-		
-		radius       0.09;                       // radius of cylinder
-	}
-}

tutorials/sphereGranFlow/toteblender/settings/settingsDict

@@ -1,34 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-objectName 	settingsDict;
-objectType 	dictionary;
-fileFormat 	ASCII;
-/*---------------------------------------------------------------------------*/
-run 	   toteblender;
-
-dt 			   0.00004; 	                     // time step for integration (s)
-
-startTime 		     0; 			             // start time for simulation 
-
-endTime 		    10;	 		                 // end time for simulation 
-
-saveInterval 	  0.05; 		                 // time interval for saving the simulation
-
-timePrecision        3;			                 // maximum number of digits for time folder 
-
-g 			(0 0 -9.8);                          // gravity vector (m/s2) 
-
-includeObjects (diameter);                       // save necessary (i.e., required) data on disk
-
-// exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
-
-integrationMethod 		AdamsBashforth2; 	     // integration method 
-
-writeFormat				          ascii;         // data writting format (ascii or binary)
-
-timersReport 			            Yes;  	     // report timers (Yes or No)
-
-timersReportInterval   	           0.02;	     // time interval for reporting timers