cmake_policy

layeredSiloFilling is Updated.

CMakeLists.txt

@@ -3,30 +3,17 @@ cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
 # set the project name and version
 project(phasicFlow VERSION 1.0 )
 
-set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
+set(CMAKE_CXX_STANDARD 20 CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_INSTALL_PREFIX ${phasicFlow_SOURCE_DIR} CACHE PATH "Install path of phasicFlow" FORCE)
-set(CMAKE_BUILD_TYPE Release CACHE STRING "build type" FORCE)
+set(CMAKE_BUILD_TYPE Release CACHE STRING "build type")
 set(BUILD_SHARED_LIBS ON CACHE BOOL "Build using shared libraries" FORCE)
 mark_as_advanced(FORCE var BUILD_SHARED_LIBS)
 
-message(STATUS ${CMAKE_INSTALL_PREFIX})
+message(STATUS "Install prefix is:" ${CMAKE_INSTALL_PREFIX})
 
 include(cmake/globals.cmake)
 
-#Kokkos directory to be included 
-set(Kokkos_Source_DIR)
-
-if(DEFINED ENV{Kokkos_DIR})
-   set(Kokkos_Source_DIR $ENV{Kokkos_DIR})
-else()
-  set(Kokkos_Source_DIR $ENV{HOME}/Kokkos/kokkos)
-endif()
-message(STATUS "Kokkos source directory is ${Kokkos_Source_DIR}")
-add_subdirectory(${Kokkos_Source_DIR} ./kokkos)
-Kokkos_cmake_settings()
-
-
 option(pFlow_STD_Parallel_Alg "Use TTB std parallel algorithms" ON)
 option(pFlow_Build_Serial "Build phasicFlow and backends for serial execution" OFF)
 option(pFlow_Build_OpenMP "Build phasicFlow and backends for OpenMP execution" OFF)
@@ -34,6 +21,8 @@ option(pFlow_Build_Cuda   "Build phasicFlow and backends for Cuda execution" OFF
 option(pFlow_Build_Double "Build phasicFlow with double precision floating-oint variables" ON)
 option(pFlow_Build_MPI    "Build for MPI parallelization. This will enable multi-gpu run, CPU run on clusters (distributed memory machine). Use this combination Cuda+MPI, OpenMP + MPI or Serial+MPI " OFF)
 
+#for installing the required packages
+include(cmake/preReq.cmake)
 
 if(pFlow_Build_Serial)
 	set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "Serial execution" FORCE) 
@@ -46,7 +35,8 @@ elseif(pFlow_Build_OpenMP )
 	set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "OpenMP execution" FORCE)
 	set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "Cuda execution" FORCE)
 	set(Kokkos_ENABLE_CUDA_LAMBDA OFF CACHE BOOL "Cuda execution" FORCE)
-	set(Kokkos_DEFAULT_HOST_PARALLEL_EXECUTION_SPACE SERIAL CACHE STRING "" FORCE)
+	set(Kokkos_DEFAULT_HOST_PARALLEL_EXECUTION_SPACE Serial CACHE STRING "" FORCE)
+	set(Kokkos_DEFAULT_DEVICE_PARALLEL_EXECUTION_SPACE OpenMP CACHE STRING "" FORCE)
 	set(Kokkos_ENABLE_CUDA_CONSTEXPR OFF CACHE BOOL "Enable constexpr on cuda code" FORCE)
 elseif(pFlow_Build_Cuda)
 	set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "Serial execution" FORCE) 
@@ -65,6 +55,7 @@ include(cmake/makeExecutableGlobals.cmake)
 
 configure_file(phasicFlowConfig.H.in phasicFlowConfig.H)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
 #add a global include directory 
 include_directories(src/setHelpers src/demComponent "${PROJECT_BINARY_DIR}")
 

cmake/preReq.cmake

@@ -0,0 +1,54 @@
+if(pFlow_STD_Parallel_Alg)
+    # Check if libtbb-dev is installed
+    execute_process(
+        COMMAND dpkg -s libtbb-dev
+        RESULT_VARIABLE TBB_IS_INSTALLED
+        OUTPUT_QUIET
+        ERROR_QUIET)
+
+    if(NOT TBB_IS_INSTALLED EQUAL 0)
+        message(STATUS "libtbb-dev not found. Installing libtbb-dev...")
+        execute_process(
+            COMMAND sudo apt-get update
+            COMMAND sudo apt-get install -y libtbb-dev
+            RESULT_VARIABLE TBB_INSTALL_RESULT)
+            
+        if(NOT TBB_INSTALL_RESULT EQUAL 0)
+            message(FATAL_ERROR "Failed to install libtbb-dev")
+        endif()
+    else()
+        message(STATUS "libtbb-dev is already installed.")
+    endif()
+endif()
+
+
+# Kokkos folder creation 
+set(Kokkos_Source_DIR $ENV{HOME}/Kokkos/kokkos)
+
+if(NOT EXISTS "${Kokkos_Source_DIR}/CMakeLists.txt")
+
+    # Check CMake version and set policy CMP0169 if CMake version is 3.30 or higher
+    if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.30")
+        cmake_policy(SET CMP0169 OLD)
+    endif()
+
+    include(FetchContent)
+    FetchContent_Declare(
+        kokkos
+        GIT_REPOSITORY https://github.com/kokkos/kokkos.git
+        GIT_TAG 4.3.01
+    )
+    
+    FetchContent_GetProperties(kokkos)
+    if(NOT kokkos_POPULATED)
+        message(STATUS "Kokkos source directory not found. Downloading Kokkos version 4.3.01 ...")
+        FetchContent_Populate(kokkos)
+        set(Kokkos_Source_DIR ${kokkos_SOURCE_DIR})
+    endif()
+
+endif()
+
+message(STATUS "Kokkos source directory is ${Kokkos_Source_DIR}")
+add_subdirectory(${Kokkos_Source_DIR} ./kokkos)
+#Kokkos_cmake_settings()
+

solvers/sphereGranFlow/sphereGranFlow.cpp

@@ -74,7 +74,7 @@ pFlow::initialize_pFlowProcessors();
 
 	do 
 	{
-		
+		//Ping;
 		if(! sphInsertion.insertParticles( 
 			Control.time().currentIter(),
 			Control.time().currentTime(),
@@ -90,21 +90,25 @@ pFlow::initialize_pFlowProcessors();
 
 		// set force to zero, predict, particle deletion and etc. 
 		sphParticles.beforeIteration();
-
+		//Ping;
 		sphInteraction.beforeIteration();
 		
 		sphInteraction.iterate();
 			
 		surfGeometry.iterate();
 
+		//Ping;
 		sphParticles.iterate();
 		
+		//Ping;
 		sphInteraction.afterIteration();
 
+		//Ping;
 		surfGeometry.afterIteration();
 
+		//Ping;
 		sphParticles.afterIteration();
-				
+		//Ping;	
 
 	}while(Control++);
 

src/Particles/globalDamping/globalDamping.cpp

@@ -35,10 +35,14 @@ pFlow::globalDamping::globalDamping(const systemControl& control)
     performDamping_ = !equal(dampingFactor_, static_cast<real>(1.0));
 
     if( performDamping_ )
+    {
       REPORT(2)<<"Global damping "<<Yellow_Text("is active")<<
 		  " and damping factor is "<<dampingFactor_<<END_REPORT;
+    }
 		else
+		{
       REPORT(2)<<"Global damping "<<Yellow_Text("is not active")<<"."<<END_REPORT;
+    }
 
 }
 

src/phasicFlow/containers/Set/Set.hpp

@@ -24,6 +24,7 @@ Licence:
 #include <set>
 
 #include "types.hpp"
+#include "iOstream.hpp"
 
 namespace pFlow
 {
@@ -34,6 +35,20 @@ using Set = std::set<Key,std::less<Key>,std::allocator<Key>>;
 
 using wordSet = Set<word>;
 
+template<typename key>
+iOstream& operator<<(iOstream& os, const Set<key>& s)
+{
+	os << beginListToken();
+	for(auto elm = s.begin(); elm!=s.end(); )
+	{
+		os<< *elm++;
+        if( elm!=s.end() )
+			os<<spaceToken();
+	}
+	os<< endListToken();
+    os.check(FUNCTION_NAME);
+    return os;
+}
 
 }
 

src/phasicFlow/repository/systemControl/systemControl.cpp

@@ -36,6 +36,8 @@ bool pFlow::systemControl::readIncludeExclue(const dictionary& dict)
 		}
 	}
     
+    REPORT(1)<<"IncludeObject list is: "<<Green_Text(includeList_)<<END_REPORT;
+
 	if (dict.containsDataEntry("excludeObjects"))
 	{
 		wordList excld = dict.getVal<wordList>("excludeObjects");
@@ -44,6 +46,8 @@ bool pFlow::systemControl::readIncludeExclue(const dictionary& dict)
 			excludeList_.insert(nm);
 		}
 	}
+
+    REPORT(1)<<"excludeObject list is: "<<Green_Text(excludeList_)<<END_REPORT;
 	return true;
 }
 

tutorials/sphereGranFlow/RotaryAirLockValve/ReadMe.md

@@ -1,7 +1,7 @@
 # Problem Definition
 The problem is to simulate a Rotary Air-Lock Valve. The external diameter of rotor is about 21 cm. There is one type of particle in this simulation. Particles are inserted into the inlet of the valve from t=**0** s.
 * **28000** particles with **5 mm** diameter are inserted into the valve with the rate of **4000 particles/s**. 
-* The rotor starts its ortation at t = 1.25 s at the rate of 2.1 rad/s. 
+* The rotor starts its rotation at t = 1.25 s at the rate of 2.1 rad/s. 
 
 
 <html>

tutorials/sphereGranFlow/RotaryAirLockValve/caseSetup/interaction

@@ -46,7 +46,7 @@ model
     nu      (0.25 0.25                           // Poisson's ratio [-]
                   0.25);
 
-    en    (0.7     0.8                           // coefficient of normal restitution
+    en      (0.70 0.80                           // coefficient of normal restitution
                    1.0);
 
     et        (1.0 1.0                           // coefficient of tangential restitution

tutorials/sphereGranFlow/RotaryAirLockValve/settings/settingsDict

@@ -6,7 +6,7 @@ objectName 	geometryDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-run		rotatingValve;
+run		       rotatingAirLockValve;
 
 dt			   0.00001; // time step for integration (s)
 
@@ -16,24 +16,21 @@ endTime			    7;                           // end time for simulation
 
 saveInterval   0.05;    // time interval for saving the simulation
 
-timePrecision	    6;                           // 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) 
 
-/*
-	Simulation domain every particles that goes outside this domain is deleted
-*/
-
-includeObjects (diameter);                       // save necessary (i.e., required) data on disk
+// save necessary (i.e., required) data on disk
+includeObjects (diameter mass);      
 
 // exclude unnecessary data from saving on disk
 excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
-integrationMethod	    AdamsBashforth2;         // integration method 
+integrationMethod	 AdamsBashforth2;  
 
 writeFormat 		 ascii; // data writting format (ascii or binary)
 
 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/binarySystemOfParticles/README.md

@@ -45,7 +45,6 @@ in <b>settings/particlesDict</b> file
 positionParticles
 {
     method ordered;         // other options: random or empty
-
     orderedInfo
     {        
            diameter 0.005;     // minimum space between centers of particles
@@ -100,6 +99,7 @@ setFields
                 end     30000;        // end index of points 
                 stride      3;        // stride for selector 
             }
+            
             fieldValue                // fields that the selector is applied to 
             {
                 /*

tutorials/sphereGranFlow/conveyorBelt/settings/geometryDict

@@ -55,15 +55,20 @@ surfaces
 	belt
 	{
 		type 	          stlWall;  	         // type of the wall
+
 		file 	         belt.stl;	             // file name in stl folder	
+
 		material          wallMat;               // material name of this wall
+
 		motion 	    conveyorBelt1;		         // motion component name 
 	}
 
 	box
 	{
 		type 	         stlWall;  	             // type of the wall
+
 		file 	         box.stl;	             // file name in stl folder
+
 		material         wallMat;                // material name of this wall
 	}
 }

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/README.md

@@ -0,0 +1,20 @@
+# Simulating a Simple Homogenization Silo Using Periodic Boundary 
+
+## Problem
+A homogenization silo is used to mix particles inside a silo using the circulation of particles. A pneumatic conveying system carries particles from the exit and re-enters them from the top. Here, we use a `periodic` boundary to simulate the action of the pneumatic conveyor system for circulating particles. Particles exiting from the bottom are re-entered from the top using this boundary (`periodic`).
+
+The simulation case setup is essentially similar to the [`layeredSiloFilling`](https://github.com/PhasicFlow/phasicFlow/tree/main/tutorials/sphereGranFlow/layeredSiloFilling) tutorial. There is also another change with regard to `layeredSiloFilling`. The exit gate is opened after the filling phase of the silo (see `settings/geometryDict` for more details).
+
+<div align ="center">
+<img src="./homoSilo.jpeg" style="width: 400px;">
+
+<b>
+
+A view of the homogenization silo
+</b>
+
+</div>
+
+***
+
+

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/caseSetup/interaction

@@ -0,0 +1,67 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+materials   (lightMat heavyMat wallMat);         // a list of materials names
+
+densities            (1000 1500.0 2500);         // density of materials [kg/m3]
+
+contactListType       sortedContactList;
+
+contactSearch
+{
+   method         NBS;                           // method for broad search particle-particle
+   
+   updateInterval 10;
+
+   sizeRatio      1.1;
+
+   cellExtent     0.55;
+
+   adjustableBox  No;
+} 
+
+model
+{
+   contactForceModel nonLinearLimited;
+
+   rollingFrictionModel        normal;
+
+   /*
+
+   Property (lightMat-lightMat   lightMat-heavyMat    lightMat-wallMat
+                                 heavyMat-heavyMat    heavyMat-wallMat
+                                                      wallMat-wallMat  );
+   */
+
+   Yeff (1.0e6 1.0e6 1.0e6                       // Young modulus [Pa]
+               1.0e6 1.0e6
+                     1.0e6);
+   
+   Geff (0.8e6 0.8e6 0.8e6                       // Shear modulus [Pa]
+               0.8e6 0.8e6
+                     0.8e6);
+
+   nu    (0.25 0.25  0.25                        // Poisson's ratio [-]
+               0.25  0.25
+                     0.25);
+
+   en (0.97  0.97    0.85                        // coefficient of normal restitution
+             0.97    0.85
+                     1.00);
+
+   mu (0.65   0.65 0.35                          // dynamic friction 
+              0.65 0.35
+                   0.35);
+
+   mur (0.1  0.1 0.1                             // rolling friction 
+             0.1 0.1
+                 0.1);       
+}
+
+
+

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/caseSetup/particleInsertion

@@ -0,0 +1,214 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName particleInsertion;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active           Yes;   // is insertion active -> yes or no
+
+/*
+   six layers of particles are packed 
+*/
+layer0
+{  
+   timeControl          simulationTime;
+
+   regionType           cylinder;          // type of insertion region
+
+   rate                 5100;          // insertion rate (particles/s)
+
+   startTime            0;          // (s)
+
+   endTime              0.5;          // (s)
+
+   insertionInterval    0.025;          // s 
+
+   cylinderInfo 
+   {
+   	radius 	  0.09;          // radius of cylinder (m)
+
+   	p1         (0.0  0.0 0.1);          // (m,m,m)
+
+   	p2         (0.0  0.0 0.11);          // (m,m,m)
+   }
+   
+   setFields
+   {
+     velocity     realx3 (0.0 0.0 -0.6);         // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+      parType1    1;          // mixture composition of inserted particles 
+   }
+}
+
+layer1
+{
+   timeControl          simulationTime;
+
+   regionType           cylinder;          // type of insertion region
+
+   rate                 5100;          // insertion rate (particles/s)
+
+   startTime            0.7;          // (s)
+
+   endTime              1.2;          // (s)
+
+   insertionInterval    0.025;          // s 
+
+   
+   cylinderInfo 
+   {
+      radius 0.09;
+      p1     (0.0  0.0 0.16 ); // (m,m,m)
+      p2     (0.0  0.0 0.17); // (m,m,m)
+   }
+   
+   setFields
+   {
+     velocity    realx3 (0.0 0.0 -0.6);
+   }
+   
+   mixture
+   {
+      parType2 1; // only parType2
+      
+   }
+}
+
+layer2
+{
+   timeControl          simulationTime;
+
+   regionType           cylinder;          // type of insertion region
+
+   rate                 5100;          // insertion rate (particles/s)
+
+   startTime            1.4;          // (s)
+
+   endTime              1.9;          // (s)
+
+   insertionInterval    0.025;          // s 
+
+   cylinderInfo 
+   {
+      radius   0.09;
+      p1 ( 0.0  0.0 0.2 ); // (m,m,m)
+      p2 ( 0.0  0.0 0.21); // (m,m,m)
+   }
+   
+   setFields
+   {
+     velocity    realx3 (0.0 0.0 -0.6);
+   }
+   
+   mixture
+   {
+      parType1 1; // only parType1
+      
+   }
+}
+
+layer3
+{
+   timeControl          simulationTime;
+
+   regionType           cylinder;      // type of insertion region
+
+   rate                 5100;          // insertion rate (particles/s)
+
+   startTime            2.1;           // (s)
+
+   endTime              2.6;           // (s)
+
+   insertionInterval    0.025;         // s 
+   
+
+   cylinderInfo 
+   {
+      radius   0.09;
+      p1 ( 0.0  0.0 0.28 ); // (m,m,m)
+      p2 ( 0.0  0.0 0.29); // (m,m,m)
+   }
+   
+   setFields
+   {
+     velocity   realx3 (0.0 0.0 -0.6);
+   }
+   
+   mixture
+   {
+      parType2 1;
+      
+   }
+}
+
+layer4
+{
+   timeControl          simulationTime;
+
+   regionType                 cylinder;          // type of insertion region
+
+   rate                          5100;          // insertion rate (particles/s)
+
+   startTime                       2.8;          // (s)
+
+   endTime                         3.3;          // (s)
+
+   insertionInterval             0.025;          // s  
+
+   cylinderInfo 
+   {
+      radius   0.09;
+      p1 ( 0.0  0.0 0.37 ); // (m,m,m)
+      p2 ( 0.0  0.0 0.38); // (m,m,m)
+   }
+   
+   setFields
+   {
+     velocity    realx3 (0.0 0.0 -0.6);
+   }
+   
+   mixture
+   {
+      parType1 1;
+      
+   }
+}
+
+layer5
+{
+   timeControl          simulationTime;
+
+   regionType                 cylinder;          // type of insertion region
+
+   rate                          5100;          // insertion rate (particles/s)
+
+   startTime                       3.4;          // (s)
+
+   endTime                         3.9;          // (s)
+
+   insertionInterval             0.025;          // s  
+
+   cylinderInfo 
+   {
+      radius   0.09;
+      p1 ( 0.0  0.0 0.38 ); // (m,m,m)
+      p2 ( 0.0  0.0 0.39); // (m,m,m)
+   }
+   
+   setFields
+   {
+     velocity    realx3 (0.0 0.0 -0.6);
+   }
+   
+   mixture
+   {
+      parType2 1;
+      
+   }
+}

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/caseSetup/shapes

@@ -2,18 +2,14 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
-objectType dicrionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
 objectName 	sphereDict;
 objectType 	sphereShape;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+names 		 (parType1 parType2); 	     // names of shapes 
 
-// names of shapes
-names 		(sphere);
+diameters 	 (0.00885 0.0089);		     // diameter of shapes 
+
+materials	 (lightMat heavyMat);		     // material names for shapes 
 
-// diameter of shapes 
-diameters 	(0.005);
 
-// material names for shapes 
-materials	(sphereMat);

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/cleanThisCase

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

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/runThisCase

@@ -0,0 +1,24 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+echo "\n<--------------------------------------------------------------------->"
+echo "1) Creating particles"
+echo "<--------------------------------------------------------------------->\n"
+particlesPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "2) Creating geometry"
+echo "<--------------------------------------------------------------------->\n"
+geometryPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "3) Running the case"
+echo "<--------------------------------------------------------------------->\n"
+sphereGranFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "4) Converting to vtk"
+echo "<--------------------------------------------------------------------->\n"
+pFlowToVTK --fields diameter velocity id --binary
+
+
+#------------------------------------------------------------------------------

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/domainDict

@@ -0,0 +1,52 @@
+/* -------------------------------*- 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 (-0.11 -0.11 -0.15);
+	
+	max ( 0.11  0.11  0.4);
+}
+
+boundaries
+{
+	
+	left
+	{
+		type exit;     
+	}
+
+	right
+	{
+		type exit;     
+	}
+
+	bottom
+	{
+		type exit;          
+	}
+
+	top
+	{
+		type exit;   
+	}
+
+	rear
+	{
+		type periodic;      
+	}
+
+	front
+	{
+		type periodic;   
+	}
+}    
+
+

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/geometryDict

@@ -0,0 +1,87 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	geometryDict;
+objectType 	dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+motionModel            rotatingAxis;   
+
+rotatingAxisInfo
+{
+	// for opening the gate of silo between time 4.1 and 5.1 s
+	gateMotion
+	{
+		p1        (-0.04 -0.04 -0.1);
+		p2        (-0.04 -0.04  0.0);
+		omega     3.14;
+		startTime 4.1;
+		endTime   5.1;
+	}
+}
+
+surfaces
+{
+	cylinderShell
+	{
+		type 		 cylinderWall;  	         // other options: cuboidWall and planeWall
+
+		p1 			(0.0 0.0 0.0);               // begin point of cylinder axis
+
+		p2 			(0.0 0.0 0.4);               // end point of cylinder axis
+
+		radius1 	          0.1;		         // radius at p1
+ 
+		radius2 	          0.1;		         // radius at p2
+
+		resolution 	           36;      	     // number of divisions
+
+		material 	      wallMat;   	         // material name of this wall
+	}
+
+	coneShell
+	{
+		type 		 cylinderWall;  	         // other options: cuboidWall and planeWall
+
+		p1 		   (0.0 0.0 -0.1);               // begin point of cylinder axis
+
+		p2 			(0.0 0.0 0.0);               // end point of cylinder axis
+
+		radius1 	         0.04;		         // radius at p1
+
+		radius2 	          0.1;		         // radius at p2
+  
+		resolution 	           36;      	     // number of divisions
+
+		material 	      wallMat;   	         // material name of this wall
+	}
+
+	/*
+		This is a plane wall at the exit of silo
+	*/
+
+	exitGate
+	{
+		type        planeWall;                   // other options: cuboidWall and cylinderWall
+
+		p1 (-0.04 -0.04 -0.1);                   // first point of the wall
+
+		p2 ( 0.04 -0.04 -0.1);                   // second point of the wall
+
+		p3 ( 0.04  0.04 -0.1);                   // third point of the wall
+
+		p4 (-0.04  0.04 -0.1);                   // fourth point of the wall
+		 
+		material      wallMat;                   // material name of the wall
+
+		motion 		gateMotion; 
+	}
+}
+
+
+
+
+
+

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/particlesDict

@@ -0,0 +1,36 @@
+/* -------------------------------*- 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	     parType1;   // name of the particle shape 
+	}
+
+	selectors
+	{}
+}
+
+positionParticles                                 
+{
+	method                empty;                 // empty simulation  
+}
+

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/settingsDict

@@ -0,0 +1,41 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	settingsDict;
+objectType 	dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run             homogenizationSilo;
+
+dt 				0.00001; 	// time step for integration (s)
+
+startTime 		0.0; 		// start time for simulation 
+
+endTime 		20;	        // 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) 
+
+
+// overrides the default behavior 
+includeObjects (diameter);    
+
+// exclude unnecessary data from saving on disk
+excludeObjects (rVelocity.dy1 rVelocity.dy2 rVelocity.dy3 
+				pStructPosition.dy1 pStructPosition.dy2 pStructPosition.dy3
+				pStructVelocity.dy1 pStructVelocity.dy2 pStructVelocity.dy3); 
+
+integrationMethod 		AdamsBashforth4; // integration method 
+
+writeFormat				binary;    // data writting format (ascii or binary)
+
+timersReport 			Yes;  	   // report timers
+
+timersReportInterval    0.1;	   // time interval for reporting timers
+
+
+

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/interaction

@@ -54,10 +54,6 @@ model
                  0.97 0.85
                       1.00);
 
-   et (1.0   1.0  1.0                            // coefficient of tangential restitution 
-             1.0  1.0
-                  1.0);
-
    mu      (0.65 0.65 0.35                       // dynamic friction 
                  0.65 0.35
                       0.35);
@@ -66,6 +62,3 @@ model
                    0.1 0.1
                        0.1);       
 }
-
-
-

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/particleInsertion

@@ -6,34 +6,26 @@ objectName particleInsertion;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-active           Yes;                            // is insertion active -> yes or no
 
-checkForCollision No;                            // is checked          -> yes or no
+// is insertion active -> yes or no
+active           Yes;
 
 /*
-   one layers of particles are packed 
+   six layers of particles are packed 
 */
-
 layer0
 {
     timeControl          simulationTime;
-
     regionType           cylinder;    // type of insertion region
-
     rate                 15000;      // insertion rate (particles/s)
-
     startTime            0;          // (s)
-
     endTime              0.5;        // (s)
-
     insertionInterval    0.025;      // s 
 
     cylinderInfo 
     {
         radius     0.09;             // radius of cylinder (m)
-
         p1         (0.0  0.0 0.1);   // (m,m,m)
-
         p2         (0.0  0.0 0.11);  // (m,m,m)
     }
 
@@ -48,7 +40,138 @@ layer0
     }
 }
 
+layer1
+{
+    timeControl          simulationTime;
+    regionType           cylinder;   // type of insertion region
+    rate                 15000;      // insertion rate (particles/s)
+    startTime            0.7;        // (s)
+    endTime              1.2;        // (s)
+    insertionInterval    0.025;      // s 
 
+    cylinderInfo 
+    {
+        radius 0.09;
+        p1     (0.0  0.0 0.16 ); // (m,m,m)
+        p2     (0.0  0.0 0.17); // (m,m,m)
+    }
 
+    setFields
+    {
+        velocity    realx3 (0.0 0.0 -0.6);
+    }
 
+    mixture
+    {
+      heavySphere 1; // only heavySphere
+    }
+}
+
+layer2
+{
+    timeControl          simulationTime;
+    regionType           cylinder;   // type of insertion region
+    rate                 15000;      // insertion rate (particles/s)
+    startTime            1.4;        // (s)
+    endTime              1.9;        // (s)
+    insertionInterval    0.025;      // s 
+
+    cylinderInfo 
+    {
+        radius   0.09;
+        p1 ( 0.0  0.0 0.2 ); // (m,m,m)
+        p2 ( 0.0  0.0 0.21); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 0.0 -0.6);
+    }
+
+    mixture
+    {
+        lightSphere 1; // only lightSphere
+    }
+}
+
+layer3
+{
+    timeControl          simulationTime;
+    regionType           cylinder;   // type of insertion region
+    rate                 15000;      // insertion rate (particles/s)
+    startTime            2.1;        // (s)
+    endTime              2.6;        // (s)
+    insertionInterval    0.025;      // s 
+
+    cylinderInfo 
+    {
+        radius   0.09;
+        p1 ( 0.0  0.0 0.28 ); // (m,m,m)
+        p2 ( 0.0  0.0 0.29); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity   realx3 (0.0 0.0 -0.6);
+    }
+
+    mixture
+    {
+        heavySphere 1;
+    }
+}
+
+layer4
+{
+    timeControl          simulationTime;
+    regionType           cylinder;   // type of insertion region
+    rate                 15000;      // insertion rate (particles/s)
+    startTime            2.8;        // (s)
+    endTime              3.3;        // (s)
+    insertionInterval    0.025;      // s  
+
+    cylinderInfo 
+    {
+        radius   0.09;
+        p1 ( 0.0  0.0 0.37 ); // (m,m,m)
+        p2 ( 0.0  0.0 0.38); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 0.0 -0.6);
+    }
+
+    mixture
+    {
+        lightSphere 1;
+    }
+}
+
+layer5
+{
+    timeControl          simulationTime;
+    regionType           cylinder;   // type of insertion region
+    rate                 15000;      // insertion rate (particles/s)
+    startTime            3.4;        // (s)
+    endTime              3.9;        // (s)
+    insertionInterval    0.025;      // s  
+
+    cylinderInfo 
+    {
+        radius   0.09;
+        p1 ( 0.0  0.0 0.38); // (m,m,m)
+        p2 ( 0.0  0.0 0.39); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 0.0 -0.6);
+    }
+
+    mixture
+    {
+        heavySphere 1;
+    }
+}
 

tutorials/sphereGranFlow/layeredSiloFilling/settings/domainDict

@@ -2,64 +2,49 @@
 |  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
+
+// Simulation domain: every particle that goes outside this domain will be deleted
+globalBox
 {
     min (-0.11 -0.11 -0.11);
-	
     max ( 0.11  0.11  0.41);
 }
 
 boundaries
 {
-	// 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 
-
-	neighborListUpdateInterval 30;
-	
-	// Determines how often do you want to update the new changes in the boundary
-
-	updateInterval             10;
-
-	// The distance from the boundary plane within which particles are marked to be in the boundary list 
-
-	neighborLength          0.004;
-
     left
     {
-		type exit;	                             // other options: periodict, reflective 
+        type exit; // other options: periodic, reflective
     }
 
     right
     {
-		type exit;                               // other options: periodict, reflective 
+        type exit; // other options: periodic, reflective
     }
 
     bottom
     {
-		type exit;                               // other options: periodict, reflective 
+        type exit; // other options: periodic, reflective
     }
 
     top
     {
-		type exit;                               // other options: periodict, reflective 
+        type exit; // other options: periodic, reflective
     }
 
     rear
     {
-		type exit;                               // other options: periodict, reflective 
+        type exit; // other options: periodic, reflective
     }
 
     front
     {
-		type exit;                               // other options: periodict, reflective 
+        type exit; // other options: periodic, reflective
     }
 }
-
-

tutorials/sphereGranFlow/layeredSiloFilling/settings/geometryDict

@@ -2,15 +2,18 @@
 |  phasicFlow File                                                            |
 |  copyright: www.cemf.ir                                                     |
 \* ------------------------------------------------------------------------- */
+
 objectName  geometryDict;
 objectType  dictionary;
 fileFormat  ASCII;
+
 /*---------------------------------------------------------------------------*/
-motionModel            stationary;               // motion model can be rotatingAxis or stationary or vibrating
+
+motionModel            stationary; // motion model can be rotatingAxis, stationary, or vibrating
 
 stationaryInfo
 {
-	
+    // No additional information needed for stationary motion model
 }
 
 surfaces
@@ -18,59 +21,35 @@ surfaces
     cylinderShell
     {
         type        cylinderWall;  // other options: cuboidWall and planeWall
-
         p1          (0.0 0.0 0.0); // begin point of cylinder axis
-
         p2          (0.0 0.0 0.4); // end point of cylinder axis
-
         radius1     0.1;           // radius at p1
- 
         radius2     0.1;           // radius at p2
-
         resolution  36;            // number of divisions
-
         material    wallMat;       // material name of this wall
     }
 
     coneShell
     {
         type        cylinderWall; // other options: cuboidWall and planeWall
-
         p1          (0.0 0.0 -0.1); // begin point of cylinder axis
-
         p2          (0.0 0.0 0.0); // end point of cylinder axis
-
         radius1     0.02;          // radius at p1
-
         radius2     0.1;           // radius at p2
-  
         resolution  36;            // number of divisions
-
         material    wallMat;       // material name of this wall
     }
 
     /*
-		This is a plane wall at the exit of silo
+        This is a plane wall at the exit of the silo that plugs the exit.
     */
-
     exitGate
     {
         type        planeWall;   // other options: cuboidWall and cylinderWall
-
         p1          (-0.02 -0.02 -0.1); // first point of the wall
-
         p2          ( 0.02 -0.02 -0.1); // second point of the wall
-
         p3          ( 0.02  0.02 -0.1); // third point of the wall
-
         p4          (-0.02  0.02 -0.1); // fourth point of the wall
-		 
         material    wallMat;       // material name of the wall
     }
 }
-
-
-
-
-
-

tutorials/sphereGranFlow/layeredSiloFilling/settings/particlesDict

@@ -10,9 +10,7 @@ setFields
 {
 	/*
 	    Default value for fields defined for particles
-
 		These fields should always be defined for simulations with 
-
 		spherical particles.
 	*/
 
@@ -20,7 +18,7 @@ setFields
 	{
 		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/s^2)
 
 		rVelocity 		realx3 	    (0 0 0);  	 // rotational velocity (rad/s)
 
@@ -31,17 +29,8 @@ setFields
 	{}
 }
 
-positionParticles                                // positions particles 
+positionParticles     
 {
-	method                empty;                 // other options: ordered and random 
-
-	regionType              box;                 // other options: cylinder and sphere  
-
-	boxInfo                                      // box region for positioning particles 
-	{
-		min (-0.08 -0.08 0.015);                 // lower corner point of the box 
-
-		max ( 0.08  0.08 0.098);	             // upper corner point of the box 
-	} 
+	method    empty;   // empty simulation 
 }
 

tutorials/sphereGranFlow/layeredSiloFilling/settings/settingsDict

@@ -6,7 +6,7 @@ objectName 	settingsDict;
 objectType      dictionary;
 fileFormat      ASCII;
 /*---------------------------------------------------------------------------*/
-run   layerdSiloFilling;
+run             layeredSiloFilling;
 
 dt              0.00001;       // time step for integration (s)
 
@@ -18,25 +18,19 @@ saveInterval 	   0.05; 		                 // time interval for saving the simula
 
 timePrecision   6;             // maximum number of digits for time folder
 
-g 			 (0 0 -9.8);                         // gravity vector (m/s2) 
+g               (0 0 -9.8);    // gravity vector (m/s^2)
 
 // save data objects that are not automatically saved on disk.
-
 // overrides the default behavior
-
-includeObjects (diameter);    
+includeObjects  (diameter mass);
 
 // 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)
+writeFormat          ascii;           // data writing format (ascii or binary)
 
 timersReport         Yes;             // report timers
 
-timersReportInterval   	           0.01;	      // time interval for reporting timers
-
-
-
+timersReportInterval 0.05;            // time interval for reporting timers

tutorials/sphereGranFlow/screwConveyor/README.md

@@ -1,23 +1,27 @@
-# Simulating a screw conveyor {#screwConveyor}
-## Problem definition
-The problem is to simulate a screw conveyorwith the diameter 0.2 m and the length 1 m and 20 cm pitch. It is filled with 30,000 4-mm spherical particles. The timestep for integration is 0.00001 s.
-<div align="center"><b>
-a view of rotating drum
+# Simulating a Screw Conveyor
 
-![]()
-</b></div>
+## Problem Definition
+
+The problem is to simulate a screw conveyor with a diameter of 0.2 m and a length of 1 m with a variable pitch. It is filled with 10 mm and 9 mm spherical particles. The timestep for integration is 0.00002 s. Particles are inserted from the top of the feeder at a rate of 2800 particles/s. The number composition of large and small particles is 2:1.
+
+<div align="center">
+
+<img src="./screw.jpeg" style="width: 400px;">
+<b>
+
+A view of the screw conveyor simulation
+</b>
+</div>
 
 ***
 
-## Setting up the case 
-PhasicFlow simulation case setup is based on the text-based scripts that we provide in two folders located in the simulation case folder: `settings` and `caseSetup` (You can find the case setup files in the above folders.
-All the commands should be entered in the terminal while the current working directory is the simulation case folder (at the top of the `caseSetup` and `settings`).
+## Setting Up the Case
 
+PhasicFlow simulation case setup is based on the text-based scripts provided in two folders located in the simulation case folder: `settings` and `caseSetup`. All commands should be entered in the terminal while the current working directory is the simulation case folder (at the top level of `caseSetup` and `settings`).
 
-### Creating particles
+### Creating Particles
 
-Open the file  `settings/particlesDict`. Two dictionaries, `positionParticles` and `setFields` position particles and set the field values for the particles. 
-In dictionary `positionParticles`, the positioning `method` is `positionOrdered`, which position particles in order in the space defined by `box`. `box` space is defined by two corner points `min` and `max`. In dictionary `positionOrderedInfo`, `numPoints` defines number of particles; `diameter`, the distance between two adjacent particles, and `axisOrder` defines the axis order for filling the space by particles. 
+Open the file `settings/particlesDict`. Two dictionaries, `positionParticles` and `setFields`, position particles and set the field values for the particles. In the dictionary `positionParticles`, the positioning `method` is `empty`, which means that there are no particles in the simulation at the start.
 
 <div align="center"> 
 in <b>settings/particlesDict</b> file
@@ -26,20 +30,20 @@ in <b>settings/particlesDict</b> file
 ```C++
 positionParticles
 {
+	// A list of options are: ordered, random
 	method empty;     		// creates the required fields with zero particles (empty). 
 
-	maxNumberOfParticles 	50000; // maximum number of particles in the simulation
-	mortonSorting 			Yes;    // perform initial sorting based on morton code?   
-
+	mortonSorting 			Yes;    // perform initial sorting based on morton    
 }
 ```
 
-Enter the following command in the terminal to create the particles and store them in `0` folder.
+Enter the following command in the terminal to create the particles and store them in the `0` folder:
 
 `> particlesPhasicFlow`
 
-### Creating geometry
-In file `settings/geometryDict` , you can provide information for creating geometry. Each simulation should have a `motionModel` that defines a model for moving the surfaces in the simulation. `rotatingAxisMotion` model defines a fixed axis which rotates around itself. The dictionary `rotAxis` defines an motion component with `p1` and `p2` as the end points of the axis and `omega` as the rotation speed in rad/s. You can define more than one motion component in a simulation. 
+### Creating Geometry
+
+In the file `settings/geometryDict`, you can provide information for creating geometry. Each simulation should have a `motionModel` that defines a model for moving the surfaces in the simulation. The `rotatingAxis` model defines a fixed axis which rotates around itself. The dictionary `rotAxis` defines a motion component with `p1` and `p2` as the endpoints of the axis and `omega` as the rotation speed in rad/s. You can define more than one motion component in a simulation.
 
 <div align="center"> 
 in <b>settings/geometryDict</b> file
@@ -47,23 +51,21 @@ in <b>settings/geometryDict</b> file
 
 ```C++
 motionModel rotatingAxisMotion; 
-.
-.
-.
+
 rotatingAxisMotionInfo
 {
 	rotAxis 
 	{
-		p1 (1.09635 0.2010556 0.22313511);	// first point for the axis of rotation 
-		p2 (0.0957492 0.201556 0.22313511);	// second point for the axis of rotation
-		omega 3; 		// rotation speed (rad/s)
-		startTime 5;
-		endTime 30;
+		p1        (0 0 0.0); // first point for the axis of rotation 
+		p2        (0 0 1.0); // second point for the axis of rotation
+		omega     3.14; 	 // rotation speed (rad/s)
+		startTime 1;         // when t>1 s, rotation starts 
+		endTime   30;        // when t>30 s, rotation stops
 	}
 }
-
 ```
-In the dictionary `surfaces` you can define all the surfaces (shell) in the simulation. Two main options are available: built-in geometries in PhasicFlow, and providing surfaces with stl file. Here we use built-in geometries. In `cylinder` dictionary, a cylindrical shell with end helix, `material` name `prop1`, `motion` component `none` is defined. `helix` define  plane helix at center of  cylindrical shell, `material` name `prop1` and `motion` component `rotAxis`.'rotAxis' is use for helix because it is rotating and 'none' is use for shell because It is motionless.
+
+In the dictionary `surfaces`, you can define all the surfaces in the simulation. Two main options are available: built-in geometries in PhasicFlow, and providing surfaces with an STL file (ASCII format). Here we use `stlWall` as a method to provide the surface information through STL files. In the `shell` dictionary, `material` is set to `prop1` and `motion` is set to `none` (meaning this surface is fixed). `helix` defines the screw at the center of the cylindrical part of the shell. For this surface, `material` is set to `prop1` and `motion` is set to `rotAxis`.
 
 <div align="center"> 
 in <b>settings/geometryDict</b> file
@@ -75,7 +77,7 @@ surfaces
 	helix
 	{
 		type 	 stlWall;  	// type of the wall
-		file 	 helix.stl;	// file name in stl folder		
+		file 	 screw.stl;	// file name in stl folder		
 		material prop1;     // material name of this wall
 		motion 	 rotAxis;	// motion component name 
 	}
@@ -85,19 +87,18 @@ surfaces
 		type 	 stlWall;  	// type of the wall
 		file 	 shell.stl;	// file name in stl folder		
 		material prop1;     // material name of this wall
-		motion 	 none;		// motion component name 
+		motion 	 none;		// this surface is not moving ==> none
 	}
-
 }
-
 ```
 
-Enter the following command in the terminal to create the geometry and store it in `0/geometry` folder.
+Enter the following command in the terminal to create the geometry and store it in the `0/geometry` folder:
 
 `> geometryPhasicFlow`
 
-### Defining properties and interactions 
-In the file `caseSetup/interaction` , you find properties of materials. `materials` defines a list of material names in the simulation and `densities` sets the corresponding density of each material name. model dictionary defines the interaction model for particle-particle and particle-wall interactions. `contactForceModel` selects the model for mechanical contacts (here nonlinear model with limited tangential displacement) and `rollingFrictionModel` selects the model for calculating rolling friction. Other required prosperities should be defined in this dictionary. 
+### Defining Properties and Interactions
+
+In the file `caseSetup/interaction`, you will find properties of materials. `materials` defines a list of material names in the simulation and `densities` sets the corresponding density of each material name. The `model` dictionary defines the interaction model for particle-particle and particle-wall interactions. `contactForceModel` selects the model for mechanical contacts (here nonlinear model with limited tangential displacement) and `rollingFrictionModel` selects the model for calculating rolling friction. Other required properties should be defined in this dictionary.
 
 <div align="center"> 
 in <b>caseSetup/interaction</b> file
@@ -105,13 +106,14 @@ in <b>caseSetup/interaction</b> file
 
 ```C++
 materials      (prop1);    // a list of materials names
-densities      (1000.0);   // density of materials [kg/m3]
+densities      (2300.0);   // density of materials [kg/m3]
 
 contactListType   sortedContactList; 
 
 model
 {
    contactForceModel    nonLinearNonLimited;
+
    rollingFrictionModel normal;
 
    Yeff  (1.0e6);       // Young modulus [Pa]
@@ -120,18 +122,15 @@ model
 
    nu    (0.25);        // Poisson's ratio [-]
 
-   en    (0.7);         // coefficient of normal restitution
-
-   et    (1.0);         // coefficient of tangential restitution 
+   en    (0.8);         // coefficient of normal restitution 
 
    mu    (0.3);         // dynamic friction 
 
-   mur   (0.1);         // rolling friction 
-        
+   mur   (0.2);         // rolling friction 
 }
 ```
 
-Dictionary `contactSearch` sets the methods for particle-particle and particle-wall contact search. `method` specifies the algorithm for finding neighbor list for particle-particle contacts and `wallMapping` shows how particles are mapped onto walls for finding neighbor list for particle-wall contacts. `updateFrequency` sets the frequency for updating neighbor list and `sizeRatio` sets the size of enlarged cells (with respect to particle diameter) for finding neighbor list. Larger `sizeRatio` include more particles in the neighbor list and you require to update it less frequent. 
+The dictionary `contactSearch` sets the methods for broad search. `method` specifies the algorithm for finding the neighbor list for particle-particle contacts. `updateInterval` sets the intervals (in terms of the number of iterations) between each occurrence of updating the neighbor list, and `sizeRatio` sets the size of enlarged cells (with respect to particle diameter) for finding the neighbor list. A larger `sizeRatio` includes more particles in the neighbor list, requiring less frequent updates.
 
 <div align="center"> 
 in <b>caseSetup/interaction</b> file
@@ -140,69 +139,61 @@ in <b>caseSetup/interaction</b> file
 ```C++
 contactSearch
 {
-   method         NBS;           // method for broad search particle-particle
-   wallMapping    cellMapping;   // method for broad search particle-wall 
+    method          NBS;   // method for broad search 
     
-   NBSInfo
-   {
-      updateFrequency 10;        // each 20 timesteps, update neighbor list 
-      sizeRatio      1.1;        // 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;
 }
 ```
 
-In the file `caseSetup/sphereShape`, you can define a list of `names` for shapes (`shapeName` in particle field), a list of diameters for shapes and their `properties` names. 
+In the file `caseSetup/shapes`, you can define a list of `names` for shapes, a list of `diameters` for shapes, and their `materials` names.
 
 <div align="center"> 
-in <b>caseSetup/sphereShape</b> file
+in <b>caseSetup/shapes</b> file
 </div>
 
 ```C++
-names 		(sphere1); 	// names of shapes 
-diameters 	(0.01);	        // diameter of shapes 
-materials	(prop1);	// material names for shapes 
+names 		(sphere1 sphere2); 	// names of shapes 
+diameters 	(0.01  	 0.009);	// diameter of shapes 
+materials	(prop1   prop1);	// material names for shapes 
 ```
 
-Other settings for the simulation can be set in file `settings/settingsDict`. The dictionary `domain` defines the a rectangular bounding box with two corner points for the simulation. Each particle that gets out of this box, will be deleted automatically. 
+Other settings for the simulation can be set in the file `settings/settingsDict`. The dictionary `domain` defines a rectangular bounding box with two corner points for the simulation. Each particle that gets out of this box will be deleted automatically.
 
 <div align="center"> 
 in <b>settings/settingsDict</b> file
 </div>
 
 ```C++
-dt 		0.0001; 	// time step for integration (s)
+dt 				0.00002; 	// time step for integration (s)
+
 startTime 		0; 			// start time for simulation 
+
 endTime 		20;	 		// end time for simulation 
-saveInterval 	0.05; 		// time interval for saving the simulation
-timePrecision   6;		// maximum number of digits for time folder 
+
+saveInterval 	0.025; 		// time interval for saving the simulation
+
+timePrecision   4;			// maximum number of digits for time folder 
+
 g 				(0 -9.8 0); // gravity vector (m/s2) 
 
-domain 
-{
-	min (0.0 -0.06 0.001);
-	max (1.2 1 0.5);
-}
-
-integrationMethod 		AdamsBashforth3; 	// integration method 
-
-timersReport 			Yes;  	                // report timers?
-
-timersReportInterval    	0.01;	                // time interval for reporting timers
+writeFormat 	binary;     // field files will be saved in binary format
+...
 ```
 
-## Running the case 
-The solver for this simulation is `sphereGranFlow`. Enter the following command in the terminal. Depending on the computational power, it may take a few minutes to a few hours to complete. 
+## Running the Case
+
+The solver for this simulation is `sphereGranFlow`. Enter the following command in the terminal. Depending on the computational power, it may take a few minutes to a few hours to complete:
 
 `> sphereGranFlow`
 
-## Post processing 
-After finishing the simulation, you can render the results in Paraview. To convert the results to VTK format, just enter the following command in the terminal. This will converts all the results (particles and geometry) to VTK format and store them in folder `VTK/`. 
+## Post Processing
 
-`> pFlowToVTK`
+After finishing the simulation, you can render the results in ParaView. To convert the results to VTK format, enter the following command in the terminal. This will convert all the results (particles and geometry) to VTK format and store them in the `VTK/` folder:
+
+`> pFlowToVTK --binary  -f diameter id velocity`

tutorials/sphereGranFlow/screwConveyor/caseSetup/interaction

@@ -6,25 +6,12 @@ objectName interaction;
 objectType dicrionary;
 fileFormat 	ASCII;
 /*---------------------------------------------------------------------------*/
-materials       (prop1);                         // a list of materials names
 
-densities      (1000.0);                         // density of materials [kg/m3]
+materials      (prop1);    // a list of materials names
+densities      (2300.0);   // 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;
@@ -37,14 +24,24 @@ model
 
    nu    (0.25);        // Poisson's ratio [-]
 
-   en      (0.7);                                // coefficient of normal restitution
-
-   et      (1.0);                                // coefficient of tangential restitution 
+   en    (0.8);         // coefficient of normal restitution 
 
    mu    (0.3);         // dynamic friction 
 
-   mur     (0.1);                                // rolling friction     
+   mur   (0.2);         // rolling friction 
+        
 }
 
 
+contactSearch
+{
+    method          NBS;   // method for broad search 
     
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;
+}

tutorials/sphereGranFlow/screwConveyor/caseSetup/particleInsertion

@@ -6,46 +6,42 @@ 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?
 
-/*
-      five layers of particles are packed one-by-one using 5 insertion steps 
-*/
 
-layer0
+feeder
 {
+   rate 	              2800;  // insertion rate (particles/s)
+   
    timeControl         simulationTime;
 
-   regionType		      cylinder;                // type of insertion region
+   startTime 	        0;
    
-   rate 	                   5000;                // Particles Insertion Rate (particles/s)
+   endTime   	        100;
    
-   startTime 	                0;                // Start time of LightParticles insertion (s)
+   insertionInterval   0.04;   //s
    
-   endTime   	              100;                // End time of LightParticles insertion (s) 
+   regionType          box;  
 
-   insertionInterval        0.03;                // Time Interval of LightParticles insertion (s) 
-
-   cylinderInfo 
+   boxInfo 
    {
-   	p1  (0.22 0.730 0.25);                     // Bottom of cylinderRegion(m,m,m)
 
-   	p2  (0.22 0.742 0.25);                     // Top of cylinderRegion (m,m,m)
-
-      radius           0.09;                     // radius of cylinder (m)
+   	min ( -0.15 0.34  0.01); // (m,m,m)
+   	max (  0.15 0.36 0.15);  // (m,m,m)
    }
    
+   // initial velocity of inserted particles
    setFields
    {
-     velocity    realx3 (0.0 -0.6 -0);           // initial velocity of inserted particles 
+     velocity    realx3 (0.0 -0.65 0);  
    }
    
+   // mixture composition of inserted particles
    mixture
    {
-      sphere1 1;                                 // mixture composition of inserted particles 
-      
+      sphere1 2; 
+      sphere2 1; 
    }
 }
 

tutorials/sphereGranFlow/screwConveyor/caseSetup/shapes

@@ -3,11 +3,10 @@
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
 objectName 	sphereDict;
-objectType 	sphereShape;
+objectType 	shapes;
 fileFormat 	ASCII;
 /*---------------------------------------------------------------------------*/
-names 		(sphere1); 	                         // names of shapes 
 
-diameters 	  (0.01);	                         // diameter of shapes 
-
-materials	 (prop1);	                         // material names for shapes 
+names 		(sphere1 sphere2); 	// names of shapes 
+diameters 	(0.01  	 0.009);	// diameter of shapes 
+materials	(prop1   prop1);	// material names for shapes 

tutorials/sphereGranFlow/screwConveyor/caseSetup/sphereShape

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

tutorials/sphereGranFlow/screwConveyor/runThisCase

@@ -15,7 +15,10 @@ echo "3) Running the case"
 echo "<--------------------------------------------------------------------->\n"
 sphereGranFlow
 
-
+echo "\n<--------------------------------------------------------------------->"
+echo "4) Converting to VTK"
+echo "<--------------------------------------------------------------------->\n"
+pFlowToVTK -f diameter velocity id 
 
 
 #------------------------------------------------------------------------------

tutorials/sphereGranFlow/screwConveyor/settings/domainDict

@@ -2,63 +2,49 @@
 |  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 (0.0 -0.06 0.001);                   // lower corner point of the box 
 
-	    max       (1.2 1 0.5);                   // upper corner point of the box 
-}
-
-decomposition
+// Simulation domain: every particle that goes outside this domain will be deleted
+globalBox
 {
-	direction z;
+    min (-0.2 -0.20 -0.01);
+    max ( 0.2  0.4   1.05);
 }
 
 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 
+        type exit;
     }
 
     right
     {
-		type     exit;                           // other options: periodict, reflective 
+        type exit; 
     }
 
     bottom
     {
-		type     exit;                           // other options: periodict, reflective 
+        type exit; 
     }
 
     top
     {
-		type     exit;                           // other options: periodict, reflective 
+        type exit; 
     }
 
     rear
     {
-		type     exit;                           // other options: periodict, reflective 
+        type exit; 
     }
 
     front
     {
-		type     exit;                           // other options: periodict, reflective 
+        type exit; 
     }
 }

tutorials/sphereGranFlow/screwConveyor/settings/geometryDict

@@ -6,47 +6,41 @@ objectName 	geometryDict;
 objectType 	dictionary;
 fileFormat 	ASCII;
 /*---------------------------------------------------------------------------*/
-motionModel rotatingAxis;                        // motion model: rotating object around an axis
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
 
 rotatingAxisInfo
 {
 	rotAxis 
 	{
-		p1  (1.09635 0.2010556 0.22313511);	     // first point for the axis of rotation 
-
-		p2 (0.0957492 0.201556 0.22313511);	     // second point for the axis of rotation
-
-		omega                            3; 	 // rotation speed (rad/s)
-
-		startTime                        5;      // Start time of Geometry Rotating 
-
-		endTime                         30;      // End time of Geometry Rotating
+		p1        (0 0 0.0); // first point for the axis of rotation 
+		p2        (0 0 1.0); // second point for the axis of rotation
+		omega     3.14; 	 // rotation speed (rad/s)
+		startTime 1;         // when t>1 s, rotation starts 
+		endTime   30;        // when t>30 s, rotation stops
 	}
 }
 
+
 surfaces
 {
 	helix
 	{
 		type 	 stlWall;  	// type of the wall
-
-		file 	 helix.stl;	                     // file name in stl folder
-
+		file 	 screw.stl;	// file name in stl folder		
 		material prop1;     // material name of this wall
-
 		motion 	 rotAxis;	// motion component name 
 	}
 
 	shell
 	{
 		type 	 stlWall;  	// type of the wall
-
 		file 	 shell.stl;	// file name in stl folder		
-
 		material prop1;     // material name of this wall
-
-		motion 	      none;		                 // motion component name 
+		motion 	 none;		// this surface is not moving ==> none
 	}
+
 }
 
 

tutorials/sphereGranFlow/screwConveyor/settings/particlesDict

@@ -6,72 +6,34 @@ objectName 	particlesDict;
 objectType 	dictionary;
 fileFormat 	ASCII;
 /*---------------------------------------------------------------------------*/
+
+
+// positions particles 
+positionParticles
+{
+	// A list of options are: ordered, random
+	method empty;     		// creates the required fields with zero particles (empty). 
+
+	mortonSorting 			Yes;    // perform initial sorting based on morton 
+}
+
 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)
+		// linear velocity (m/s)
+		velocity 	  realx3 (0 0 0);
 
-		acceleration 	realx3 	(0 0 0);         // linear acceleration (m/s2)
+		// linear acceleration (m/s2)
+		acceleration  realx3 (0 0 0);
 
-		rVelocity 	    realx3 	(0 0 0);	     // rotational velocity (rad/s)
+		// rotational velocity (rad/s)
+		rVelocity 	  realx3 (0 0 0);
 
-		shapeName 	    word	sphere1;         // name of the particle shape
+		// name of the particle shape
+		shapeName 	  word	  sphere1;
 	}
 
 	selectors
-	{
-		shapeAssigne
-		{
-			selector 	stridedRange; 	         // other options: box, cylinder, sphere, randomPoints 
- 
-			stridedRangeInfo
-			{
-				begin 	    0;			         // begin index of points
-
-				end 	5000;		 			 // 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;     		             // other options: random and empty
-
-	mortonSorting    Yes;                        // perform initial sorting based on morton code?   
-
-	orderedInfo
-	{
-		diameter     0.01; 						 // minimum space between centers of particles
-
-		numPoints   5000; 	                     // 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 1);	             // upper corner point of the box 
-	}
-}
-

tutorials/sphereGranFlow/screwConveyor/settings/settingsDict

@@ -6,29 +6,37 @@ objectName 	settingsDict;
 objectType 	dictionary;
 fileFormat 	ASCII;
 /*---------------------------------------------------------------------------*/
+
 run 			screwConveyor;
 
-dt 				0.0001; 	                     // time step for integration (s)
+dt 				0.00002; 	// time step for integration (s)
 
 startTime 		0; 			// start time for simulation 
 
 endTime 		20;	 		// end time for simulation 
 
-saveInterval 	  0.05; 		                 // time interval for saving the simulation
+saveInterval 	0.025; 		// time interval for saving the simulation
 
-timePrecision        6;			                 // maximum number of digits for time folder 
+timePrecision   4;			// maximum number of digits for time folder 
 
 g 				(0 -9.8 0); // gravity vector (m/s2) 
 
-includeObjects (diameter);                       // save necessary (i.e., required) data on disk
+writeFormat 	binary;     // field files will be saved in binary format
+
+// A list of options: AB2, AB3, AB4, AB5
+integrationMethod 		AdamsBashforth4; 	// integration method
+
+// overrides the default behavior 
+includeObjects (diameter);
+
+
 
 // exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+excludeObjects (rVelocity.dy1 rVelocity.dy2 rVelocity.dy3 
+				pStructPosition.dy1 pStructPosition.dy2 pStructPosition.dy3
+				pStructVelocity.dy1 pStructVelocity.dy2 pStructVelocity.dy3);
 				 
-integrationMethod 		AdamsBashforth2; 	     // integration method 
 
-writeFormat				          ascii;         // data writting format (ascii or binary)
+timersReport 			Yes;  	// report timers?
 
-timersReport 			            Yes;  	     // report timers (Yes or No)
-
-timersReportInterval   	           0.01;	     // time interval for reporting timers
+timersReportInterval   	0.1;	// time interval for reporting timers

utilities/particlesPhasicFlow/empty/empty.cpp

@@ -30,7 +30,7 @@ pFlow::empty::empty(
 	positionParticles(control, dict),
 	position_
 	(
-		"empty",maxNumberOfParticles(), 0, RESERVE()
+		"empty",1, 0, RESERVE()
 	)
 {
 }

utilities/particlesPhasicFlow/positionOrdered/positionOrdered.cpp

@@ -146,7 +146,7 @@ pFlow::positionOrdered::positionOrdered
 	position_
 	(
 		"positionOrdered", 
-		max(maxNumberOfParticles(), numPoints_), 
+		numPoints_, 
 		numPoints_,
 		RESERVE()
 	)

utilities/particlesPhasicFlow/positionParticles/positionParticles.cpp

@@ -32,45 +32,10 @@ pFlow::realx3Vector pFlow::positionParticles::sortByMortonCode(
 		uint64 index;
 	};
 
-	/*realx3 minP = min(position);
-	realx3 maxP = max(position);
-	real cellsize = maxDiameter();
-	cells<uint64> allCells( box(minP, maxP), cellsize);
-
-	Vector<indexMorton> indMor(position.size(),RESERVE());
-
-	indMor.clear();
-
-	uint64 ind=0;
-	for(const auto& p:position)
-	{
-		auto cellInd = allCells.pointIndex(p);
-		indMor.push_back( 
-			{ xyzToMortonCode64(cellInd.x(), cellInd.y(), cellInd.z()),
-			ind++});
-	}
-
-	INFORMATION<<"Performing morton sorting."<<END_INFO;
-	std::sort(
-		indMor.begin(),
-		indMor.end(),
-		[]( const indexMorton &lhs, const indexMorton &rhs){
-			return lhs.morton < rhs.morton; } );
-
-	realx3Vector sortedPos(position.capacity(), RESERVE());
-	sortedPos.clear();
-
-
-	for(auto& ind:indMor)
-	{
-		sortedPos.push_back( position[ind.index] );
-	}*/
-
     WARNING<<"Morton sorting is inactive!"<<END_WARNING;
 	return position;
 }
 
-
 pFlow::positionParticles::positionParticles
 (
 	systemControl& control,
@@ -78,12 +43,8 @@ pFlow::positionParticles::positionParticles
 )
 :
 	regionType_(dict.getValOrSet<word>("regionType", "domain")),
-	maxNumberOfParticles_(dict.getValOrSet(
-		"maxNumberOfParticles", 
-		static_cast<uint32>(10000))),
 	mortonSorting_(dict.getValOrSet("mortonSorting", Logical("Yes")))
 {
-
 	if( regionType_ != "domain" )	
 	{
 		pRegion_ = peakableRegion::create(
@@ -92,7 +53,7 @@ pFlow::positionParticles::positionParticles
 	}	
 	else
 	{
-		fileDictionary domainDict
+		fileDictionary domainDictionary
 		(
 			objectFile
 			{
@@ -103,12 +64,10 @@ pFlow::positionParticles::positionParticles
 			},
 			&control.settings()
 		);
-		pRegion_ = peakableRegion::create(regionType_,domainDict.subDict("globalBox"));
+		pRegion_ = peakableRegion::create("box", domainDictionary.subDict("globalBox"));
 	}
-	
 }
 
-
 pFlow::realx3Vector pFlow::positionParticles::getFinalPosition()
 {
 	if(mortonSorting_)
@@ -130,10 +89,8 @@ pFlow::uniquePtr<pFlow::positionParticles>
     const dictionary & dict
 )
 {
-
 	word method = dict.getVal<word>("method");
 
-
 	if( dictionaryvCtorSelector_.search(method) )
 	{
 		return dictionaryvCtorSelector_[method] (control, dict);

utilities/particlesPhasicFlow/positionParticles/positionParticles.hpp

@@ -40,12 +40,8 @@ private:
 
 	word 			regionType_;
 
-	uint32  		maxNumberOfParticles_ = 10000;
-
 	Logical 		mortonSorting_;
 
-	
-
 	realx3Vector sortByMortonCode(const realx3Vector& position)const;
 
 protected:
@@ -83,12 +79,6 @@ public:
 		return mortonSorting_();
 	} 
 
-	inline
-	auto maxNumberOfParticles()const
-	{
-		return maxNumberOfParticles_;
-	}
-
 	virtual uint32 numPoints()const = 0;
 
 	virtual uint32 size()const = 0;

utilities/particlesPhasicFlow/positionRandom/positionRandom.cpp

@@ -122,14 +122,14 @@ pFlow::positionRandom::positionRandom
 	position_
 	(
 		"position",
-		maxNumberOfParticles(),
+		1,
 		0,
 		RESERVE()
 	),
 	diameters_
 	(
 		"diameters",
-		maxNumberOfParticles(),
+		1,
 		0,
 		RESERVE()
 	)