Merge pull request #238 from wanqing0421/main

fixed the error when insert particles from file with integer number

benchmarks/helicalMixer/caseSetup/particleInsertion

@@ -1,67 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-
-objectName particleInsertion;
-objectType dicrionary;
-
-
-active  yes;          // is insertion active?
-
-collisionCheck No;   // not implemented for yes
-
-
-
-particleInlet1
-{
-   type		      boxRegion; // type of insertion region
-   rate 	         1000000;  // insertion rate (particles/s)
-   startTime 	   0;      // (s)
-   endTime   	   2.0;    // (s)
-   interval       0.05;  //s  
-
-   boxRegionInfo 
-   {
-   	min ( -0.17 0.23 0.46); // (m,m,m)
-   	max (  0.17 0.24 0.88); // (m,m,m)
-   }
-   
-   setFields
-   {
-     velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
-   }
-   
-   mixture
-   {
-      smallParticle 1; // mixture composition of inserted particles 
-      
-   }
-}
-
-particleInlet2
-{
-   type           boxRegion; // type of insertion region
-   rate           1000000;  // insertion rate (particles/s)
-   startTime      0;      // (s)
-   endTime        2.0;    // (s)
-   interval       0.05;  //s  
-
-   boxRegionInfo 
-   {
-      min ( -0.17 0.23 0.02); // (m,m,m)
-      max (  0.17 0.24 0.44); // (m,m,m)
-   }
-   
-   setFields
-   {
-     velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
-   }
-   
-   mixture
-   {
-      largeParticle 1; // mixture composition of inserted particles 
-      
-   }
-}
-

benchmarks/helicalMixer/caseSetup/sphereShape

@@ -1,11 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-
-objectName 	sphereDict;
-objectType 	sphereShape;
-
-names 		(smallParticle largeParticle); 	// names of shapes 
-diameters 	(0.002 0.00201);				// diameter of shapes 
-materials	(glassMat glassMat);		// material names for shapes 

benchmarks/helicalMixer/helicalMixer_1m/caseSetup/interaction

@@ -2,18 +2,21 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-
 objectName interaction;
 objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
 
 materials   (glassMat wallMat); // a list of materials names
+
 densities   (2500.0 2500);      // density of materials [kg/m3]
 
 contactListType   sortedContactList;
 
 model
 {
-   contactForceModel nonLinearLimited;
+   contactForceModel    nonLinearLimited;
+   
    rollingFrictionModel normal;
 
    Yeff (1.0e6 1.0e6  // Young modulus [Pa]
@@ -28,9 +31,6 @@ model
    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);
 
@@ -41,19 +41,13 @@ model
 
 contactSearch
 {
-   method         NBS;           
+    method         NBS;  
-   wallMapping    cellMapping;   
 
-   NBSInfo
+    updateInterval   10;
-   {
-      updateFrequency 10;        // each 20 timesteps, update neighbor list 
-      sizeRatio      1.1;       // bounding box size to particle diameter (max)
-   }
 
-   cellMappingInfo
+    sizeRatio       1.1;
-   {
-      updateFrequency 10;        // each 20 timesteps, update neighbor list  
-      cellExtent     0.6;        // bounding box for particle-wall search (> 0.5)
-   }
 
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
 }

benchmarks/helicalMixer/helicalMixer_1m/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           250000;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           250000;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_1m/caseSetup/shapes

@@ -2,13 +2,11 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
+objectName  shapes;
-objectType dicrionary;
+objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 
-active  no;          // is insertion active?
+names       (smallParticle largeParticle);  // names of shapes 
-
+diameters   (0.004 0.00401);                // diameter of shapes 
-collisionCheck No;   // not implemented for yes
+materials   (glassMat glassMat);            // material names for shapes 
-
-

benchmarks/helicalMixer/helicalMixer_1m/cleanThisCase

@@ -3,5 +3,5 @@ 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 
-
+rm -rf stl
 #------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_1m/runThisCase

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+
+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 -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_1m/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+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/helicalMixer/helicalMixer_1m/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_1m/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_1m/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             7.5;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/helicalMixer_250K/caseSetup/interaction

@@ -0,0 +1,53 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+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);
+
+   mu (0.65  0.65   // dynamic friction 
+             0.65);
+
+   mur (0.1  0.1    // rolling friction 
+             0.1);
+        
+}
+
+contactSearch
+{
+    method         NBS;  
+
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
+}

benchmarks/helicalMixer/helicalMixer_250K/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           62500;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           62500;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_250K/caseSetup/shapes

@@ -0,0 +1,12 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  shapes;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.006 0.00601);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_250K/cleanThisCase

@@ -0,0 +1,8 @@
+#!/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
+rm -rf stl 
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_250K/runThisCase

@@ -1,5 +1,12 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"
 echo "<--------------------------------------------------------------------->\n"
@@ -18,6 +25,6 @@ sphereGranFlow
 echo "\n<--------------------------------------------------------------------->"
 echo "4) Converting to VtK"
 echo "<--------------------------------------------------------------------->\n"
-pFlowToVTK -f diameter id velocity
+pFlowToVTK -f diameter id velocity --binary
 
 #------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_250K/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+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/helicalMixer/helicalMixer_250K/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_250K/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_250K/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             7.5;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/helicalMixer_2m/caseSetup/interaction

@@ -0,0 +1,53 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+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);
+
+   mu (0.65  0.65   // dynamic friction 
+             0.65);
+
+   mur (0.1  0.1    // rolling friction 
+             0.1);
+        
+}
+
+contactSearch
+{
+    method         NBS;  
+
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
+}

benchmarks/helicalMixer/helicalMixer_2m/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           500000;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           500000;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_2m/caseSetup/shapes

@@ -0,0 +1,12 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  shapes;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.003 0.00301);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_2m/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 
+rm -rf stl
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_2m/runThisCase

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+
+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 -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_2m/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+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/helicalMixer/helicalMixer_2m/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_2m/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_2m/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             7.5;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/helicalMixer_4m/caseSetup/interaction

@@ -0,0 +1,53 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+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);
+
+   mu (0.65  0.65   // dynamic friction 
+             0.65);
+
+   mur (0.1  0.1    // rolling friction 
+             0.1);
+        
+}
+
+contactSearch
+{
+    method         NBS;  
+
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
+}

benchmarks/helicalMixer/helicalMixer_4m/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           1000000;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           1000000;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_4m/caseSetup/shapes

@@ -0,0 +1,12 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  shapes;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.002 0.00201);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_4m/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 
+rm -rf stl
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_4m/runThisCase

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+
+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 -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_4m/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+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/helicalMixer/helicalMixer_4m/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_4m/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_4m/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             7.5;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/helicalMixer_500k/caseSetup/interaction

@@ -0,0 +1,53 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+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);
+
+   mu (0.65  0.65   // dynamic friction 
+             0.65);
+
+   mur (0.1  0.1    // rolling friction 
+             0.1);
+        
+}
+
+contactSearch
+{
+    method         NBS;  
+
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
+}

benchmarks/helicalMixer/helicalMixer_500k/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           125000;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           125000;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_500k/caseSetup/shapes

@@ -0,0 +1,12 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  shapes;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.005 0.00501);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_500k/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 
+rm -rf stl
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_500k/runThisCase

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+
+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 -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_500k/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+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/helicalMixer/helicalMixer_500k/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_500k/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_500k/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             7.5;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/readme.md

@@ -1 +1,101 @@
 # Helical Mixer Benchmark (phasicFlow v-1.0)
+
+## Overview
+
+This benchmark compares the performance of phasicFlow with a well-stablished commercial DEM software for simulating a helical mixer with varying particle counts (250k to 4M particles). The benchmark measures both computational efficiency and memory usage across different hardware configurations.
+
+**Summary of Results:**
+
+- phasicFlow achieves similar performance to the commercial DEM software on the same hardware.
+- phasicFlow shows a 30% performance improvement when using the NVIDIA RTX A4000 compared to the RTX 4050Ti.
+- Memory usage is approximately 50% lower in phasicFlow compared to the commercial software, with phasicFlow using about 0.7 GB of memory per million particles, while the commercial software uses about 1.5 GB per million particles.
+
+## Simulation Setup
+
+<div align="center">
+    <img src="./images/commericalDEMsnapshot.png"/>
+    <div align="center">  
+        <p>Figure 1. Commercial DEM simulation snapshot</p>
+    </div>
+</div>
+
+<div align="center">
+    <img src="./images/phasicFlow_snapshot.png"/>
+    <div align="center">  
+        <p>Figure 2. phasicFlow simulation snapshot and visualized using Paraview</p>
+    </div>
+</div>
+
+### Hardware Specifications
+
+<div align="center">
+    Table 1. Hardware specifications used for benchmarking.
+</div>
+
+|  System     |           CPU            |             GPU              | Operating System |
+| :---------: | :----------------------: | :--------------------------: | :--------------: |
+|   Laptop    | Intel i9-13900HX 2.2 GHz | NVIDIA GeForce RTX 4050Ti 6G | Windows 11 24H2  |
+| Workstation | Intel Xeon 4210 2.2 GHz  |     NVIDIA RTX A4000 16G     |   Ubuntu 22.04   |
+
+### Simulation Parameters
+
+<div align="center">
+    Table 2. Parameters for helical mixer simulations.
+</div>
+
+| Case     | Particle Diameter | Particle Count | 
+| :-------: | :---------------: | :--------------: | 
+| 250k     | 6 mm              | 250,000        | 
+| 500k     | 5 mm              | 500,000        | 
+| 1M       | 4 mm              | 1,000,000      | 
+| 2M       | 3 mm              | 2,000,000      | 
+| 4M       | 2 mm              | 4,000,000      |
+
+The time step for all simulations was set to 1.0e-5 seconds and the simulation ran for 7.5 seconds.
+
+## Performance Comparison
+
+### Execution Time
+
+<div align="center">
+    Table 3. Total calculation time (minutes) for different configurations.
+</div>
+
+|     Software      | 250k   | 500k   | 1M     | 2M     | 4M     | 
+| :---------------: | :----: | :-----: | :-----: | :-----: | :-----: |
+| phasicFlow-4050Ti | 110 min | 215 min | 413 min | - | -       | 
+| Commercial DEM-4050Ti | 111 min | 210 min | 415 min | - | -       | 
+| phasicFlow-A4000  | 82 min | 150 min  | 300 min | 613 min | 1236 min |
+
+The execution time scales linearly with particle count. phasicFlow demonstrates approximately:
+
+- the computing speed is basically the same as well-established commercial DEM software on the same hardware
+- 30% performance improvement when using the NVIDIA RTX A4000 compared to the RTX 4050Ti
+
+<div align="center">
+    <img src="./images/performance.png"/>
+    <p>Figure 3. Calculation time comparison between phasicFlow and the well-established commercial DEM software.</p>
+</div>
+
+### Memory Usage
+
+<div align="center">
+    Table 4. Memory consumption for different configurations.
+</div>
+
+|     Software      | 250k   | 500k   | 1M      | 2M      | 4M      | 
+| :---------------: | :-----: | :-----: | :-----: | :-----: | :-----: | 
+| phasicFlow-4050Ti | 260 MB  | 404 MB  | 710 MB  | - | -       | 
+| Commercial DEM-4050Ti | 460 MB | 920 MB | 1574 MB | - | -       | 
+| phasicFlow-A4000  | 352 MB  | 496 MB  | 802 MB  | 1376 MB | 2310 MB |
+
+Memory efficiency comparison:
+
+- phasicFlow uses approximately 0.7 GB of memory per million particles
+- Commercial DEM software uses approximately 1.5 GB of memory per million particles
+- phasicFlow shows ~50% lower memory consumption compared to the commercial alternative
+- The memory usage scales linearly with particle count in both software packages. But due to memory limitations on GPUs, it is possible to run larger simulation on GPUs with phasicFlow.
+
+## Run Your Own Benchmarks
+
+The simulation case setup files are available in this folder for users interested in performing similar benchmarks on their own hardware. These files can be used to reproduce the tests and compare performance across different systems.

benchmarks/helicalMixer/settings/geometryDict

@@ -1,56 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-
-objectName 	geometryDict;
-objectType 	dictionary;
-
-// motion model: rotating object around an axis
-motionModel rotatingAxisMotion; 
-
-surfaces
-{
-	
-	helix
-	{
-		type 	 stlWall;   // type of the wall
-		file 	 helix2.stl;	// file name in stl folder
-		material wallMat;   // material name of this wall
-		motion 	 rotAxis;	// motion component name 
-	}
-
-	
-	shell
-	{
-		type 	 stlWall;  	// type of the wall
-		file 	 shell2.stl;	// file name in stl folder		
-		material wallMat;   // material name of this wall
-		motion 	 none;		// motion component name 
-	}
-
-		
-	plug
-	{
-		type 	planeWall;
-		p1 (-0.075 -0.185 0.375);
-		p2 ( 0.075 -0.185 0.375);
-		p3 ( 0.075 -0.185 0.525);
-		p4 (-0.075 -0.185 0.525);
-		material wallMat;   // material name of this wall
-		motion 	 none;		// motion component name 
-	}
-	
-	
-}
-
-// information for rotatingAxisMotion motion model 
-rotatingAxisMotionInfo
-{
-	rotAxis 
-	{
-		p1 ( 0 0 0);
-		p2 ( 0 0 1);
-		omega 0; //3.1428; 		// rotation speed (rad/s) => 30 rpm
-	}
-}

benchmarks/helicalMixer/settings/particlesDict

@@ -1,31 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-
-objectName 	particlesDict;
-objectType 	dictionary;
-
-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	smallParticle; 	// name of the particle shape 
-	}
-
-	selectors
-	{}
-}
-
-// positions particles 
-positionParticles
-{
-	method empty;     		// creates the required fields with zero particles (empty). 
-
-	maxNumberOfParticles 	4100000; // maximum number of particles in the simulation
-	mortonSorting 			Yes;    // perform initial sorting based on morton code?   
-
-}

benchmarks/helicalMixer/settings/settingsDict

@@ -1,36 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-objectName 	settingsDict;
-objectType 	dictionary;;
-
-run 			inclinedScrewConveyor;
-
-dt 				0.00001; 	// time step for integration (s)
-
-startTime 		2.9; 			// start time for simulation 
-
-endTime 		7;			// end time for simulation 
-
-saveInterval 	0.05; 		// time interval for saving the simulation
-
-timePrecision   3;			// maximum number of digits for time folder 
-
-g 				(0 -9.8 0); // gravity vector (m/s2) 
-
-/*
-	Simulation domain 
-	every particles that goes outside this domain is deleted.
-*/
-domain 
-{
-	min (-0.19  -0.19 -0.02);
-	max ( 0.19   0.26  0.92);
-}
-
-integrationMethod 		AdamsBashforth2; 	// integration method 
-
-timersReport 			Yes;  	// report timers?
-
-timersReportInterval   	0.01;	// time interval for reporting timers

benchmarks/readme.md

@@ -1,7 +1,9 @@
 
 # Benchmarks
 
-Benchmakrs has been done on two different simulations: a simulation with simple geometry (rotating drum) and a simulation with complex geometry (helical mixer).
+Benchmakrs has been done on two different simulations: simulation with simple geometry (rotating drum) and a simulation with complex geometry (helical mixer). These benchmarks are used to show how PhasicFlow performs in different scenarios.
 
-- [rotating drum](./rotatingDrum/readme.md)
+- [rotating drum](./rotatingDrum/)
-- [helical mixer](./helicalMixer/readme.md)
+- [helical mixer](./helicalMixer/)
+
+**Note:** If you have performed benchmarks with PhasicFlow using other hardware or software other than PhasicFlow, we would be happy to include them in this section. Please open an issue for more arrangements or send a pull request with the benchmarks results.

benchmarks/rotatingDrum/readme.md

@@ -4,6 +4,12 @@
 
 This benchmark compares the performance of phasicFlow with a well-stablished commercial DEM software for simulating a rotating drum with varying particle counts (250k to 8M particles). The benchmark measures both computational efficiency and memory usage across different hardware configurations.
 
+**Summary of Results:**
+
+- phasicFlow achieves approximately 20% faster calculation than the commercial DEM software on the same hardware.
+- phasicFlow shows a 30% performance improvement when using the NVIDIA RTX A4000 compared to the RTX 4050Ti.
+- Memory usage is approximately 42% lower in phasicFlow compared to the commercial software, with phasicFlow using about 0.7 GB of memory per million particles, while the commercial software uses about 1.2 GB per million particles
+
 ## Simulation Setup
 
 <div align="center">

benchmarks/rotatingDrum/rotatingDrum_1mParticles/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

benchmarks/rotatingDrum/rotatingDrum_250kParticles/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

benchmarks/rotatingDrum/rotatingDrum_2mParticles/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

benchmarks/rotatingDrum/rotatingDrum_4mParticles/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

benchmarks/rotatingDrum/rotatingDrum_8mParticles/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

src/PostprocessData/CMakeLists.txt

@@ -13,6 +13,7 @@ set(SourceFiles
     region/regionPoints/lineRegionPoints/lineRegionPoints.cpp
     region/regionPoints/centerPointsRegionPoints/centerPointsRegionPoints.cpp
     region/regionPoints/multipleSpheresRegionPoints/multipleSpheresRegionPoints.cpp
+    region/regionPoints/rectMeshRegionPoints/rectMeshRegionPoints.cpp
 
     # Postprocess components
     postprocessComponent/postprocessComponent/postprocessComponent.cpp

src/PostprocessData/operation/PostprocessOperation/PostprocessOperationAverage.cpp

@@ -178,4 +178,26 @@ bool PostprocessOperationAverage::write(const fileSystem &parDir) const
     return true;
 }
 
+bool PostprocessOperationAverage::write(iOstream &os) const
+{
+    if(! postprocessOperation::write(os))
+    {
+        return false;
+    }
+    if(!calculateFluctuation2_())
+    {
+        return true;
+    }
+    
+    return 
+        std::visit
+        (
+            [&](auto&& arg)->bool
+            {
+                return arg.writeFieldToVtk(os);
+            },
+            fluctuation2FieldPtr_()
+        );
+}
+
 } // namespace pFlow::postprocessData

src/PostprocessData/operation/PostprocessOperation/PostprocessOperationAverage.hpp

@@ -195,6 +195,8 @@ public:
     /// write to os stream
     bool write(const fileSystem &parDir)const override;
 
+    bool write(iOstream& os)const override;
+
 
     /// @brief Execute average operation on field values
     /// @param weights Weight factors for particles

src/PostprocessData/operation/PostprocessOperation/operationFunctions.hpp

@@ -142,7 +142,7 @@ regionField<T> executeFluctuation2Operation
 )
 {
     const auto& regPoints = fieldAvg.regPoints();
-    regionField<T> processedField(regFieldName, regPoints, T{});
+    regionField<T> processedField(regFieldName+"_fluctuation2", regPoints, T{});
     auto vols = regPoints.volumes();
 
     for(uint32 reg =0; reg<regPoints.size(); reg++)

src/PostprocessData/operation/postprocessOperation/postprocessOperation.cpp

@@ -124,6 +124,25 @@ bool postprocessOperation::write(const fileSystem &parDir) const
     return true;
 }
 
+bool postprocessOperation::write(iOstream& os)const
+{
+    if(!regPoints().writeToSameTimeFile())
+    {
+        const auto& field = processedField();
+
+        return 
+        std::visit
+        (
+            [&](auto&& arg)->bool
+            {
+                return arg.writeFieldToVtk(os);
+            },
+            field
+        );
+    }
+    return false;
+}
+
 uniquePtr<postprocessOperation> postprocessOperation::create
 (
     const dictionary &opDict,

src/PostprocessData/operation/postprocessOperation/postprocessOperation.hpp

@@ -99,7 +99,7 @@ public:
 private:
 
     /// Dictionary containing operation-specific parameters.
-    pFlow::dictionary              operationDict_;
+    pFlow::dictionary       operationDict_;
 
     /// This Threshold is used to exclude the regions which contain
     /// fewer than this value. 
@@ -255,7 +255,7 @@ public:
     /// write the result to output stream (possibly a file)
     /// @param os Output stream to write the result.
     virtual 
-    bool write(iOstream& os)const {return true;}
+    bool write(iOstream& os)const;
 
     /// Create the polymorphic object using the virtual constructor.
     /// @param opDict Dictionary containing operation-specific parameters.

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponent.cpp

@@ -152,11 +152,25 @@ bool pFlow::postprocessData::PostprocessComponent<RegionType, ProcessMethodType>
     }
     else
     {
-        notImplementedFunction;
+        word chNum = real2FixedStripZeros(database().time().currentTime() *1000000, 0);
-        return false;
+        fileSystem  file = parDir + (name() +"-"+chNum+".vtk");
-    }
-    
 
+        auto osPtr = makeUnique<oFstream>(file);
+
+        regPoints().write(osPtr());
+
+        for(auto& operation:operatios_)
+        {
+            if(!operation->write(osPtr()))
+            {
+                fatalErrorInFunction
+                    <<"Error occurred in writing operation defined in dict "
+                    << operation->operationDict()
+                    <<endl;
+                return false;
+            }
+        }   
+    }
 
     return true;
 }

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponent.hpp

@@ -53,7 +53,7 @@ private:
 
     regionField<real>               volumeFactor_;
 
-    bool    executed_{false};
+    bool                            executed_{false};
 
     dictionaryList                  operationDicts_;
 
@@ -122,8 +122,6 @@ public:
 
 };
 
-
-
 }
 
 #include "PostprocessComponent.cpp"

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponentGaussian.hpp

@@ -47,8 +47,8 @@ public:
     :
         PostprocessComponent<RegionType,GaussianDistribution>(dict, fieldsDB, defaultTimeControl)
     {
-        /// initializes the Gaussian distribution for all elements of region
+
-        //const uint32 n = this->regPoints().size();
+        this->regPoints().applyRegionExtension();
         auto d = this->regPoints().eqDiameters();
         auto c = this->regPoints().centers();
         auto& regs = this->regionProecessMethod();

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponents.cpp

@@ -26,6 +26,7 @@ Licence:
 #include "sphereRegionPoints.hpp"
 #include "lineRegionPoints.hpp"
 #include "multipleSpheresRegionPoints.hpp"
+#include "rectMeshRegionPoints.hpp"
 
 namespace pFlow::postprocessData
 {
@@ -37,6 +38,10 @@ template class PostprocessComponentGaussian<multipleSpheresRegionPoints>;
 template class PostprocessComponentUniform<multipleSpheresRegionPoints>;
 template class PostprocessComponentArithmetic<multipleSpheresRegionPoints>;
 
+template class PostprocessComponentGaussian<rectMeshRegionPoints>;
+template class PostprocessComponentUniform<rectMeshRegionPoints>;
+template class PostprocessComponentArithmetic<rectMeshRegionPoints>;
+
 template class PostprocessComponentGaussian<lineRegionPoints>;
 template class PostprocessComponentUniform<lineRegionPoints>;
 template class PostprocessComponentArithmetic<lineRegionPoints>;

src/PostprocessData/readme.md

@@ -2,17 +2,16 @@
 
 The `PostprocessData` module in phasicFlow provides powerful tools for analyzing particle-based simulations both during runtime (in-simulation) and after simulation completion (post-simulation). This document explains how to configure and use the postprocessing features through the dictionary-based input system.
 
-- in-simulation: this is postprocessing that is active during simulation. When running a solver, it allows for real-time data analysis and adjustments based on the simulation's current state. See below to see how you can activate in-simulation postprocessing.
+- **In-simulation**: This is postprocessing that is active during simulation. When running a solver, it allows for real-time data analysis and adjustments based on the simulation's current state. See below to learn how you can activate in-simulation postprocessing.
-- post-simulation: this is postprocessing that is done after the simulation is completed. It allows for detailed analysis of the simulation results, including data extraction and visualization based on the results that are stored in time-folders. If you want to use post-simulation, you need to run utility `postprocessPhasicFlow` in terminal (in the simulation case setup folder) to run the postprocessing. This utility reads the `postprocessDataDict` file and performs the specified operations on the simulation data.
+- **Post-simulation**: This is postprocessing that is done after the simulation is completed. It allows for detailed analysis of the simulation results, including data extraction and visualization based on the results stored in time folders. If you want to use post-simulation, you need to run the utility `postprocessPhasicFlow` in the terminal (in the simulation case setup folder) to execute the postprocessing. This utility reads the `postprocessDataDict` file and performs the specified operations on the simulation data.
-
 
 ### Important Notes
 
-* **NOTE 1:**
+* **NOTE 1:**  
-postprocessing for in-simulation, is not implemented for MPI execution. So, do not use it when using MPI execution. For post-simulation postprocessing, you can use the `postprocessPhasicFlow` utility without MPI, even though the actual simulation has been done using MPI.
+Postprocessing for in-simulation is not implemented for MPI execution. So, do not use it when using MPI execution. For post-simulation postprocessing, you can use the `postprocessPhasicFlow` utility without MPI, even though the actual simulation has been done using MPI.
 
-* **NOTE 2:**
+* **NOTE 2:**  
-In post-simulation mode, all timeControl settings are ignored. The postprocessing will be done for all the time folders that are available in the case directory or if you specify the time range in the command line, the postprocessing will be done for the time folders that are in the specified range of command line.
+In post-simulation mode, all `timeControl` settings are ignored. The postprocessing will be done for all the time folders that are available in the case directory, or if you specify the time range in the command line, the postprocessing will be done for the time folders within the specified range.
 
 ## Table of Contents
 
@@ -32,12 +31,14 @@ In post-simulation mode, all timeControl settings are ignored. The postprocessin
   - [7.1. Example 1: Probing Individual Particles](#71-example-1-probing-individual-particles)
   - [7.2. Example 2: Processing in a Spherical Region](#72-example-2-processing-in-a-spherical-region)
   - [7.3. Example 3: Processing Along a Line](#73-example-3-processing-along-a-line)
+  - [7.4. Example 4: Processing in a Rectangular Mesh](#74-example-4-processing-in-a-rectangular-mesh)
+  - [7.5. Example 5: Tracking particles](#75-example-5-tracking-particles)
 - [8. Advanced Features](#8-advanced-features)
-  - [8.1. Special functions applied on fields](#81-special-functions-applied-on-fields)
+  - [8.1. Special Functions Applied on Fields](#81-special-functions-applied-on-fields)
-  - [8.2. Particle Filtering with includeMask](#82-particle-filtering-with-includemask)
+  - [8.2. Particle Filtering with IncludeMask](#82-particle-filtering-with-includemask)
   - [8.3. Implementation Notes](#83-implementation-notes)
 - [9. Mathematical Formulations](#9-mathematical-formulations)
-- [10. A complete dictionary file (postprocessDataDict)](#10-a-complete-dictionary-file-postprocessdatadict)
+- [10. A Complete Dictionary File (postprocessDataDict)](#10-a-complete-dictionary-file-postprocessdatadict)
 
 ## 1. Overview
 
@@ -46,12 +47,12 @@ Postprocessing in phasicFlow allows you to:
 - Extract information about particles in specific regions of the domain
 - Calculate statistical properties such as averages and sums of particle attributes
 - Track specific particles throughout the simulation
-- Apply different weighing methods when calculating statistics
+- Apply different weighting methods when calculating statistics
 - Perform postprocessing at specific time intervals
 
 ## 2. Setting Up Postprocessing
 
-Postprocessing is configured through a dictionary file named `postprocessDataDict` which should be placed in the `settings` directory. Below is a detailed explanation of the configuration options.
+Postprocessing is configured through a dictionary file named `postprocessDataDict`, which should be placed in the `settings` directory. Below is a detailed explanation of the configuration options.
 
 ### 2.1. Basic Configuration
 
@@ -60,7 +61,6 @@ The input dictionary, **settings/postprocessDataDict**, may look like this:
 ```cpp
 // PostprocessData dictionary
 
-
 // Enable/disable postprocessing during simulation
 runTimeActive yes;  // Options: yes, no
 
@@ -70,7 +70,7 @@ shapeType sphere;   // Options depend on the simulation type: sphere, grain, etc
 // Default time control for postprocessing components
 defaultTimeControl
 {
-    timeControl         timeStep;  // Options: timeStep, simulationTime, settings
+    timeControl         timeStep;  // Options: timeStep, simulationTime, settingsDict
     startTime           0;         // Start time for postprocessing
     endTime             1000;      // End time for postprocessing
     executionInterval   150;       // How frequently to run postprocessing
@@ -83,7 +83,6 @@ components
 );
 ```
 
-
 If you want to activate in-simulation postprocessing, you need to add these lines to the `settings/settingsDict` file:
 
 ```cpp
@@ -92,7 +91,7 @@ libs   ("libPostprocessData.so");
 auxFunctions    postprocessData;
 ```
 
-This will link the postprocessing library to your simulation, allowing you to use its features. Note that, anytime you want to deactivate the in-simulation postprocessing, you can simply change the `runTimeActive` option to `no` in `postprocessDataDict` file.
+This will link the postprocessing library to your simulation, allowing you to use its features. Note that anytime you want to deactivate the in-simulation postprocessing, you can simply change the `runTimeActive` option to `no` in the `postprocessDataDict` file.
 
 ## 3. Time Control Options
 
@@ -102,8 +101,8 @@ Each postprocessing component can either use the default time control settings o
 |--------|-------------|---------------------|
 | `timeStep` | Controls execution based on simulation time steps | `startTime`, `endTime`, `executionInterval` |
 | `simulationTime` | Controls execution based on simulation time | `startTime`, `endTime`, `executionInterval` |
-| `settings` | Uses parameters from settingsDict file | None (defined elsewhere) |
+| `settingsDict` | Uses parameters from settingsDict file | None (defined elsewhere) |
-| `default` | Uses the default time control settings (uses `defaultTimeControl` settings)| None (uses default) |
+| `default` | Uses the default time control settings (uses `defaultTimeControl` settings) | None (uses default) |
 
 If no time control is specified, the `default` option is used automatically.
 
@@ -111,14 +110,14 @@ If no time control is specified, the `default` option is used automatically.
 
 The postprocessing module provides several methods for processing particle data. They are categorized into two main groups: bulk and individual methods.
 
-- **Bulk Methods**: Operate on all particles that are located in a specified locations/regions (cells, spheres, etc.).
+- **Bulk Methods**: Operate on all particles that are located in specified locations/regions (cells, spheres, etc.).
 - **Individual Methods**: Operate on specific particles, allowing for targeted particle property extraction.
 
-| Method | Property type | Description | Formula |
+| Method | Property Type | Description | Formula |
-|--------|------------------|-------------|---------|
+|--------|---------------|-------------|---------|
 | `arithmetic` | bulk | Simple arithmetic mean/sum with equal weights | Each particle contributes equally |
 | `uniformDistribution` | bulk | Each particle contributes inversely proportional to the total number of particles | $w_i = 1/n$ where $n$ is the number of particles |
-| `GaussianDistribution` | bulk | Weight contribution based on distance from center with Gaussian falloff | $w_i = \exp(-\|x_i - c\|^2/(2\sigma^2))/\sqrt{2\pi\sigma^2}$ |
+| `GaussianDistribution` | bulk | Weight contribution based on distance from the center with Gaussian falloff | $w_i = \exp(-\|x_i - c\|^2/(2\sigma^2))/\sqrt{2\pi\sigma^2}$ |
 | `particleProbe` | individual | Extracts values from specific particles | Direct access to particle properties |
 
 ## 5. Region Types
@@ -131,11 +130,13 @@ Regions define where in the domain the postprocessing operations are applied:
 | `multipleSpheres` | Multiple spherical regions | `centers`, `radii` defined in `multiplSpheresInfo` dict | bulk |
 | `line` | Spheres along a line with specified radius | `p1`, `p2`, `nSpheres`, `radius` defined in `lineInfo` dict| bulk |
 | `box`| A cuboid region | `min`, `max` defined in `boxInfo` dict | bulk |
-| `centerPoints`* | Specific particles selected by ID | `ids` | individual |
+| `rectMesh`** | creates a rectangular mesh and each direction is divided into equal spaces| corner points of mesh, and `nx`, `ny`, `nz`: number of divisions in each direction | bulk |
-| `centerPoints`* | Specific particles selected by center points located in a box | `boxInfo` | individual |
+| `centerPoints`* | if `selector` is set to `id`, particles selected by ID list | `ids`: a list of particle ids | individual |
-| `centerPoints`* | Specific particles selected by center points located in a sphere | `sphereInfo` | individual |
+| `centerPoints`* | if `selector` is set to `box`, particles are selected by center points located in a box | corner points of the box are given in `boxInfo` sub-dict | individual |
-| `centerPoints`* | Specific particles selected by center points located in a cylinder | `cylinderInfo` | individual |
+| `centerPoints`* | if `selector` is set to `sphere`, particles are selected by center points located in a sphere | center and radius of a sphere given in `sphereInfo` sub-dict | individual |
-| <td colspan="4">\* Particles selection is done when simulation reaches the time that is specified by `startTime` of the post-process component and this selection remains intact up to the end of simulation. This is very good for particle tracking purposes or when you want to analyze specific particles behavior over time.</td> |
+| `centerPoints`* | if `selector` is set to `cylinder`, particles are selected by center points located in a cylinder | axis info and radius of cylinder at end points that are given in `cylinderInfo` sub-dict | individual |
+| <td colspan="3">\* Particles selection is done when simulation reaches the time that is specified by `startTime` of the post-process component and this selection remains intact up to the end of simulation. This is very good for particle tracking purposes or when you want to analyze specific particles behavior over time.</td> |
+| <td colspan="3">\** This region creates a rectangular mesh and particles are located into cells according to their center points. When using `GaussianDistribution` as `processMethod`, a larger neighbor radius is considered for each cell and particles inside this neighbor radius are included in the calculations.</td> |
 
 ## 6. Processing Operations for Bulk Properties
 
@@ -166,7 +167,7 @@ where:
 
 ### 6.2. About fluctuation2 in average function
 
-Fluctuation2 is an optional parameter that can be used to account for fluctuations in the particle field values with respect to mean value of the field.
+`fluctuation2` is an optional parameter that can be used to account for fluctuations in the particle field values with respect to mean value of the field.
 It is used in the `average` function to calculate the fluctuation of the field values around the mean. The formula for fluctuation2 is:
 
 $$\text{fluctuation}^2 = \frac{\sum_j w_j \cdot \phi_j \cdot (\text{field}_j - \text{mean})^2}{\sum_i w_i \cdot \phi_i}$$
@@ -349,6 +350,90 @@ along_a_line
 
 This example creates 10 spherical regions along a line from (0,0,0) to (0,0.15,0.15) and calculates the bulk density and volume density in each region.
 
+### 7.4 Example 4: Processing in a Rectangular Mesh
+
+In this example, a rectangular mesh is defined. The `rectMeshInfo` section specifies the minimum and maximum corner points of the box, the number of divisions in each direction, and an optional cell extension factor which is effective for GaussianDistribution only. In the `operations` section, two operations are defined: one for calculating the average velocity and another for calculating the solid volume fraction.
+
+```cpp
+on_a_rectMesh
+{
+    processMethod   GaussianDistribution;
+    processRegion   rectMesh;
+
+    timeControl     settingsDict; // uses settings from settingsDict file
+
+    rectMeshInfo 
+    {
+        min (-0.12 -0.12 0.00); // lower corner point of the box 
+        max (0.12   0.12 0.11); // upper corner point of the box
+        
+        nx 30; // number of divisions in x direction
+        ny 30; // number of divisions in y direction
+        nz 15; // number of divisions in z direction
+
+        // optional (default is 2.0)
+        // for each cell, a neighbor radius is considered. This neighbor radius is equal to 
+        // cellExtension * equivalent diameter of the cell. 
+        // cell extension is only effective when using GaussianDistribution as processMethod.
+        cellExtension 3; 
+    }
+
+    operations
+    (
+        avVelocity
+        {
+            function     average;
+            field        velocity;
+            fluctuation2 yes;
+            threshold    4;
+            phi          mass;
+        }
+
+        solidVolumeFraction
+        {
+            function sum;
+            field    volume;
+            divideByVolume yes;
+        }
+    );
+}
+```
+
+### 7.5 Example 5: Tracking particles
+
+Suppose we want to mark and track the position of particles that are located inside a box region at t = 1 s. All particles that are inside the box at t = 1 s will be marked/selected and then the position of them are recorded along the simulation time. The following example shows how to do this. Note that marking/selecting of particles is done at the instance that is defined by `startTime`.  
+
+```C++
+particlesTrack
+{
+    processMethod      particleProbe;
+    
+    processRegion      centerPoints;
+    
+    // all particles whose ceters are located inside this box 
+    // are selected. Selection occurs at startTime: particles 
+    // that are inside the box at t = startTime. 
+    selector           box;
+    boxInfo
+    {
+        min            (0 0 0);
+        max            (0.1 0.05 0.05);
+    }
+    
+    // center position of selected particles are processed 
+    field              position;
+    
+    timeControl        simulationTime;
+    // execution starts at 1.0 s
+    startTime           1.0;
+    // execution ends at 100 s
+    endTime             100;
+    // execution interval of this compoenent 
+    executionInterval   0.02;
+
+}
+```
+
 ## 8. Advanced Features
 
 ### 8.1. Special functions applied on fields
@@ -464,7 +549,7 @@ components
         field            component(velocity,y);
         ids              (0 10 100);
         timeControl      default; // other options are settings, timeStep, simulationTime 
-        // settings: uses parameters from settingsDict file
+        // settingsDict: uses parameters from settingsDict file
         // timeStep: uses the time step of the simulation controlling the execution of postprocessing
         // simulationTime: uses the simulation time of the simulation controlling the execution of postprocessing
         // default: uses the default time control (defined in defaultTimeControl).
@@ -499,6 +584,49 @@ components
         executionInterval   0.02;
 
     }
+
+    on_a_rectMesh
+    {
+        processMethod   GaussianDistribution;
+        processRegion   rectMesh;
+
+        timeControl     settingsDict; // uses settings from settingsDict file
+
+        rectMeshInfo 
+        {
+            min (-0.12 -0.12 0.00); // lower corner point of the box 
+            max (0.12   0.12 0.11); // upper corner point of the box
+            
+            nx 30; // number of divisions in x direction
+            ny 30; // number of divisions in y direction
+            nz 15; // number of divisions in z direction
+
+            // optional (default is 2.0)
+            // for each cell, a neighbor radius is considered. This neighbor radius is equal to 
+            // cellExtension * equivalent diameter of the cell. 
+            // cell extension is only effective when using GaussianDistribution as processMethod.
+            cellExtension 3; 
+        }
+
+        operations
+        (
+            avVelocity
+            {
+                function     average;
+                field        velocity;
+                fluctuation2 yes;
+                threshold    4;
+                phi          mass;
+            }
+
+            solidVolumeFraction
+            {
+                function sum;
+                field    volume;
+                divideByVolume yes;
+            }
+        );
+    }
     
     on_single_sphere
     {

src/PostprocessData/region/regionFields/regionField.hpp

@@ -24,6 +24,7 @@ Licence:
 #include "types.hpp"
 #include "regionPoints.hpp"
 #include "Field.hpp"
+#include "cellMapper.hpp"
 
 namespace pFlow::postprocessData
 {
@@ -101,6 +102,11 @@ public:
         return field_.size();
     }
 
+    uint32x3 shape()const
+    {
+        return regionPoints_.shape();
+    }
+
     bool empty()const
     {
         return field_.empty();

src/PostprocessData/region/regionFields/regionFieldTemplate.cpp

@@ -1,3 +1,6 @@
+
+
+
 namespace pFlow::postprocessData
 {
 
@@ -9,6 +12,86 @@ regionField<T>::regionField(
 :
     field_(name, "regionFieldValue", rPoints.size(), rPoints.size(), defaultVal),
     regionPoints_(rPoints)
+
 {}
 
+template<typename T>
+inline
+bool regionField<T>::writeFieldToVtk(iOstream& os)const
+{
+    fatalErrorInFunction<< "This type is not supported for vtk conversion:"<<
+	field_.typeName()<<endl;
+	fatalExit;
+    return false;
+}
+
+template<>
+inline
+bool regionField<real>::writeFieldToVtk(iOstream& os)const
+{
+    os<<"FIELD FieldData 1 " << field_.name() << " 1 "<< field_.size() << " float\n";
+    
+    
+    const auto mapper = cellMapper{shape()};
+
+    for(uint32 k=0; k<mapper.nz(); k++)
+    {
+        for(uint32 j=0; j<mapper.ny(); j++)
+        {
+            for(uint32 i=0; i<mapper.nx(); i++)
+            {
+                os<< field_[ mapper(i,j,k) ]<<'\n';
+            }
+        }
+    }
+    os<<endl;
+    return true;
+}
+
+template<>
+inline
+bool regionField<realx3>::writeFieldToVtk(iOstream& os)const
+{
+    os<<"FIELD FieldData 1 " << field_.name() << " 3 "<< field_.size() << " float\n";
+    
+    
+    const auto mapper = cellMapper{shape()}; 
+
+    for(uint32 k=0; k<mapper.nz(); k++)
+    {
+        for(uint32 j=0; j<mapper.ny(); j++)
+        {
+            for(uint32 i=0; i<mapper.nx(); i++)
+            {
+                os<<field_[mapper(i,j,k)].x()<<' '<<field_[mapper(i,j,k)].y()<<' '<<field_[mapper(i,j,k)].z()<<'\n';
+            }
+        }
+    }
+    os<<endl;
+    return true;
+}
+
+template<>
+inline
+bool regionField<uint32>::writeFieldToVtk(iOstream& os)const
+{
+    os<<"FIELD FieldData 1 " << field_.name() << " 1 "<< field_.size() << " int\n";
+    
+    
+    const auto mapper = cellMapper{shape()} ; 
+
+    for(uint32 k=0; k<mapper.nz(); k++)
+    {
+        for(uint32 j=0; j<mapper.ny(); j++)
+        {
+            for(uint32 i=0; i<mapper.nx(); i++)
+            {
+                os<< field_[ mapper(i,j,k) ]<<'\n';
+            }
+        }
+    }
+    os<<endl;
+    return true;
+}
+
 } // End namespace pFlow::postprocessData

src/PostprocessData/region/regionPoints/rectMeshRegionPoints/cellMapper.hpp

@@ -0,0 +1,56 @@
+
+#ifndef __cellMapper_hpp__
+#define __cellMapper_hpp__
+
+#include "types.hpp"
+
+namespace pFlow::postprocessData
+{
+
+struct cellMapper
+{
+    uint32x3 cells_;
+
+    cellMapper()
+    :
+        cells_()
+    {}
+
+    explicit cellMapper(uint32x3 cells)
+    :
+        cells_(cells)
+    {}
+
+    cellMapper(const cellMapper&) = default;
+    cellMapper(cellMapper&&) = default;
+    cellMapper& operator=(const cellMapper&) = default;
+    cellMapper& operator=(cellMapper&&) = default;
+    ~cellMapper() = default;
+
+    inline
+    uint32 operator()(uint32 i, uint32 j, uint32 k)const
+    {
+        return (k*(cells_.y()*cells_.x()))+j*cells_.x() + i;
+    }
+
+    uint32 nx()const
+    {
+        return cells_.x();
+    }
+
+    uint32 ny()const
+    {
+        return cells_.y();
+    }
+
+    uint32 nz()const
+    {
+        return cells_.z();
+    }
+
+};
+
+
+} //pFlow::postprocessData
+
+#endif //__cellMapper_hpp__

src/PostprocessData/region/regionPoints/rectMeshRegionPoints/rectMeshRegionPoints.cpp

@@ -0,0 +1,224 @@
+#include "rectMeshRegionPoints.hpp"
+#include "fieldsDataBase.hpp"
+#include "numericConstants.hpp"
+
+void pFlow::postprocessData::rectMeshRegionPoints::findPointsBeyoundCells()
+{
+    // check if pointsBeyoundCells_ is initialized
+    if(!pointsBeyoundCells_)
+    {
+        pointsBeyoundCells_ = makeUnique<decltype(pointsOnCells_)>
+        (
+            "selectedPoints2",
+            this->size()
+        );
+    }
+
+    // get the reference to pointsBeyoundCells_ and clear it
+    auto& selectedPoints = pointsBeyoundCells_();
+
+    // point positions are obtained from the database
+    const auto points = database().updatePoints();
+
+    // iterate through all cells to find points that are within the search radius
+    for(int32 i=0; i<mapper_.nx(); i++)
+    {
+        for(int32 j=0; j<mapper_.ny(); j++)
+        {
+            for(int32 k=0; k<mapper_.nz(); k++)
+            {
+                uint32 cellIndex = mapper_(i,j,k);
+
+                // copy the points in the center cell
+                auto& cellIndices = selectedPoints[cellIndex];
+                cellIndices.clear();
+                
+                
+                if(pointsOnCells_[cellIndex].empty())
+                    continue;
+
+                const auto cellCenter = centerPoints_[cellIndex];
+                const auto rad = 0.5*diameter_[cellIndex];
+                
+                for(int32 ii=-2; ii <= 2; ++ii)
+                {
+                    for(int32 jj=-2; jj <= 2; ++jj)
+                    {
+                        for(int32 kk=-2; kk <= 2; ++kk)
+                        {
+
+                            int32 ni = i + ii;
+                            int32 nj = j + jj;
+                            int32 nk = k + kk;
+                            if(ni < 0 || nj < 0 || nk < 0)
+                                continue;
+                            
+                            if(ni >= mapper_.nx() || nj >= mapper_.ny() || nk >= mapper_.nz())
+                                continue;
+                            
+                            uint32 neighborIndex = mapper_(ni, nj, nk);
+
+                            const auto& neighborPoints = pointsOnCells_[neighborIndex];
+
+                            for(auto nIndx : neighborPoints)
+                            {
+                                if( (points[nIndx]-cellCenter).length() < rad )
+                                {
+                                    cellIndices.push_back(nIndx);
+                                }
+                            }
+
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
+
+
+pFlow::postprocessData::rectMeshRegionPoints::rectMeshRegionPoints
+(
+    const dictionary &dict, 
+    fieldsDataBase &fieldsDataBase
+)
+:
+    regionPoints(dict, fieldsDataBase),
+    boxRegion_(dict.subDict("rectMeshInfo")),
+    cellExtension_(dict.subDict("rectMeshInfo").getValOrSet<real>("cellExtension", 2.0)),
+    pointsOnCells_("selectedPoints"),
+    selectedPoints_(pointsOnCells_)
+{
+    cellExtension_ = max(cellExtension_, one);
+
+    const auto& rectMeshInfo = dict.subDict("rectMeshInfo");
+    
+    auto nx = rectMeshInfo.getValMax<uint32>("nx", 1);
+    auto ny = rectMeshInfo.getValMax<uint32>("ny", 1);
+    auto nz = rectMeshInfo.getValMax<uint32>("nz", 1);
+    
+    mapper_ = cellMapper(uint32x3(nx, ny, nz));
+    uint32 nCells = mapper_.nx() * mapper_.ny() * mapper_.nz();
+    real vol = boxRegion_.volume() / nCells;
+    volumes_.resize(nCells, vol);
+    diameter_.resize(nCells, 2 * pow(3 * vol / 4.0 / Pi, 0.3333333));
+    pointsOnCells_.resize(nCells);
+    centerPoints_.resize(nCells);
+
+    real dx = (boxRegion_.maxPoint().x() - boxRegion_.minPoint().x()) / mapper_.nx();
+    real dy = (boxRegion_.maxPoint().y() - boxRegion_.minPoint().y()) / mapper_.ny();
+    real dz = (boxRegion_.maxPoint().z() - boxRegion_.minPoint().z()) / mapper_.nz();
+    
+    for(uint32 i = 0; i < nx; ++i)
+    {
+        for(uint32 j = 0; j < ny; ++j)
+        {
+            for(uint32 k = 0; k < nz; ++k)
+            {
+                realx3 center = boxRegion_.minPoint() + 
+                    realx3(
+                        ( static_cast<real>(i) + 0.5) * dx,
+                        ( static_cast<real>(j) + 0.5) * dy,
+                        ( static_cast<real>(k) + 0.5) * dz
+                    );
+                centerPoints_[mapper_(i, j, k)] = center;
+            }
+        }
+    }
+}
+
+void pFlow::postprocessData::rectMeshRegionPoints::applyRegionExtension()
+{
+    // it cannot be lower than 1
+    cellExtension_ = max(one, cellExtension_);
+
+    real vf = pow(cellExtension_, 3);
+    for(auto& v:volumes_)
+    {
+        v *= vf;
+    }
+
+    for(auto& d:diameter_)
+    {
+        d *= cellExtension_;
+    }
+}
+
+bool pFlow::postprocessData::rectMeshRegionPoints::update()
+{
+    const auto points = database().updatePoints();
+    for (auto& elem : pointsOnCells_)
+    {
+        elem.clear();
+    }
+ 
+    real dx = (boxRegion_.maxPoint().x() - boxRegion_.minPoint().x()) / mapper_.nx();
+    real dy = (boxRegion_.maxPoint().y() - boxRegion_.minPoint().y()) / mapper_.ny();
+    real dz = (boxRegion_.maxPoint().z() - boxRegion_.minPoint().z()) / mapper_.nz();
+
+    for (uint32 i = 0; i < points.size(); ++i)
+    {
+        if(boxRegion_.isInside(points[i]))
+        {
+            uint32 indexX = (points[i] - boxRegion_.minPoint()).x() / dx;
+            uint32 indexY = (points[i] - boxRegion_.minPoint()).y() / dy;
+            uint32 indexZ = (points[i] - boxRegion_.minPoint()).z() / dz;
+            pointsOnCells_[mapper_(indexX, indexY, indexZ)].push_back(i);
+        }
+    }
+
+    // search beyound cells is not required
+    if( equal(cellExtension_,one))
+    {
+        selectedPoints_ = pointsOnCells_;
+        return true;
+    }
+
+    // search beyound cells is required
+    findPointsBeyoundCells();
+    selectedPoints_ = pointsBeyoundCells_();
+
+    return true;
+}
+
+bool pFlow::postprocessData::rectMeshRegionPoints::write(iOstream &os) const
+{
+
+    auto [x, y , z] = boxRegion_.minPoint();
+    auto [nx, ny, nz] = mapper_.cells_;
+    real dx = (boxRegion_.maxPoint().x() - boxRegion_.minPoint().x()) / mapper_.nx();
+    real dy = (boxRegion_.maxPoint().y() - boxRegion_.minPoint().y()) / mapper_.ny();
+    real dz = (boxRegion_.maxPoint().z() - boxRegion_.minPoint().z()) / mapper_.nz();
+
+
+    os << "# vtk DataFile Version 3.0" << endl;
+    os << "postProcessData" << endl;
+    os << "ASCII" << endl;
+    os << "DATASET RECTILINEAR_GRID" << endl;
+	os << "DIMENSIONS " << nx + 1 << " " << ny + 1 << " " << nz + 1 << endl;
+	
+    os << "X_COORDINATES " << nx + 1 << " float\n";
+    for(int32 i = 0; i < nx + 1; i++)
+    {
+        os << x << "\n";
+        x += dx;
+    }
+
+    os << "Y_COORDINATES " << ny + 1 << " float\n";
+    for(int32 j = 0; j < ny + 1; j++)
+    {
+        os << y << "\n";
+        y += dy;
+    }
+
+    os << "Z_COORDINATES " << nz + 1 << " float\n";
+    for(int32 j = 0; j < nz + 1; j++)
+    {
+        os << z << "\n";
+        z += dz;
+    }
+
+    os << "CELL_DATA " << nx * ny * nz << endl;
+
+    return true;
+}

src/PostprocessData/region/regionPoints/rectMeshRegionPoints/rectMeshRegionPoints.hpp

@@ -0,0 +1,222 @@
+/*------------------------------- phasicFlow ---------------------------------
+      O        C enter of
+     O O       E ngineering and
+    O   O      M ultiscale modeling of
+   OOOOOOO     F luid flow
+------------------------------------------------------------------------------
+  Copyright (C): www.cemf.ir
+  email: hamid.r.norouzi AT gmail.com
+------------------------------------------------------------------------------
+Licence:
+  This file is part of phasicFlow code. It is a free software for simulating
+  granular and multiphase flows. You can redistribute it and/or modify it under
+  the terms of GNU General Public License v3 or any other later versions.
+
+  phasicFlow is distributed to help others in their research in the field of
+  granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
+  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+-----------------------------------------------------------------------------*/
+
+/**
+ * @file rectMeshRegionPoints.hpp
+ * @brief A class representing a rectMesh region for point selection
+ * 
+ * This class provides functionality to select points within a rectMesh region
+ * and to compute related properties such as volume and equivalent diameter.
+ * It inherits from regionPoints and implements all required virtual methods.
+ * 
+ * @see regionPoints
+ * @see fieldsDataBase
+ */
+
+#ifndef __rectMeshRegionPoints_hpp__
+#define __rectMeshRegionPoints_hpp__
+
+#include "regionPoints.hpp"
+#include "box.hpp"
+#include "Vectors.hpp"
+#include "cellMapper.hpp"
+
+
+namespace pFlow::postprocessData
+{
+
+
+class rectMeshRegionPoints
+:
+    public regionPoints
+{
+private:
+
+    /// box object defining the region for point selection
+    box             boxRegion_;
+
+    /// store the cells that are inside the box region
+    cellMapper      mapper_;
+
+    /// Center points of each cell in the rectMesh region
+    realx3Vector    centerPoints_;
+
+    /// Volume of each cell in the rectMesh region
+    realVector      volumes_;
+
+    /// Diameter of each cell in the rectMesh region
+    realVector      diameter_;
+
+    real            cellExtension_;
+
+    Vector<uint32Vector>            pointsOnCells_;
+
+    uniquePtr<Vector<uint32Vector>> pointsBeyoundCells_;
+
+    /// Indices of points that are selected by this region
+    Vector<uint32Vector>&           selectedPoints_;
+
+
+    void findPointsBeyoundCells();
+
+public:
+
+    TypeInfo("rectMesh");
+
+    /**
+     * @brief Construct a rectMesh region for point selection
+     * 
+     * @param dict Dictionary containing sphereInfo dictionary 
+     * @param fieldsDataBase Database containing fields data
+     */
+    rectMeshRegionPoints(
+        const dictionary& dict,
+        fieldsDataBase& fieldsDataBase);
+
+    /// Destructor
+    ~rectMeshRegionPoints() override = default;
+    
+    /**
+     * @brief Get the number of regions
+     */
+    uint32 size()const override
+    {
+        return volumes_.size();
+    }
+
+    /**
+     * return the shape of the field 
+     */
+    uint32x3 shape()const override
+    {
+        return mapper_.cells_;
+    }
+
+    const cellMapper&  mapper()const
+    {
+        return mapper_;
+    }
+
+    /**
+     * @brief Update the points selected by this region
+     * @return True if update was successful
+     */
+    bool empty()const override
+    {
+        return volumes_.empty();
+    }
+
+    void applyRegionExtension() override;
+
+     
+    real regionExtensionRatio()const override
+    {
+        return cellExtension_;
+    }
+
+    /**
+     * @brief Get the volume of the rectMesh region
+     * @return A span containing the volume of the region
+     */
+    span<const real> volumes()const override
+    {
+        return span<const real>(volumes_.data(), volumes_.size());
+    }
+
+    /**
+     * @brief Get the equivalent diameter of the rectMesh region
+     * @return A span containing the diameter of the region
+     */
+    span<const real> eqDiameters()const override
+    {
+        return span<const real>(diameter_.data(), diameter_.size());
+    }
+
+    /**
+     * @brief Get the center of the rectMesh region
+     * @return A span containing the center point of the region
+     */
+    span<const realx3> centers()const override
+    {
+        return span<const realx3>(centerPoints_.data(), centerPoints_.size());
+    }
+    
+    /**
+     * @brief Get the indices of points within the region (const version)
+     * @param elem Element index (ignored as there's only one sphere)
+     * @return A span containing indices of points within the region
+     */    
+    span<const uint32> indices(uint32 elem)const override
+    {
+        if (elem >= size())
+        {
+        fatalErrorInFunction
+            << "The element index is out of range. elem: " << elem
+            << " size: " << size() << endl;
+            fatalExit;
+        }
+
+        return span<const uint32>(selectedPoints_[elem].data(), selectedPoints_[elem].size());
+    }
+
+    /**
+     * @brief Get the indices of points within the region (non-const version)
+     * @param elem Element index (ignored as there's only one sphere)
+     * @return A span containing indices of points within the region
+     */
+    span<uint32> indices(uint32 elem) override
+    {
+        if (elem >= size())
+        {
+            fatalErrorInFunction
+            << "The element index is out of range. elem: " << elem
+            << " size: " << size() << endl;
+            fatalExit;
+        }
+
+        return span<uint32>(selectedPoints_[elem].data(), selectedPoints_[elem].size());
+    }
+
+    /**
+     * @brief Update the points selected by this region
+     * @return True if update was successful
+     */
+    bool update()override;
+
+    /**
+     * @brief Determine if data should be written to the same time file
+     */
+    bool writeToSameTimeFile()const override
+    {
+        return false;
+    }
+
+    /**
+     * @brief Write region data to output stream
+     * @param os Output stream to write to
+     * @return True if write was successful
+     */
+    bool write(iOstream& os)const override;
+    
+};
+
+}
+
+#endif // __sphereRegionPoints_hpp__

src/PostprocessData/region/regionPoints/regionPoints/regionPoints.hpp

@@ -49,10 +49,10 @@ class fieldsDataBase;
  */
 class regionPoints
 {
-        using PointsTypeHost = typename pointStructure::PointsTypeHost;
+    using PointsTypeHost = typename pointStructure::PointsTypeHost;
 
     /// Reference to the fields database containing simulation data
-    fieldsDataBase& fieldsDataBase_;
+    fieldsDataBase& fieldsDataBase_;  
 
 public:
 
@@ -78,11 +78,29 @@ public:
     /// @brief size of elements 
     virtual 
     uint32 size()const = 0;
+
+    virtual 
+    uint32x3 shape()const
+    {
+      return uint32x3(size(), 1u, 1u);
+    }
     
     /// @brief  check if the region is empty
     virtual 
     bool empty()const = 0;  
     
+    /// by default it does nothing
+    /// But, it can be used for the methods that needs to search for 
+    /// particles which are beyound the region 
+    virtual void applyRegionExtension()
+    {}
+
+    virtual 
+    real regionExtensionRatio()const
+    {
+        return 1.0;
+    }
+
     /// @brief  volume of elements
     /// @return sapn for accessing the volume of elements 
     virtual 

src/PostprocessData/sampleDictionary/postprocessDataDict

@@ -39,7 +39,7 @@ components
         field            component(velocity,y);
         ids              (0 10 100);
         timeControl      default; // other options are settings, timeStep, simulationTime 
-        // settings: uses parameters from settingsDict file
+        // settingsDict: uses parameters from settingsDict file
         // timeStep: uses the time step of the simulation controlling the execution of postprocessing
         // simulationTime: uses the simulation time of the simulation controlling the execution of postprocessing
         // default: uses the default time control (defined in defaultTimeControl).
@@ -74,6 +74,49 @@ components
         executionInterval   0.02;
 
     }
+
+    on_a_rectMesh
+    {
+        processMethod   GaussianDistribution;
+        processRegion   rectMesh;
+
+        timeControl     settingsDict; // uses settings from settingsDict file
+
+        rectMeshInfo 
+        {
+            min (-0.12 -0.12 0.00); // lower corner point of the box 
+            max (0.12   0.12 0.11); // upper corner point of the box
+            
+            nx 30; // number of divisions in x direction
+            ny 30; // number of divisions in y direction
+            nz 15; // number of divisions in z direction
+
+            // optional (default is 2.0)
+            // for each cell, a neighbor radius is considered. This neighbor radius is equal to 
+            // cellExtension * equivalent diameter of the cell. 
+            // cell extension is only effective when using GaussianDistribution as processMethod.
+            cellExtension 3; 
+        }
+
+        operations
+        (
+            avVelocity
+            {
+                function     average;
+                field        velocity;
+                fluctuation2 yes;
+                threshold    4;
+                phi          mass;
+            }
+
+            solidVolumeFraction
+            {
+                function sum;
+                field    volume;
+                divideByVolume yes;
+            }
+        );
+    }
     
     on_single_sphere
     {
@@ -134,7 +177,7 @@ components
             {
                 function        sum;
                 field           one;
-                phi             one; 
+                phi             one;
                 divideByVolume  yes;
                 
             }
@@ -153,15 +196,14 @@ components
         startTime   1.0;
         endTime     3.0;
         executionInterval 0.1;
-
+        
-
         // 10 spheres with radius 0.01 along the straight line defined by p1 and  p2 
         lineInfo
         {
-            p1        (0 0 0);
+          p1        (0 0 0);
-            p2        (0 0.15 0.15);
+          p2        (0 0.15 0.15);
-            nSpheres  10;
+          nSpheres  10;
-            radius    0.01;
+          radius    0.01;
         }
 
         operations

src/phasicFlow/repository/IOobject/IOPattern.hpp

@@ -181,4 +181,4 @@ public:
 
 }
 
-#endif //__IOPattern_hpp__
+#endif //__IOPattern_hpp__

src/phasicFlow/repository/systemControl/auxFunctions/auxFunctions.hpp

@@ -62,4 +62,5 @@ public:
 
 } // namespace pFlow
 
-#endif 
+#endif 
+

src/phasicFlow/structuredData/box/box.hpp

@@ -111,6 +111,14 @@ public:
             return max_;
         }
 
+		INLINE_FUNCTION_HD
+		real volume()const
+		{
+			return (max_.x() - min_.x()) * 
+                   (max_.y() - min_.y()) * 
+                   (max_.z() - min_.z()); 
+		}
+
 	//// - IO operation 
 		FUNCTION_H
 		bool read(iIstream & is);

tutorials/grainGranFlow/rotatingDrum/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

tutorials/iterateGeometry/inclinedScrewConveyor/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 
 echo "\n<--------------------------------------------------------------------->"

tutorials/postprocessPhasicFlow/segregation/README.md

@@ -0,0 +1,184 @@
+# Post-processing for Evaluating Segregation of Particles
+ 
+    - Compatibility: phasicFlow-v-1.0
+    - Solvers and tools: sphereGranFlow, postprocessPhasicFlow 
+
+## Background
+
+In particle-based simulations, it's often necessary to perform operations on particle fields to obtain bulk properties of the powder system (such as sums or averages). For example, we may need to calculate the mass-averaged velocity of particles in a granular flow. For bulk-processing of particle fields, we can use a mesh structure to obtain bulk properties of the powder in each cell. In this tutorial, we use a rectangular mesh in which a cuboid is divided into equal sub-spaces (cells).
+
+This tutorial demonstrates how to obtain three important bulk properties:
+
+- Mass-averaged solid velocity (and its fluctuations)
+- Solid volume fraction
+- Volume fraction of small particles (segregation measurement)
+
+## Problem Definition
+
+We will post-process the simulation results from the case [rotating drum with binary particles](../sphereGranFlow/binarySystemOfParticles/). The goal is to create a rectangular mesh with cuboid cells and calculate bulk properties on this mesh to analyze particle segregation patterns.
+
+***
+
+## Case Setup
+
+This tutorial focuses solely on the post-processing aspect of the simulation. It assumes you have already executed the simulation and the results are available for post-processing.
+
+**Important Note:** Postprocessing in phasicFlow can be performed in two modes:
+1. **In-simulation postprocessing**: Activated during simulation runtime, allowing calculations on live simulation data
+2. **Post-simulation postprocessing**: Performed after the simulation has completed
+
+For more detailed information about different modes of postprocessing, please refer to the [official documentation page](../../../src/PostprocessData/readme.md).
+
+### Configuration File
+
+In `settings/postprocessDataDict`, you configure the post-processing parameters:
+
+```C++
+// file: settings/postprocessDataDict
+
+// Enable in-simulation postprocessing (set to "no" for post-simulation only)
+runTimeActive       yes;
+
+// Shape type used in the simulation
+shapeType           sphere;
+
+components
+(
+    on_rectMesh
+    {
+        // Use Gaussian distribution for sampling and distributing 
+        // particle properties over cells 
+        processMethod   GaussianDistribution;
+        
+        processRegion   rectMesh;
+
+        // Use time control in settingsDict file
+        timeControl     settingsDict;
+
+        // A rectangular mesh is constructed using corner points of the 
+        // mesh region and number of divisions in each direction 
+        rectMeshInfo 
+        {
+            min (-0.12 -0.12 0.00);       
+            max (0.12   0.12 0.1);
+            nx 36;
+            ny 36;
+            nz 15;
+        }
+
+        operations  
+        (
+            // Calculate mass-averaged particle velocity 
+            avVelocity
+            {
+                function     average;
+                
+                field        velocity;
+                
+                fluctuation2 yes;
+                
+                threshold    4;
+                
+                phi          mass;
+            }
+
+            // Calculate solid volume fraction 
+            solidVolFraction
+            {
+                function    sum;
+
+                field       volume;
+                
+                divideByVolume yes;
+                
+                threshold   4;
+            }
+
+            // Calculate volume fraction of small particles 
+            smallSphereVolFraction
+            {
+                function        average;
+                
+                field           one;
+
+                phi             volume;
+                
+                divideByVolume  no;
+
+                threshold       4;
+                
+                includeMask     lessThan;
+                
+                lessThanInfo
+                {
+                    field   diameter;
+                  
+                    value   0.0031;  
+                }
+            }
+        );
+
+    }
+);
+```
+
+### Understanding the Configuration
+
+#### Mesh Configuration
+In the `rectMeshInfo` dictionary:
+- `min` and `max` define the corner points of the entire domain
+- `nx`, `ny`, and `nz` define the number of divisions in each direction
+
+#### Operations
+We define three operations to extract bulk properties:
+
+1. **avVelocity**: Calculates mass-averaged particle velocity
+   
+   The `average` function is defined mathematically as:
+
+   $$\text{average} = \frac{\sum_j w_j \cdot \phi_j \cdot \text{field}_j}{\sum_i w_i \cdot \phi_i}$$
+
+   When `field` is set to velocity and `phi` is set to mass, we calculate the mass-averaged velocity of particles in each cell. With `fluctuation2` set to yes, we also calculate velocity fluctuations around the mean value.
+   
+   Note that:
+   - Cells with fewer than 4 particles are excluded (via the `threshold` parameter)
+   - $w_j$ is the weight factor determined by the Gaussian distribution function
+
+2. **solidVolFraction**: Calculates solid volume fraction in each cell
+   
+   The `sum` function is defined as:
+
+   $$\text{sum} = \sum_j w_j \cdot \phi_j \cdot \text{field}_j$$
+
+   By setting `field` to volume and `divideByVolume` to yes, we sum the volumes of all particles in each cell and divide by the cell volume, giving us the solid volume fraction.
+
+3. **smallSphereVolFraction**: Calculates volume fraction of small particles in each cell
+   
+   This operation measures the volume fraction of small particles relative to total particle volume. The `includeMask` parameter filters particles by diameter, selecting only those smaller than 0.0031 units. 
+   
+   The numerator of the `average` function calculates the sum of small particle volumes, while the denominator calculates the total volume of all particles.
+
+### Particle Filtering with includeMask
+
+The `includeMask` parameter allows filtering particles based on field values. Available options include:
+
+* `all`: Include all particles (default)
+* `lessThan`: Include particles where field < value
+* `lessThanEq`: Include particles where field ≤ value 
+* `greaterThan`: Include particles where field > value
+* `greaterThanEq`: Include particles where field ≥ value
+* `equal`: Include particles where field = value
+* `between`: Include particles where value1 < field < value2
+* `betweenEq`: Include particles where value1 ≤ field ≤ value2
+
+## Running the Post-processing Tool
+
+After completing the simulation, execute the post-processing tool with:
+
+```bash
+postprocessPhasicFlow
+```
+
+The results will be stored in the `./postprocessData` folder.
+
+**Tip:** Run `postprocessPhasicFlow -h` to see all available command-line options, including time range selection for post-processing.

tutorials/postprocessPhasicFlow/segregation/caseSetup/interaction

@@ -7,47 +7,42 @@ objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 
-materials      (prop1);    // a list of materials names
+materials                   (prop1);  // a list of materials names
-densities      (1000.0);   // density of materials [kg/m3]
+
+densities                  (1000.0);  // density of materials [kg/m3]
 
 contactListType   sortedContactList; 
 
-model
-{
-   contactForceModel nonLinearNonLimited;
-   rollingFrictionModel normal;
-
-   Yeff  (1.0e6);       // Young modulus [Pa]
-
-   Geff  (0.8e6);       // Shear modulus [Pa]
-
-   nu    (0.25);        // Poisson's ratio [-]
-
-   en    (0.7);         // coefficient of normal restitution
-
-   et    (1.0);         // coefficient of tangential restitution 
-
-   mu    (0.3);         // dynamic friction 
-
-   mur   (0.1);         // rolling friction 
-        
-}
-
 contactSearch
 {
-   method         multiGridNBS;           // method for broad search particle-particle
+  
-   wallMapping    multiGridMapping;   // method for broad search particle-wall 
+    method          NBS;  
 
-   multiGridNBSInfo
+    updateInterval   10;
-   {
-      updateFrequency 10;        // each 10 timesteps, update neighbor list 
-      sizeRatio      1.1;        // bounding box size to particle diameter (max)
-   }
 
-   multiGridMappingInfo
+    sizeRatio       1.1;
-   {
-      updateFrequency 10;        // each 10 timesteps, update neighbor list  
-      cellExtent     0.6;        // bounding box for particle-wall search (> 0.5)
-   }
 
+    cellExtent     0.55;
+
+    adjustableBox   Yes;
+} 
+
+model
+{
+    contactForceModel    nonLinearNonLimited;
+
+    rollingFrictionModel              normal;
+
+    Yeff  (1.0e6);   // Young modulus [Pa]
+
+    Geff  (0.8e6);   // Shear modulus [Pa]
+
+    nu    (0.25);    // Poisson's ratio [-]
+
+    en    (0.7);     // coefficient of normal restitution
+
+    mu    (0.3);     // dynamic friction 
+
+    mur   (0.1);     // rolling friction      
 }
+

tutorials/postprocessPhasicFlow/segregation/caseSetup/shapes

@@ -7,6 +7,8 @@ objectType 	sphereShape;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 
-names 		(smallSphere largeSphere); 	// names of shapes 
+names 		(smallSphere largeSphere); 	// names of shapes
+
 diameters 	(0.003 	0.005);	// diameter of shapes 
+
 materials	(prop1  prop1);	// material names for shapes 

tutorials/postprocessPhasicFlow/segregation/cleanThisCase

@@ -3,5 +3,5 @@ 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 
-
+rm -rf postprocessData
 #------------------------------------------------------------------------------

tutorials/postprocessPhasicFlow/segregation/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

tutorials/postprocessPhasicFlow/segregation/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- 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 (-0.12 -0.12 0.00);                  // lower corner point of the box 
+
+    max (0.12   0.12 0.11);                  // upper corner point of the box 
+}
+
+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 
+    }
+}

tutorials/postprocessPhasicFlow/segregation/settings/geometryDict

@@ -2,70 +2,89 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
-objectName 	geometryDict;
+objectName  geometryDict;
-objectType 	dictionary;
+objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 
-// motion model: rotating object around an axis
+motionModel rotatingAxis; 
-motionModel rotatingAxisMotion; 
+
+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      1.214;   // rotation speed (rad/s)
+
+        startTime    0.5;
+    }
+}
 
 surfaces
 {
-	/*
+    /*
-	    A cylinder with begin and end radii 0.12 m and axis points at (0 0 0) 
+        A cylinder with begin and end radii 0.12 m and axis points at (0 0 0) and (0 0 0.1)
-	and (0 0 0.1)
+    */
-	*/
+    cylinder
-	cylinder
+    {
-	{
+        type cylinderWall;  // type of the wall
-		type cylinderWall;  // type of the wall
-		p1 (0.0 0.0 0.0);   // begin point of cylinder axis
-		p2 (0.0 0.0 0.1);   // end point of cylinder axis
-		radius1 0.12;		// radius at p1
-		radius2 0.12;		// radius at p2
-		resolution 24;      // number of divisions
-		material prop1;     // material name of this wall
-		motion rotAxis;		// motion component name 
-	}
 
-	/*
+        p1  (0.0 0.0 0.0);  // begin point of cylinder axis
-	This is a plane wall at the rear end of cylinder
-	*/
-	wall1
-	{
-		type planeWall;			// type of the wall
-		p1 (-0.12 -0.12 0.0);	// first point of the wall
-		p2 ( 0.12 -0.12 0.0);   // second point
-		p3 ( 0.12  0.12 0.0);   // third point
-		p4 (-0.12  0.12 0.0);   // fourth point 
-		material prop1;         // material name of the wall  
-		motion rotAxis;			// motion component name 
-	}
 
-	/*
+        p2  (0.0 0.0 0.1);  // end point of cylinder axis
-	This is a plane wall at the front end of cylinder
+
-	*/
+        radius1      0.12;  // radius at p1
-	wall2
+
-	{
+        radius2      0.12;  // radius at p2
-		type planeWall;
+
-		p1 (-0.12 -0.12 0.1);
+        resolution     24;  // number of divisions
-		p2 ( 0.12 -0.12 0.1);
+
-		p3 ( 0.12  0.12 0.1);
+        material    prop1;  // material name of this wall
-		p4 (-0.12  0.12 0.1);
+
-		material prop1;
+        motion    rotAxis;  // motion component name 
-		motion rotAxis;
+    }
-	}
+
-		
+    /*
-	
+        This is a plane wall at the rear end of cylinder
+    */
+    wall1
+    {
+        type       planeWall;  // type of the wall
+
+        p1 (-0.12 -0.12 0.0);  // first point of the wall
+
+        p2 ( 0.12 -0.12 0.0);  // second point
+
+        p3 ( 0.12  0.12 0.0);  // third point
+
+        p4 (-0.12  0.12 0.0);  // fourth point 
+
+        material       prop1;  // material name of the wall
+
+        motion       rotAxis;  // motion component name 
+    }
+
+    /*
+        This is a plane wall at the front end of cylinder
+    */
+    wall2
+    {
+        type       planeWall;  // type of the wall
+
+        p1 (-0.12 -0.12 0.1);  // first point of the wall
+
+        p2 ( 0.12 -0.12 0.1);  // second point
+
+        p3 ( 0.12  0.12 0.1);  // third point
+
+        p4 (-0.12  0.12 0.1);  // fourth point 
+
+        material       prop1;  // material name of the wall
+
+        motion       rotAxis;  // motion component name 
+    }
 }
 
-// information for rotatingAxisMotion motion model 
-rotatingAxisMotionInfo
-{
-	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 1.214; 		// rotation speed (rad/s)
-	}
-}

tutorials/postprocessPhasicFlow/segregation/settings/particlesDict

@@ -10,21 +10,20 @@ fileFormat  ASCII;
 // positions particles 
 positionParticles
 {
-	method positionOrdered;     // ordered positioning
+	method ordered;     
 
-	maxNumberOfParticles 30001; // maximum number of particles in the simulation
+	regionType cylinder;
-	mortonSorting Yes;          // perform initial sorting based on morton code?   
+        
-
+	cylinderInfo   
-	cylinder  // cylinder region for positioning particles 
 	{
 		p1 (0.0 0.0 0.003); 	// begin point of cylinder axis
 		p2 (0.0 0.0 0.097);		// end point of cylinder axis
 		radius 		0.117;		// radius of cylinder 
 	}
 		
-	positionOrderedInfo
+	orderedInfo
 	{		
-		distance 0.005; 	// minimum distance between particles centers
+		distance 0.005; 	// minimum space between centers of particles
 		numPoints 30000; 	// number of particles in the simulation 
 		axisOrder (z x y);  // axis order for filling the space with particles
 	}
@@ -35,8 +34,8 @@ setFields
 	/*
 	    Default value for fields defined for particles
 	These fields should always be defined for simulations with 
-	spherical particles.*/
+	spherical particles.
-
+	*/
 	defaultValue 
 	{
 		velocity 		realx3 	(0 0 0); // linear velocity (m/s)
@@ -49,17 +48,17 @@ setFields
 	{
 		shapeAssigne
 		{
-			selector 	selectRandom; // type of point selector
+			selector 	randomPoints; // type of point selector
-			selectRandomInfo
+			
+			randomPointsInfo
 			{
 				begin 	0;			// begin index of points
-				end 	29999;		// end index of points
+				end 	29999;		// end index of points 
-				number 	10000;	    // number of points to be selected 
+				number  10000;
 			}
+
 			fieldValue  // fields that the selector is applied to 
 			{
-				/*
-				sets shapeName of the selected points to largeSphere*/
 				shapeName 	word 	largeSphere;
 			}
 		}

tutorials/postprocessPhasicFlow/segregation/settings/postprocessDataDict

@@ -0,0 +1,82 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  processDataDict;
+objectType  dictionary;;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+runTimeActive       yes;
+
+shapeType           sphere;
+
+components
+(
+    on_rectMesh
+    {
+        processMethod   GaussianDistribution;
+        processRegion   rectMesh;
+
+        timeControl     settingsDict;
+
+        rectMeshInfo 
+        {
+            min (-0.12 -0.12 0.00);       
+            max (0.12   0.12 0.1);
+            nx 36;
+            ny 36;
+            nz 15;
+        }
+
+        operations
+        (
+            avVelocity
+            {
+                function     average;
+                
+                field        velocity;
+                
+                fluctuation2 yes;
+                
+                threshold    4;
+                
+                phi          mass;
+            }
+
+            solidVolFraction
+            {
+                function    sum;
+
+                field       volume;
+                
+                divideByVolume yes;
+                
+                threshold   4;
+            }
+
+            smallSphereVolFraction
+            {
+                function        average;
+                
+                field           one;
+
+                phi             volume;
+                
+                divideByVolume  no;
+
+                threshold       4;
+                
+                includeMask     lessThan;
+                
+                lessThanInfo
+                {
+                    field   diameter;
+                  
+                    value   0.0031;  
+                }
+            }
+        );
+
+    }
+);

tutorials/postprocessPhasicFlow/segregation/settings/postprocessDict

@@ -1,54 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-objectName 	postprocessDict;
-objectType 	dictionary;;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-
-rectMesh
-{
-	min (-0.12 -0.12 0.0);  //minimum corner point 
-	max (0.12   0.12 0.1);  //maximum corner point 
-	nx 24; 		// number of divisions in x direction
-	ny 24; 		// number of divisions in y direction
-	nz 10; 		// number of divisions in z direction 
-}
-
-
-numberBased
-{
-	// num particles in a cell 
-	numParticles
-	{
-		field 		real 1.0; // uniform field with value 1 
-		operation	sum; 	  // sum over all particles in a cell 
-		includeMask all; 	  // select all
-	}
-
-	// concentration of small particles (number based)
-	smallConc
-	{
-		field 		real 1.0; 	// uniform field with value 1 
-		operation	average;	// average over all particles in a cell	
-		threshold 	1; 			// exclude cells with number of particles less than 1
-		includeMask lessThan;   // include mask 
-		lessThanInfo
-		{ 
-			field diameter;     // include particles with diameter less than 0.004
-			value 0.004;
-		}
-	}
-
-	// average velocity of particles 
-	avVelocity
-	{
-		field 	    velocity;   // read velocity field from time folder 
-		operation   average;    // average over all particles in the cell
-		threshold   3; 			// exclude cells with number of particles less than 3
-		includeMask all;		// select all
-		
-	}
-	
-}

tutorials/postprocessPhasicFlow/segregation/settings/settingsDict

@@ -2,39 +2,37 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */  
-objectName 	settingsDict;
+objectName  settingsDict;
-objectType 	dictionary;;
+objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 
-run 			rotatingDrumSmall;
+run   			rotatingDrumSmall;
 
-dt 				0.00001; 	// time step for integration (s)
+libs   	("libPostprocessData.so");
 
-startTime 		0; 			// start time for simulation 
+auxFunctions      postprocessData;
 
-endTime 		10; 		// end time for simulation 
+dt              0.00001;                         // time step for integration (s)
 
-saveInterval 	0.1; 		// time interval for saving the simulation
+startTime             0;                         // start time for simulation 
 
-timePrecision   6;			// maximum number of digits for time folder 
+endTime              10;                         // end time for simulation 
 
-g 				(0 -9.8 0); // gravity vector (m/s2) 
+saveInterval        0.1;                         // time interval for saving the simulation
 
-/*
+timePrecision         6;                         // maximum number of digits for time folder 
-	Simulation domain 
-	every particles that goes outside this domain is deleted.
-*/
-domain 
-{
-	min (-0.12 -0.12 0);
-	max (0.12   0.12 0.1);
-}
 
-integrationMethod 		AdamsBashforth2; 	// integration method 
+g            (0 -9.8 0);                         // gravity vector (m/s2) 
 
-writeFormat 			ascii;
+includeObjects (diameter);                       // save necessary (i.e., required) data on disk
 
-timersReport 			Yes;  	// report timers?
+integrationMethod       AdamsBashforth2;         // integration method
 
-timersReportInterval   	0.01;	// time interval for reporting timers
+integrationHistory                  off; 
+
+writeFormat                       ascii;         // data writting format (ascii or binary)
+
+timersReport                        Yes;         // report timers (Yes or No)
+
+timersReportInterval               0.01;         // time interval for reporting timers

tutorials/sphereGranFlow/RotaryAirLockValve/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

tutorials/sphereGranFlow/RotatingDrumWithBaffles/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"

tutorials/sphereGranFlow/V-blender/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"