Merge 99269b9682 into acdad47823

binarySystemOfParticles updated V1.0

.gitignore

@@ -61,3 +61,8 @@ doc/DTAGS
 **/[0-9]*.[0-9][0-9][0-9][0-9][0-9][0-9][0-9]
 **/[0-9]*.[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]
 **/VTK
+utilities/postprocessPhasicFlow/includeMask.hpp
+utilities/postprocessPhasicFlow/ProcessField.hpp
+utilities/postprocessPhasicFlow/ProcessField.hpp
+*.hpp
+*.cpp

tutorials/sphereGranFlow/RotatingDrumWithBaffles/caseSetup/interaction

@@ -62,7 +62,7 @@ contactSearch
 
    NBSInfo
    {
-    // each 20 timesteps, update neighbor list
+   // each 20 timesteps, update neighbor list
       updateFrequency 10;
    // bounding box size to particle diameter (max)           
       sizeRatio      1.1;        

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/geometryDict

@@ -14,66 +14,66 @@ surfaces
 {
 	body
 	{
-		// type of the wall
+// type of the wall
 		type 	 stlWall;
-		// file name in stl folder  	
+// file name in stl folder  	
 		file 	 Body.stl;
-		// material name of this wall		
+// material name of this wall		
 		material wallMat;
-		// motion component name   
+// motion component name   
 		motion 	 rotAxis;		 
 	}
 	/*	This is a Cylinder Wall at the rear of cylinder	*/
 	rearEnd
 	{
-		// type of the wall
+// type of the wall
 		type cylinderWall;
-		// first point for the axis of rotation			
+// first point for the axis of rotation			
 		p1 (-0.1974  0.2269  -0.001);
-		// second point for the axis of rotation	 
+// second point for the axis of rotation	 
 		p2 (-0.1974  0.2269   0.0);
-		// Radius of p1	
+// Radius of p1	
 		radius1 0.0001;
-		// Radius of p2
+// Radius of p2
 		radius2 0.12;
-		// material name of the wall
+// material name of the wall
 		material wallMat;
-		// motion component name          
+// motion component name          
 		motion rotAxis;			 
 	}
 	/*	This a cylinder Wall at the front of Cylinder */
 	frontEnd
 	{
-		// type of the wall
+// type of the wall
 		type cylinderWall;
-		// first point for the axis of rotation			
+// first point for the axis of rotation			
 		p1 (-0.1974  0.2269   0.0989);
-		// second point for the axis of rotation	 
+// second point for the axis of rotation	 
 		p2 (-0.1974  0.2269   0.0990);	
-		// Radius of p1
+// Radius of p1
 		radius1 0.0001;
-		// Radius of p2
+// Radius of p2
 		radius2 0.12;
-		// material name of the wall
+// material name of the wall
 		material wallMat; 
-		// motion component name          
+// motion component name          
 		motion rotAxis;			 
 	}
 }
-	// information for rotatingAxisMotion motion model 
+// information for rotatingAxisMotion motion model 
 rotatingAxisMotionInfo
 {
 	rotAxis 
 	{
-		// first point for the axis of rotation
+// first point for the axis of rotation
 		p1 (-0.1974  0.2269  0);
-		// second point for the axis of rotation	 
+// second point for the axis of rotation	 
 		p2 (-0.1974  0.2269  0.1);
-		// rotation speed (rad/s) => 15 rpm	
+// rotation speed (rad/s) => 15 rpm	
 		omega 2.38733;
-		// Start time of Geometry Rotating 		
+// Start time of Geometry Rotating 		
 		startTime 2;
-		// End time of Geometry Rotating
+// End time of Geometry Rotating
 		endTime 9.5;
 	}
 }

tutorials/sphereGranFlow/binarySystemOfParticles/caseSetup/interaction

@@ -6,16 +6,16 @@ objectName  interaction;
 objectType  dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-materials     (prop1);          // properties of material
+materials                     (prop1);           // properties of material
 
-densities     (1000.0);         // density of materials [kg/m3]
+densities                    (1000.0);           // density of materials [kg/m3]
 
 contactListType     sortedContactList;
 
 contactSearch
 {
   
-   method          NBS;          // method for broad search 
+   method          NBS;                          // method for broad search 
     
    updateInterval   10;
 
@@ -34,18 +34,18 @@ model
 
    // Property (solid-solid Properties)
 
-   Yeff     (1.0e6);          // Young modulus [Pa]
+   Yeff     (1.0e6);                             // Young modulus [Pa]
 
-   Geff     (0.8e6);          // Shear modulus [Pa]
+   Geff     (0.8e6);                             // Shear modulus [Pa]
 
-   nu       (0.25);           // Poisson's ratio [-]
+   nu       (0.25);                              // Poisson's ratio [-]
 
-   en       (0.7);            // coefficient of normal restitution
+   en       (0.7);                               // coefficient of normal restitution
 
-   et       (1.0);            // coefficient of tangential restitution 
+   et       (1.0);                               // coefficient of tangential restitution 
 
-   mu       (0.3);            // dynamic friction 
+   mu       (0.3);                               // dynamic friction 
 
-   mur      (0.1);            // rolling friction     
+   mur      (0.1);                               // rolling friction     
 }
 

tutorials/sphereGranFlow/binarySystemOfParticles/caseSetup/particleInsertion

@@ -6,6 +6,6 @@ objectName 	particleInsertion;
 objectType 	dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-collisionCheck     No;          // is checked          -> yes or no
+collisionCheck     No;                           // is checked          -> yes or no
 
-active             No;          // is insertion active -> yes or no
+active             No;                           // is insertion active -> yes or no

tutorials/sphereGranFlow/binarySystemOfParticles/caseSetup/shapes

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

tutorials/sphereGranFlow/binarySystemOfParticles/settings/domainDict

@@ -6,7 +6,7 @@ objectName 	domainDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox          // Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
 {
 	min     (-0.12 -0.12 0);
 
@@ -21,43 +21,48 @@ decomposition
 boundaries
 {
 	// Determines how often (how many iterations) do you want to 
+
 	// rebuild the list of particles in the neighbor list 
+
 	// of all boundaries in the simulation domain 
+
 	neighborListUpdateInterval     50; 
 
 	// Determines how often do you want to update the new changes in the boundary
+
 	updateInterval                 10;
 
 	// The distance from the boundary plane within which particles are marked to be in the boundary list 
+
 	neighborLength              0.004;
 
 	left
 	{
-		type     exit;	        // other options: periodict, reflective 
+		type     exit;	                         // other options: periodict, reflective 
 	}
 
 	right
 	{
-		type     exit;          // other options: periodict, reflective 
+		type     exit;                           // other options: periodict, reflective 
 	}
 
 	bottom
 	{
-		type     exit;          // other options: periodict, reflective 
+		type     exit;                           // other options: periodict, reflective 
 	}
 
 	top
 	{
-		type     exit;          // other options: periodict, reflective 
+		type     exit;                           // other options: periodict, reflective 
 	}
 
 	rear
 	{
-		type     exit;          // other options: periodict, reflective 
+		type     exit;                           // other options: periodict, reflective 
 	}
 
 	front
 	{
-		type     exit;          // other options: periodict, reflective 
+		type     exit;                           // other options: periodict, reflective 
 	}
 }

tutorials/sphereGranFlow/binarySystemOfParticles/settings/geometryDict

@@ -6,17 +6,17 @@ objectName 	geometryDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-motionModel     rotatingAxis;          // motion model can be rotatingAxis or stationary or vibrating
+motionModel     rotatingAxis;                    // motion model can be rotatingAxis or stationary or vibrating
 
-rotatingAxisInfo          // information for rotatingAxis motion model 
+rotatingAxisInfo                                 // information for rotatingAxis motion model 
 {
 	rotAxis 
 	{
-		p1 (0.0 0.0 0.0);	       // first point for the axis of rotation 
+		p1 (0.0 0.0 0.0);	                     // first point for the axis of rotation 
 
-		p2 (0.0 0.0 1.0);	       // second point for the axis of rotation
+		p2 (0.0 0.0 1.0);	                     // second point for the axis of rotation
 		
-		omega      1.214; 		   // rotation speed (rad/s)
+		omega      1.214; 		                 // rotation speed (rad/s)
 	}
 }
 
@@ -24,21 +24,21 @@ surfaces
 {
 	cylinder
 	{
-		type     cylinderWall;          // other options: cuboidWall and planeWall
+		type     cylinderWall;                   // other options: cuboidWall and planeWall
 
-		p1 (0.0 0.0 0.0);          // begin point of cylinder axis
+		p1 (0.0 0.0 0.0);                        // begin point of cylinder axis
 
-		p2 (0.0 0.0 0.1);          // end point of cylinder axis
+		p2 (0.0 0.0 0.1);                        // end point of cylinder axis
 
-		radius1     0.12;		   // radius at p1
+		radius1     0.12;		                 // radius at p1
 
-		radius2     0.12;		   // radius at p2
+		radius2     0.12;		                 // radius at p2
 
-		resolution    24;          // number of divisions
+		resolution    24;                        // number of divisions
 
-		material   prop1;          // material name of this wall
+		material   prop1;                        // material name of this wall
 
-		motion   rotAxis;		   // motion component name 
+		motion   rotAxis;		                 // motion component name 
 	}
 
 	/*
@@ -47,19 +47,19 @@ surfaces
 
 	wall1
 	{
-		type     planeWall;			 // other options: cuboidWall and  cylinderWall
+		type       planeWall;			         // other options: cuboidWall and  cylinderWall
 
-		p1 (-0.12 -0.12 0.0);	       // first point of the wall
+		p1 (-0.12 -0.12 0.0);	                 // first point of the wall
 
-		p2  (0.12 -0.12 0.0);          // second point of the wall
+		p2  (0.12 -0.12 0.0);                    // second point of the wall
 
-		p3   (0.12 0.12 0.0);          // third point of the wall
+		p3   (0.12 0.12 0.0);                    // third point of the wall
 
-		p4  (-0.12 0.12 0.0);          // fourth point of the wall
+		p4  (-0.12 0.12 0.0);                    // fourth point of the wall
 
-		material       prop1;          // material name of the wall 
+		material       prop1;                    // material name of the wall 
 
-		motion       rotAxis;		   // motion component name 
+		motion       rotAxis;		             // motion component name 
 	}
 
 	/*
@@ -68,18 +68,18 @@ surfaces
 
 	wall2
 	{
-		type     planeWall;          // other options: cuboidWall and  cylinderWall 
+		type       planeWall;                    // other options: cuboidWall and  cylinderWall 
 
-		p1 (-0.12 -0.12 0.1);          // first point of the wall
+		p1 (-0.12 -0.12 0.1);                    // first point of the wall
 
-		p2  (0.12 -0.12 0.1);          // second point of the wall
+		p2  (0.12 -0.12 0.1);                    // second point of the wall
 
-		p3   (0.12 0.12 0.1);          // third point of the wall
+		p3   (0.12 0.12 0.1);                    // third point of the wall
 
-		p4  (-0.12 0.12 0.1);          // fourth point of the wall
+		p4  (-0.12 0.12 0.1);                    // fourth point of the wall
 
-		material       prop1;          // material name of the wall 
+		material       prop1;                    // material name of the wall 
 
-		motion       rotAxis;          // motion component name 
+		motion       rotAxis;                    // motion component name 
 	}
 }

tutorials/sphereGranFlow/binarySystemOfParticles/settings/particlesDict

@@ -9,65 +9,66 @@ fileFormat  ASCII;
 setFields
 {
 	/*
-	    	Default value for fields defined for particles:
+	    Default value for fields defined for particles:
+
 		These fields should always be defined for simulations with spherical particles
 	*/
 
 	defaultValue 
 	{
-		velocity 		realx3 	(0 0 0); 			       // linear velocity (m/s)
+		velocity 		     realx3 (0 0 0);     // linear velocity (m/s)
 
-		acceleration 	realx3 	(0 0 0); 			       // linear acceleration (m/s2)
+		acceleration 	     realx3 (0 0 0); 	 // linear acceleration (m/s2)
 
-		rVelocity 		realx3 	(0 0 0); 			       // rotational velocity (rad/s)
+		rVelocity 		     realx3 (0 0 0); 	 // rotational velocity (rad/s)
 
-		shapeName 		word	smallSphere; 		       // name of the particle shape 
+		shapeName 		word    smallSphere; 	 // name of the particle shape 
 	}
 
 	selectors
 	{
 		shapeAssigne
 		{
-			selector 	stridedRange; 				       // other options: box, cylinder, sphere, randomPoints 
+			selector 	stridedRange; 	         // other options: box, cylinder, sphere, randomPoints 
  
 			stridedRangeInfo
 			{
-				begin 	0;			 				       // begin index of points
+				begin 	    0;			         // begin index of points
 
-				end 	30000;		 				       // end index of points 
+				end 	30000;		 			 // end index of points 
 
-				stride  3;			 				       // stride for selector 
+				stride      3;			 		 // stride for selector 
 			}
 
-			fieldValue  							       // fields that the selector is applied to 
+			fieldValue  					     // fields that the selector is applied to 
 			{
-				shapeName 	word 	largeSphere;           // sets shapeName of the selected points to largeSphere
+				shapeName 	word    largeSphere; // sets shapeName of the selected points to largeSphere
 			}
 		}
 	}
 }
 
-positionParticles 				                           // positions particles 
+positionParticles 				                 // positions particles 
 {
-	method ordered;                                        // other options: random and empty
+	method ordered;                              // other options: random and empty
 
 	orderedInfo
 	{		
-		diameter  0.005; 	                               // diameter of particles
+		diameter  0.005; 	                     // diameter of particles
 
-		numPoints 30000; 	                               // number of particles in the simulation
+		numPoints 30000; 	                     // number of particles in the simulation
 
-		axisOrder (z x y);                                 // axis order for filling the space with particles
+		axisOrder (z x y);                       // axis order for filling the space with particles
 	}
 	
-	regionType cylinder;                                   // other options: box and sphere  
+	regionType cylinder;                         // other options: box and sphere  
 
-	cylinderInfo  				                           // cylinder information for positioning particles 
+	cylinderInfo  				                 // cylinder information for positioning particles 
 	{
-		p1 (0.0 0.0 0.003); 	                           // begin point of cylinder axis
+		p1 (0.0 0.0 0.003); 	                 // begin point of cylinder axis
 
-		p2 (0.0 0.0 0.097);		                           // end point of cylinder axis
+		p2 (0.0 0.0 0.097);		                 // end point of cylinder axis
 
-		radius 		0.117;		                           // radius of cylinder 
+		radius 		0.117;		                 // radius of cylinder 
 	}
 }

tutorials/sphereGranFlow/binarySystemOfParticles/settings/settingsDict

@@ -8,28 +8,31 @@ fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 run 	binarySystemofParticles;
 
-dt       0.00001; 	       // time step for integration (seconds)
+dt       0.00001; 	                             // time step for integration (seconds)
 
-startTime    0.0; 		   // start time for simulation 
+startTime    0.0; 		                         // start time for simulation 
 
-endTime     10.0; 		   // end time for simulation 
+endTime     10.0; 		                         // end time for simulation 
 
-saveInterval 0.1; 		   // time interval for saving the simulation
+saveInterval 0.1; 		                         // time interval for saving the simulation
 
-timePrecision  6;		   // maximum number of digits for time folder 
+timePrecision  6;		                         // maximum number of digits for time folder 
 
-g 	  (0 -9.8 0);          // gravity vector (m/s2) 
+g 	  (0 -9.8 0);                                // gravity vector (m/s2) 
 
 // save necessary (i.e., required) data on disk
-includeObjects (diameter);                                                 
+
+includeObjects (diameter);  
+
 // exclude unnecessary data from saving on disk
+
 excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
-integrationMethod 		AdamsBashforth2; 	      // integration method 
+integrationMethod 		AdamsBashforth2; 	     // integration method 
 
-writeFormat 			          ascii;          // data writting format (ascii or binary)
+writeFormat 			          ascii;         // data writting format (ascii or binary)
 
-timersReport 			            Yes;  	      // report timers
+timersReport 			            Yes;  	     // report timers
 
-timersReportInterval   	           0.01;	      // time interval for reporting timers
+timersReportInterval   	           0.01;	     // time interval for reporting timers
  

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/interaction

@@ -6,11 +6,11 @@ objectName interaction;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-materials   (lightMat heavyMat wallMat);          // a list of materials names
+materials   (lightMat heavyMat wallMat);         // a list of materials names
 
-densities            (1000 1500.0 2500);          // density of materials [kg/m3]
+densities            (1000 1500.0 2500);         // density of materials [kg/m3]
 
-contactListType   sortedContactList;
+contactListType       sortedContactList;
 
 contactSearch
 {
@@ -29,39 +29,40 @@ model
 {
    contactForceModel nonLinearLimited;
 
-   rollingFrictionModel normal;
+   rollingFrictionModel        normal;
 
    /*
+
    Property (lightMat-lightMat   lightMat-heavyMat    lightMat-wallMat
                                  heavyMat-heavyMat    heavyMat-wallMat
-                                                      wallMat-wallMat );
+                                                      wallMat-wallMat  );
    */
 
-   Yeff (1.0e6 1.0e6 1.0e6            // Young modulus [Pa]
+   Yeff (1.0e6 1.0e6 1.0e6                       // Young modulus [Pa]
                1.0e6 1.0e6
                      1.0e6);
    
-   Geff (0.8e6 0.8e6 0.8e6            // Shear modulus [Pa]
+   Geff (0.8e6 0.8e6 0.8e6                       // Shear modulus [Pa]
                0.8e6 0.8e6
                      0.8e6);
 
-   nu    (0.25 0.25  0.25             // Poisson's ratio [-]
+   nu    (0.25 0.25  0.25                        // Poisson's ratio [-]
                0.25  0.25
                      0.25);
 
-   en (0.97  0.97    0.85             // coefficient of normal restitution
+   en (0.97  0.97    0.85                        // coefficient of normal restitution
              0.97    0.85
                      1.00);
 
-   et (1.0   1.0  1.0                 // coefficient of tangential restitution 
+   et (1.0   1.0  1.0                            // coefficient of tangential restitution 
              1.0  1.0
                   1.0);
 
-   mu (0.65   0.65 0.35               // dynamic friction 
+   mu (0.65   0.65 0.35                          // dynamic friction 
               0.65 0.35
                    0.35);
 
-   mur (0.1  0.1 0.1                  // rolling friction 
+   mur (0.1  0.1 0.1                             // rolling friction 
              0.1 0.1
                  0.1);       
 }

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/particleInsertion

@@ -6,9 +6,9 @@ objectName particleInsertion;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-active           Yes;          // is insertion active -> yes or no
+active           Yes;                            // is insertion active -> yes or no
 
-checkForCollision No;          // is checked          -> yes or no
+checkForCollision No;                            // is checked          -> yes or no
 
 /*
    one layers of particles are packed 

tutorials/sphereGranFlow/layeredSiloFilling/settings/domainDict

@@ -6,7 +6,7 @@ objectName 	domainDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox                    // Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
 {
 	min (-0.11 -0.11 -0.11);
 	
@@ -16,44 +16,49 @@ globalBox                    // Simulation domain: every particles that goes out
 boundaries
 {
 	// Determines how often (how many iterations) do you want to 
+
 	// rebuild the list of particles in the neighbor list 
+
 	// of all boundaries in the simulation domain 
+
 	neighborListUpdateInterval 30;
 	
 	// Determines how often do you want to update the new changes in the boundary
+
 	updateInterval             10;
 
 	// The distance from the boundary plane within which particles are marked to be in the boundary list 
+
 	neighborLength          0.004;
 
 	left
 	{
-		type exit;	         // other options: periodict, reflective 
+		type exit;	                             // other options: periodict, reflective 
 	}
 
 	right
 	{
-		type exit;           // other options: periodict, reflective 
+		type exit;                               // other options: periodict, reflective 
 	}
 
 	bottom
 	{
-		type exit;           // other options: periodict, reflective 
+		type exit;                               // other options: periodict, reflective 
 	}
 
 	top
 	{
-		type exit;           // other options: periodict, reflective 
+		type exit;                               // other options: periodict, reflective 
 	}
 
 	rear
 	{
-		type exit;           // other options: periodict, reflective 
+		type exit;                               // other options: periodict, reflective 
 	}
 
 	front
 	{
-		type exit;           // other options: periodict, reflective 
+		type exit;                               // other options: periodict, reflective 
 	}
 }    
 

tutorials/sphereGranFlow/layeredSiloFilling/settings/geometryDict

@@ -6,7 +6,7 @@ objectName 	geometryDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-motionModel stationary;          // motion model can be rotatingAxis or stationary or vibrating
+motionModel            stationary;               // motion model can be rotatingAxis or stationary or vibrating
 
 stationaryInfo
 {
@@ -17,36 +17,36 @@ surfaces
 {
 	cylinderShell
 	{
-		type 		 cylinderWall;  	    // other options: cuboidWall and planeWall
+		type 		 cylinderWall;  	         // other options: cuboidWall and planeWall
 
-		p1 			(0.0 0.0 0.0);          // begin point of cylinder axis
+		p1 			(0.0 0.0 0.0);               // begin point of cylinder axis
 
-		p2 			(0.0 0.0 0.4);          // end point of cylinder axis
+		p2 			(0.0 0.0 0.4);               // end point of cylinder axis
 
-		radius1 	          0.1;		    // radius at p1
+		radius1 	          0.1;		         // radius at p1
  
-		radius2 	          0.1;		    // radius at p2
+		radius2 	          0.1;		         // radius at p2
 
-		resolution 	           36;      	// number of divisions
+		resolution 	           36;      	     // number of divisions
 
-		material 	      wallMat;   	    // material name of this wall
+		material 	      wallMat;   	         // material name of this wall
 	}
 
 	coneShell
 	{
-		type 		 cylinderWall;  	    // other options: cuboidWall and planeWall
+		type 		 cylinderWall;  	         // other options: cuboidWall and planeWall
 
-		p1 		   (0.0 0.0 -0.1);          // begin point of cylinder axis
+		p1 		   (0.0 0.0 -0.1);               // begin point of cylinder axis
 
-		p2 			(0.0 0.0 0.0);          // end point of cylinder axis
+		p2 			(0.0 0.0 0.0);               // end point of cylinder axis
 
-		radius1 	         0.02;		    // radius at p1
+		radius1 	         0.02;		         // radius at p1
 
-		radius2 	          0.1;		    // radius at p2
+		radius2 	          0.1;		         // radius at p2
+  
+		resolution 	           36;      	     // number of divisions
 
-		resolution 	           36;      	// number of divisions
+		material 	      wallMat;   	         // material name of this wall
-
-		material 	      wallMat;   	    // material name of this wall
 	}
 
 	/*
@@ -55,17 +55,17 @@ surfaces
 
 	exitGate
 	{
-		type planeWall;                     // other options: cuboidWall and cylinderWall
+		type        planeWall;                   // other options: cuboidWall and cylinderWall
 
-		p1 (-0.02 -0.02 -0.1);              // first point of the wall
+		p1 (-0.02 -0.02 -0.1);                   // first point of the wall
 
-		p2 ( 0.02 -0.02 -0.1);              // second point of the wall
+		p2 ( 0.02 -0.02 -0.1);                   // second point of the wall
 
-		p3 ( 0.02  0.02 -0.1);              // third point of the wall
+		p3 ( 0.02  0.02 -0.1);                   // third point of the wall
 
-		p4 (-0.02  0.02 -0.1);              // fourth point of the wall
+		p4 (-0.02  0.02 -0.1);                   // fourth point of the wall
 		 
-		material wallMat;                   // material name of the wall 
+		material      wallMat;                   // material name of the wall 
 	}
 }
 

tutorials/sphereGranFlow/layeredSiloFilling/settings/particlesDict

@@ -9,37 +9,39 @@ fileFormat  ASCII;
 setFields
 {
 	/*
-	    	Default value for fields defined for particles
+	    Default value for fields defined for particles
+
 		These fields should always be defined for simulations with 
+
 		spherical particles.
 	*/
 
 	defaultValue 
 	{
-		velocity 		realx3 	    (0 0 0); 		  // linear velocity (m/s)
+		velocity 		realx3 	    (0 0 0);     // linear velocity (m/s)
 
-		acceleration 	realx3 	    (0 0 0); 		  // linear acceleration (m/s2)
+		acceleration 	realx3 	    (0 0 0);     // linear acceleration (m/s2)
 
-		rVelocity 		realx3 	    (0 0 0);  		  // rotational velocity (rad/s)
+		rVelocity 		realx3 	    (0 0 0);  	 // rotational velocity (rad/s)
 
-		shapeName 		word	lightSphere; 	      // name of the particle shape 
+		shapeName 		word	lightSphere; 	 // name of the particle shape 
 	}
 
 	selectors
 	{}
 }
 
-positionParticles                                          // positions particles 
+positionParticles                                // positions particles 
 {
-	method                empty;          // other options: ordered and random 
+	method                empty;                 // other options: ordered and random 
 
-	regionType              box;          // other options: cylinder and sphere  
+	regionType              box;                 // other options: cylinder and sphere  
 
-	boxInfo                               // box region for positioning particles 
+	boxInfo                                      // box region for positioning particles 
 	{
-		min (-0.08 -0.08 0.015);          // lower corner point of the box 
+		min (-0.08 -0.08 0.015);                 // lower corner point of the box 
 
-		max ( 0.08  0.08 0.098);	      // upper corner point of the box 
+		max ( 0.08  0.08 0.098);	             // upper corner point of the box 
 	} 
 }
 

tutorials/sphereGranFlow/layeredSiloFilling/settings/settingsDict

@@ -8,22 +8,26 @@ fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 run   layerdSiloFilling;
 
-dt 				0.00001; 	      // time step for integration (s)
+dt 				0.00001; 	                     // time step for integration (s)
 
-startTime 		    0.0; 		  // start time for simulation 
+startTime 		    0.0; 		                 // start time for simulation 
 
-endTime 		    5.0;	      // end time for simulation 
+endTime 		    5.0;	                     // end time for simulation 
 
-saveInterval 	   0.05; 		  // time interval for saving the simulation
+saveInterval 	   0.05; 		                 // time interval for saving the simulation
 
-timePrecision         6;	      // maximum number of digits for time folder 
+timePrecision         6;	                     // maximum number of digits for time folder 
 
-g 			 (0 0 -9.8);          // gravity vector (m/s2) 
+g 			 (0 0 -9.8);                         // gravity vector (m/s2) 
 
 // save data objects that are not automatically saved on disk.
+
 // overrides the default behavior 
-includeObjects (diameter);                                                 
+
+includeObjects (diameter);    
+
 // exclude unnecessary data from saving on disk
+
 excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
 integrationMethod 		AdamsBashforth2; 	      // integration method 

tutorials/sphereGranFlow/toteBlender/ReadMe.md

@@ -0,0 +1,244 @@
+# Problem Definition
+The problem is to simulate a double pedestal tote blender with the diameter **0.03 m** and **0.1 m** respectively, the length **0.3 m**, rotating at **28 rpm**. This blender is filled with **20000** Particles. The timestep for integration is **0.00001 s**. There is one type of Particle in this blender that are being inserted during simulation to fill the drum.
+* **20000** particles with **4 mm** diameter, at the rate of 20000 particles/s for 1 sec.
+
+<html>
+<body>
+<div align="center"><b>
+	a view of the tote-blender while rotating 
+</div></b>
+<div align="center">
+<img src="sample sample sample sample", width=700px>
+</div>
+</body>
+</html>
+
+# Setting up the Case
+As it has been explained in the previous cases, the simulation case setup is based on text-based scripts. Here, the simulation case setup are sotred in two folders: `caseSetup`, `setting`. (see the above folders). Unlike the previous cases, this case does not have the `stl` file. and the geometry is described in the `geometryDict` file.
+
+## Defining particles 
+Then in the `caseSetup/sphereShape` the diameter and the material name of the particles are defined.
+```C++
+// names of shapes 
+names 		(sphere1); 	
+// diameter of shapes (m)
+diameters 	(0.004);
+// material names for shapes 	
+materials	(prop1);	
+```
+## Particle Insertion
+In this case we have a region for ordering particles. These particles are placed in this blender. For example the script for the inserted particles is shown below.
+
+<div align="center"> 
+in <b>caseSetup/particleInsertion</b> file
+</div>
+
+```C++
+// positions particles 
+positionParticles
+{
+// ordered positioning
+	method positionOrdered;     
+// maximum number of particles in the simulation
+	maxNumberOfParticles 40000;
+// perform initial sorting based on morton code? 
+	mortonSorting Yes;             
+// box for positioning particles 
+	box  
+	{
+// lower corner point of the box 	
+		min (-0.06 -0.06 0.08);
+// upper corner point of the box 
+		max (0.06 0.06 0.18);
+	}
+```
+ ## Interaction between particles
+ In `caseSetup/interaction` file, material names and properties and interaction parameters are defined: interaction between the particles of rotating drum. Since we are defining 1 material for simulation, the interaction matrix is 1x1 (interactions are symetric). 
+```C++
+ // a list of materials names
+materials      (prop1);
+// density of materials [kg/m3]
+densities      (1000.0);   
+
+contactListType   sortedContactList; 
+
+model
+{
+   contactForceModel nonLinearNonLimited;
+   rollingFrictionModel normal;
+   /*
+   Property (prop1-prop1);
+   */
+// Young modulus [Pa]
+   Yeff  (1.0e6);       
+// Shear modulus [Pa]
+   Geff  (0.8e6);       
+// Poisson's ratio [-]
+   nu    (0.25);        
+// coefficient of normal restitution
+   en    (0.7);         
+// coefficient of tangential restitution
+   et    (1.0);          
+// dynamic friction
+   mu    (0.3);          
+// rolling friction
+   mur   (0.1);          
+        
+}
+```
+## Settings
+### Geometry
+In the `settings/geometryDict` file, the geometry and axis of rotation is defined for the drum. The geometry is composed of a cylinder inlet and outlet, cone shell top and down, a cylinder shell and enter and exit Gate.
+```C++
+surfaces
+{
+	enterGate
+	{
+	// type of wall
+		type planeWall;
+	// coords of wall
+		p1 (-0.05    -0.05    0.3);
+		p2 (-0.05    0.05     0.3);
+		p3 ( 0.05    0.05     0.3);
+		p4 (0.05     -0.05    0.3);
+	// material of wall
+		material prop1;
+	// motion component name
+		motion rotAxis;	
+	}
+	
+    cylinderinlet
+	{
+	// type of the wall
+		type 		cylinderWall;
+	// begin point of cylinder axis 	
+		p1 			(0.0 0.0 0.28);
+	// end point of cylinder axis  
+		p2 			(0.0 0.0 0.3);
+	// radius at p1  
+		radius1 	0.03;
+	// radius at p2		
+		radius2 	0.03;
+	// number of divisions		
+		resolution 	36;
+	// material name of this wall
+		material 	prop1;
+	// motion component name   	
+		motion rotAxis;		
+	}
+
+	coneShelltop
+	{
+	// type of the wall	
+		type 		cylinderWall;
+	// begin point of cylinder axis  	
+		p1 			(0.0 0.0 0.2);
+	// end point of cylinder axis  
+		p2 			(0.0 0.0 0.28);
+	// radius at p1  
+		radius1 	0.1;
+	// radius at p2		
+		radius2 	0.03;
+	// number of divisions		
+		resolution 	36;
+	// material name of this wall      	
+		material 	prop1;
+	// motion component name   	
+		motion rotAxis;		
+	}
+
+	cylinderShell
+	{
+	// type of the wall
+		type 		cylinderWall;
+	// begin point of cylinder axis  	
+		p1 			(0.0 0.0 0.1);
+	// end point of cylinder axis
+		p2 			(0.0 0.0 0.2);
+	// radius at p1	  
+		radius1 	0.1;
+	// radius at p2			
+		radius2 	0.1;
+	// number of divisions		
+		resolution 	36;
+	// material name of this wall	      	
+		material 	prop1; 
+	// motion component name  	
+		motion rotAxis;		
+	}
+
+	coneShelldown
+	{
+	// type of the wall
+		type 		cylinderWall;
+	// begin point of cylinder axis  	
+		p1 			(0.0 0.0 0.02);
+	// end point of cylinder axis  
+		p2 			(0.0 0.0 0.1);
+	// radius at p1  
+		radius1 	0.03;
+	// radius at p2		
+		radius2 	0.1;
+	// number of divisions		
+		resolution 	36;
+	// material name of this wall	      	
+		material 	prop1;
+	// motion component name   	
+		motion rotAxis;		
+	}
+	/*
+	This is a plane wall at the exit of silo
+	*/
+
+	    cylinderoutlet
+	{
+	// type of the wall
+		type 		cylinderWall;  	
+	// begin point of cylinder axis	
+		p1 			(0.0 0.0 0.0);
+	// end point of cylinder axis	  
+		p2 			(0.0 0.0 0.02);
+	// radius at p1  
+		radius1 	0.03;
+	// radius at p2			
+		radius2 	0.03;
+	// number of divisions			
+		resolution 	36;
+	// material name of this wall	      	
+		material 	prop1;
+	// motion component name	   	
+		motion rotAxis;		
+	}
+	exitGate
+	{
+		type planeWall;
+		p1 (-0.05    -0.05    0);
+		p2 (-0.05    0.05     0);
+		p3 ( 0.05    0.05     0);
+		p4 (0.05     -0.05    0);
+		material prop1;
+		motion rotAxis;		
+	}
+		
+}
+```
+### Rotating Axis Info
+In this part of `geometryDict` the information of rotating axis and speed of rotation are defined. Unlike the previous cases, the rotation of this blender starts at time=**0 s**.
+```C++
+rotatingAxisMotionInfo
+{
+	rotAxis 
+	{
+		p1 (-0.1 0.0 0.15);	// first point for the axis of rotation 
+		p2 (0.1 0.0 0.15);	// second point for the axis of rotation
+		omega 3; 		// rotation speed (rad/s)
+	}
+}
+```
+## Performing Simulation
+To perform simulations, enter the following commands one after another in the terminal. 
+
+Enter `$ particlesPhasicFlow` command to create the initial fields for particles.  
+Enter `$ geometryPhasicFlow` command to create the Geometry.  
+At last, enter `$ sphereGranFlow` command to start the simulation.  
+After finishing the simulation, you can use  `$ pFlowtoVTK` to convert the results into vtk format storred in ./VTK folder.

tutorials/sphereGranFlow/toteBlender/caseSetup/interaction

@@ -0,0 +1,61 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+/* ------------------------------------------------------------------------- */
+// a list of materials names
+materials      (prop1);
+// density of materials [kg/m3]
+densities      (1000.0);   
+
+contactListType   sortedContactList; 
+
+model
+{
+   contactForceModel nonLinearNonLimited;
+   rollingFrictionModel normal;
+   /*
+   Property (prop1-prop1);
+   */
+// Young modulus [Pa]
+   Yeff  (1.0e6);       
+// Shear modulus [Pa]
+   Geff  (0.8e6);       
+// Poisson's ratio [-]
+   nu    (0.25);        
+// coefficient of normal restitution
+   en    (0.7);         
+// coefficient of tangential restitution
+   et    (1.0);          
+// dynamic friction
+   mu    (0.3);          
+// rolling friction
+   mur   (0.1);          
+        
+}
+contactSearch
+{
+// method for broad search particle-particle
+   method         NBS;
+// method for broad search particle-wall           
+   wallMapping    cellMapping;   
+
+   NBSInfo
+   {
+   // each 20 timesteps, update neighbor list 
+      updateFrequency 20; 
+   // bounding box size to particle diameter (max)       
+      sizeRatio      1.1;        
+   }
+
+   cellMappingInfo
+   {
+   // each 20 timesteps, update neighbor list
+      updateFrequency 20;
+   // bounding box for particle-wall search (> 0.5)          
+      cellExtent     0.7;        
+   }
+
+}

tutorials/sphereGranFlow/toteBlender/caseSetup/particleInsertion

@@ -0,0 +1,13 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName particleInsertion;
+objectType dicrionary;
+/* ------------------------------------------------------------------------- */
+// is insertion active?
+active  no;         
+// not implemented for yes
+collisionCheck No;   
+
+

tutorials/sphereGranFlow/toteBlender/caseSetup/sphereShape

@@ -0,0 +1,13 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName 	sphereDict;
+objectType 	sphereShape;
+/* ------------------------------------------------------------------------- */
+// names of shapes 
+names 		(sphere1); 	
+// diameter of shapes (m)
+diameters 	(0.004);
+// material names for shapes 	
+materials	(prop1);	

tutorials/sphereGranFlow/toteBlender/cleanThisCase

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

tutorials/sphereGranFlow/toteBlender/runThisCase

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

tutorials/sphereGranFlow/toteBlender/settings/geometryDict

@@ -0,0 +1,151 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	geometryDict;
+objectType 	dictionary;
+/* ------------------------------------------------------------------------- */
+// motion model: rotating object around an axis
+motionModel rotatingAxisMotion; 
+
+surfaces
+{
+	enterGate
+	{
+	// type of wall
+		type planeWall;
+	// coords of wall
+		p1 (-0.05    -0.05    0.3);
+		p2 (-0.05    0.05     0.3);
+		p3 ( 0.05    0.05     0.3);
+		p4 (0.05     -0.05    0.3);
+	// material of wall
+		material prop1;
+	// motion component name
+		motion rotAxis;	
+	}
+	
+    cylinderinlet
+	{
+	// type of the wall
+		type 		cylinderWall;
+	// begin point of cylinder axis 	
+		p1 			(0.0 0.0 0.28);
+	// end point of cylinder axis  
+		p2 			(0.0 0.0 0.3);
+	// radius at p1  
+		radius1 	0.03;
+	// radius at p2		
+		radius2 	0.03;
+	// number of divisions		
+		resolution 	36;
+	// material name of this wall
+		material 	prop1;
+	// motion component name   	
+		motion rotAxis;		
+	}
+
+	coneShelltop
+	{
+	// type of the wall	
+		type 		cylinderWall;
+	// begin point of cylinder axis  	
+		p1 			(0.0 0.0 0.2);
+	// end point of cylinder axis  
+		p2 			(0.0 0.0 0.28);
+	// radius at p1  
+		radius1 	0.1;
+	// radius at p2		
+		radius2 	0.03;
+	// number of divisions		
+		resolution 	36;
+	// material name of this wall      	
+		material 	prop1;
+	// motion component name   	
+		motion rotAxis;		
+	}
+
+	cylinderShell
+	{
+	// type of the wall
+		type 		cylinderWall;
+	// begin point of cylinder axis  	
+		p1 			(0.0 0.0 0.1);
+	// end point of cylinder axis
+		p2 			(0.0 0.0 0.2);
+	// radius at p1	  
+		radius1 	0.1;
+	// radius at p2			
+		radius2 	0.1;
+	// number of divisions		
+		resolution 	36;
+	// material name of this wall	      	
+		material 	prop1; 
+	// motion component name  	
+		motion rotAxis;		
+	}
+
+	coneShelldown
+	{
+	// type of the wall
+		type 		cylinderWall;
+	// begin point of cylinder axis  	
+		p1 			(0.0 0.0 0.02);
+	// end point of cylinder axis  
+		p2 			(0.0 0.0 0.1);
+	// radius at p1  
+		radius1 	0.03;
+	// radius at p2		
+		radius2 	0.1;
+	// number of divisions		
+		resolution 	36;
+	// material name of this wall	      	
+		material 	prop1;
+	// motion component name   	
+		motion rotAxis;		
+	}
+	/*
+	This is a plane wall at the exit of silo
+	*/
+
+	    cylinderoutlet
+	{
+	// type of the wall
+		type 		cylinderWall;  	
+	// begin point of cylinder axis	
+		p1 			(0.0 0.0 0.0);
+	// end point of cylinder axis	  
+		p2 			(0.0 0.0 0.02);
+	// radius at p1  
+		radius1 	0.03;
+	// radius at p2			
+		radius2 	0.03;
+	// number of divisions			
+		resolution 	36;
+	// material name of this wall	      	
+		material 	prop1;
+	// motion component name	   	
+		motion rotAxis;		
+	}
+	exitGate
+	{
+		type planeWall;
+		p1 (-0.05    -0.05    0);
+		p2 (-0.05    0.05     0);
+		p3 ( 0.05    0.05     0);
+		p4 (0.05     -0.05    0);
+		material prop1;
+		motion rotAxis;		
+	}
+		
+}
+// information for rotatingAxisMotion motion model 
+rotatingAxisMotionInfo
+{
+	rotAxis 
+	{
+		p1 (-0.1 0.0 0.15);	// first point for the axis of rotation 
+		p2 (0.1 0.0 0.15);	// second point for the axis of rotation
+		omega 3; 		// rotation speed (rad/s)
+	}
+}

tutorials/sphereGranFlow/toteBlender/settings/particlesDict

@@ -0,0 +1,59 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	particlesDict;
+objectType 	dictionary;
+/* ------------------------------------------------------------------------- */
+setFields
+{
+	/*
+	    Default value for fields defined for particles
+	These fields should always be defined for simulations with 
+	spherical particles.
+	*/
+
+	defaultValue 
+	{
+// linear velocity (m/s)	
+		velocity 		realx3 	(0 0 0); 
+// linear acceleration (m/s2)		
+		acceleration 	realx3 	(0 0 0);
+// rotational velocity (rad/s)		 
+		rotVelocity 	realx3 	(0 0 0);
+// name of the particle shape 		 
+		shapeName 		word	sphere1; 
+	}
+
+	selectors
+	{}
+}
+
+// positions particles 
+positionParticles
+{
+// ordered positioning
+	method positionOrdered;     
+// maximum number of particles in the simulation
+	maxNumberOfParticles 40000;
+// perform initial sorting based on morton code? 
+	mortonSorting Yes;             
+// box for positioning particles 
+	box  
+	{
+// lower corner point of the box 	
+		min (-0.06 -0.06 0.08);
+// upper corner point of the box 
+		max (0.06 0.06 0.18);
+	}
+
+	positionOrderedInfo
+	{
+// minimum space between centers of particles
+		diameter 0.004;
+// number of particles in the simulation 	 	
+		numPoints 20000;
+// axis order for filling the space with particles		 	
+		axisOrder (z y x);  
+	}
+}

tutorials/sphereGranFlow/toteBlender/settings/settingsDict

@@ -0,0 +1,34 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	settingsDict;
+objectType 	dictionary;;
+/*---------------------------------------------------------------------------*/
+run 			toteBlender;
+// time step for integration (s)
+dt 				0.00001; 	
+// start time for simulation 
+startTime 		0; 			
+// end time for simulation 
+endTime 		10; 		
+// time interval for saving the simulation
+saveInterval 	0.1; 		
+// maximum number of digits for time folder
+timePrecision   6;			 
+// gravity vector (m/s2)
+g 				(0 0 -9.8);  
+
+/* Simulation domain */
+/*	every particles that goes outside this domain is deleted. */
+domain 
+{
+	min (-0.5 -0.5 -0.5);
+	max (0.5 0.5 0.5);
+}
+// integration method
+integrationMethod 		AdamsBashforth2; 	 
+// report timers?
+timersReport 			Yes;  	
+// time interval for reporting timers
+timersReportInterval   	0.01;