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/binarySystemOfParticles/settings/domainDict

@@ -21,14 +21,19 @@ 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

tutorials/sphereGranFlow/binarySystemOfParticles/settings/particlesDict

@@ -10,6 +10,7 @@ setFields
 {
 	/*
 	    Default value for fields defined for particles:
+
 		These fields should always be defined for simulations with spherical particles
 	*/
 

tutorials/sphereGranFlow/binarySystemOfParticles/settings/settingsDict

@@ -21,8 +21,11 @@ timePrecision  6;		   // 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 (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
 integrationMethod 		AdamsBashforth2; 	     // integration method 

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/interaction

@@ -32,6 +32,7 @@ model
    rollingFrictionModel        normal;
 
    /*
+
    Property (lightMat-lightMat   lightMat-heavyMat    lightMat-wallMat
                                  heavyMat-heavyMat    heavyMat-wallMat
                                                       wallMat-wallMat  );

tutorials/sphereGranFlow/layeredSiloFilling/settings/domainDict

@@ -16,14 +16,19 @@ 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

tutorials/sphereGranFlow/layeredSiloFilling/settings/particlesDict

@@ -10,7 +10,9 @@ setFields
 {
 	/*
 	    Default value for fields defined for particles
+
 		These fields should always be defined for simulations with 
+
 		spherical particles.
 	*/
 

tutorials/sphereGranFlow/layeredSiloFilling/settings/settingsDict

@@ -21,9 +21,13 @@ timePrecision         6;	      // maximum number of digits for time folder
 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);    
+
 // 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;