Merge pull request #114 from ramin1728/main

binary system of particles tutorial is updated

tutorials/sphereGranFlow/binarySystemOfParticles/README.md

@@ -1,6 +1,6 @@
 # Problem definition
-A rotating drum with two particle sizes is randomly filled and let it rotate to see the segregation of particles.
+
-The focus of this tutorial is to show how to use the pre-processing tool, `particlesPhasicFlow`, to create the initial mixture of small and large particles. 
+A rotating drum is randomly filled with two particle sizes and rotated to observe particle segregation. The focus of this tutorial is to show how to use the preprocessing tool `particlesPhasicFlow` to create the initial mixture of small and large particles. 
 
 **Note:** It is supposed that you have reviewed [simulating a rotating drum](https://github.com/PhasicFlow/phasicFlow/wiki/Simulating-a-rotating-drum) tutorial before starting this tutorial.
 
@@ -14,11 +14,13 @@ a view of the rotating drum with small and large particles after 7 seconds of ro
 ***
 
 # Case setup
-PhasicFlow simulation case setup is based on the text-based files that we provide in two folders located in the simulation case folder: `settings` and `caseSetup`. Here we will have a look at some important files and the rest can be found in the tutorial folder of this case setup. 
+
+In the file `caseSetup/sphereShape` two particle types with the names `smallSphere` and `largeSphere` and the diameters 3 and 5 mm are defined. 
 
 [Simulation case setup files can be found in tutorials/sphereGranFlow folder.](https://github.com/PhasicFlow/phasicFlow/tree/main/tutorials/sphereGranFlow/binarySystemOfParticles)
 ### Shape definition 
-In file `caseSetup/sphereShape`, two particle types with names `smallSphere` and `largeSphere` and diameters 3 and 5 mm are defined. 
+
+In the file `caseSetup/sphereShape` two particle types with the names `smallSphere` and `largeSphere` and the diameters 3 and 5 mm are defined. 
 
 <div align="center"> 
 in <b>caseSetup/sphereShape</b> file
@@ -31,7 +33,7 @@ materials    (prop1  prop1);       // material names for shapes
 ```
 ### Positioning and initial mixture 
 
-In dictionary `positionParticles` located in file `settings/particlesDict`, 30000 particles are located in a cylindrical region. These particles are positioned in order along `z`, `x` and then `y` axis with 0.005 m distance between their centers. 
+In the dictionary `positionParticles` located in file `settings/particlesDict`, 30000 particles are located in a cylindrical region. These particles are positioned in order along `z`, `x` and then `y` axis with 0.005 m distance between their centers. 
 
 <div align="center"> 
 in <b>settings/particlesDict</b> file
@@ -42,10 +44,16 @@ in <b>settings/particlesDict</b> file
 // positions particles 
 positionParticles
 {
-    method positionOrdered;     // ordered positioning
+    method ordered;     // other options: random or empty
 
-    maxNumberOfParticles 30001; // maximum number of particles in the simulation
+    orderedInfo
-    mortonSorting Yes;          // perform initial sorting based on morton code?   
+    {        
+        diameter 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
+    }
+
+    regionType cylinder;                                   // other options: box and sphere 
 
     cylinder  // cylinder region for positioning particles 
     {
@@ -53,17 +61,9 @@ positionParticles
         p2 (0.0 0.0 0.097);     // end point of cylinder axis (m m m)
         radius       0.117;     // radius of cylinder (m)
     }
-        
-    positionOrderedInfo
-    {        
-        diameter 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
-    }
 }
 ```
-
+In the `setFields` dictionary, located in the `settings/particlesDict` file, you define the initial `velocity`, `acceleration`, `rotVelocity` and `shapeName` fields for all 30000 particles in the simulation. In the `selectors' dictionary, you can select subsets of particles and set the field value for those subsets. The `selectRange` selector is defined in the `shapeAssigne` subdictionary. It defines a range with `begin`, `end` and `stride` to select particles. And in the `fieldValue` subdictionary the field values for selected particles are set (any number of field values can be set here).
-In dictionary `setFields` located in file `settings/particlesDict`, you define the initial `velocity`, `acceleration`, `rotVelocity`, and  `shapeName` fields for all 30000 particles in the simulation. In `selectors` dictionary, you can select  subsets of particles and set the field value for these subsets. In `shapeAssigne` sub-dictionary, the `selectRange` selector is defined. It defines a range with `begin` (begin index), `end` (end index) and `stride` to select particles. And in `fieldValue` sub-dictionary, the fields values for selected particles are set (any number of field values can be set here).
 
 **Note:** Other selectors are: `selectBox` that selects particles inside a box and `randomSelect` that selects particles randomly from a given index range. 
 
@@ -77,7 +77,8 @@ setFields
     /*
         Default value for fields defined for particles
     These fields should always be defined for simulations with 
-    spherical particles.*/
+    spherical particles.
+*/
 
     defaultValue 
     {
@@ -91,8 +92,9 @@ setFields
     {
         shapeAssigne
         {
-            selector     selectRange; // type of point selector
+            selector     stridedRange; 				       // other options: box, cylinder, sphere, randomPoints
-            selectRangeInfo
+
+            stridedRangeInfo
             {
                 begin   0;            // begin index of points
                 end     30000;        // end index of points 
@@ -101,10 +103,10 @@ setFields
             fieldValue  // fields that the selector is applied to 
             {
                 /*
-                sets shapeName of the selected points to largeSphere*/
+                    sets shapeName of the selected points to largeSphere
+                */
                 shapeName     word     largeSphere;
             }
-        
     }
 }
 

tutorials/sphereGranFlow/binarySystemOfParticles/caseSetup/interaction

@@ -49,4 +49,3 @@ model
    mur      (0.1);            // rolling friction     
 }
 
-

tutorials/sphereGranFlow/binarySystemOfParticles/caseSetup/particleInsertion

@@ -6,9 +6,6 @@ objectName 	particleInsertion;
 objectType 	dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-active  No;                                      // is insertion active -> yes or no
-
 collisionCheck     No;          // is checked          -> yes or no
 
-
+active             No;          // is insertion active -> yes or no
-

tutorials/sphereGranFlow/binarySystemOfParticles/caseSetup/shapes

@@ -11,4 +11,3 @@ names 		(smallSphere largeSphere); 	         // names of shapes
 diameters (0.003 0.005);	                     // diameter of shapes 
 
 materials (prop1 prop1);	                     // material names for shapes 
-   

tutorials/sphereGranFlow/binarySystemOfParticles/settings/geometryDict

@@ -24,7 +24,7 @@ surfaces
 {
 	cylinder
 	{
-		type cylinderWall;             // type of the wall
+		type     cylinderWall;          // other options: cuboidWall and planeWall
 
 		p1 (0.0 0.0 0.0);          // begin point of cylinder axis
 
@@ -47,7 +47,7 @@ surfaces
 
 	wall1
 	{
-		type planeWall;			       // type of the wall
+		type     planeWall;			 // other options: cuboidWall and  cylinderWall
 
 		p1 (-0.12 -0.12 0.0);	       // first point of the wall
 
@@ -68,7 +68,7 @@ surfaces
 
 	wall2
 	{
-		type planeWall;                // type of the wall   
+		type     planeWall;          // other options: cuboidWall and  cylinderWall 
 
 		p1 (-0.12 -0.12 0.1);          // first point of the wall
 
@@ -83,5 +83,3 @@ surfaces
 		motion       rotAxis;          // motion component name 
 	}
 }
-
-

tutorials/sphereGranFlow/binarySystemOfParticles/settings/particlesDict

@@ -9,9 +9,8 @@ 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 
+		These fields should always be defined for simulations with spherical particles
-		spherical particles.
 	*/
 
 	defaultValue 
@@ -72,5 +71,3 @@ positionParticles 				                           // positions particles
 		radius 		0.117;		                           // radius of cylinder 
 	}
 }
-
-

tutorials/sphereGranFlow/binarySystemOfParticles/settings/settingsDict

@@ -8,11 +8,11 @@ fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
 run 	binarySystemofParticles;
 
-dt 				0.00001; 	                     // time step for integration (s)
+dt       0.00001; 	       // time step for integration (seconds)
 
-startTime 		0; 			                     // start time for simulation 
+startTime    0.0; 		   // start time for simulation 
 
-endTime 		10; 		                     // end time for simulation 
+endTime     10.0; 		   // end time for simulation 
 
 saveInterval 0.1; 		   // time interval for saving the simulation
 
@@ -32,3 +32,4 @@ writeFormat 			ascii;                   // data writting format (ascii or binary
 timersReport 			            Yes;  	      // report timers
 
 timersReportInterval   	           0.01;	      // time interval for reporting timers
+ 

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/interaction

@@ -64,6 +64,7 @@ model
    mur (0.1  0.1 0.1                  // rolling friction 
              0.1 0.1
                  0.1);       
-        
 }
 
+
+

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/particleInsertion

@@ -6,7 +6,7 @@ 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
 
@@ -50,3 +50,5 @@ layer0
 
 
 
+
+

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/shapes

@@ -11,3 +11,5 @@ names 		(lightSphere heavySphere); 	         // names of shapes
 diameters 	             (0.007 0.007);		     // diameter of shapes 
 
 materials	       (lightMat heavyMat);		     // material names for shapes 
+
+

tutorials/sphereGranFlow/layeredSiloFilling/caseSetup/sphereShape

@@ -1,12 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName 	sphereDict;
-objectType 	sphereShape;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-
-names 		(lightSphere heavySphere); 	// names of shapes 
-diameters 	(0.007 0.007);				// diameter of shapes 
-materials	(lightMat heavyMat);		// material names for shapes 

tutorials/sphereGranFlow/layeredSiloFilling/settings/domainDict

@@ -56,3 +56,5 @@ boundaries
 		type exit;           // other options: periodict, reflective 
 	}
 }    
+
+

tutorials/sphereGranFlow/layeredSiloFilling/settings/geometryDict

@@ -17,7 +17,7 @@ surfaces
 {
 	cylinderShell
 	{
-		type 		cylinderWall;  	   // type of the wall
+		type 		 cylinderWall;  	    // other options: cuboidWall and planeWall
 
 		p1 			(0.0 0.0 0.0);          // begin point of cylinder axis
 
@@ -34,7 +34,7 @@ surfaces
 
 	coneShell
 	{
-		type 		cylinderWall;  	   // type of the wall
+		type 		 cylinderWall;  	    // other options: cuboidWall and planeWall
 
 		p1 		   (0.0 0.0 -0.1);          // begin point of cylinder axis
 
@@ -55,7 +55,7 @@ surfaces
 
 	exitGate
 	{
-		type planeWall;                // type of the wall
+		type planeWall;                     // other options: cuboidWall and cylinderWall
 
 		p1 (-0.02 -0.02 -0.1);              // first point of the wall
 
@@ -70,3 +70,7 @@ surfaces
 }
 
 
+
+
+
+

tutorials/sphereGranFlow/layeredSiloFilling/settings/particlesDict

@@ -42,3 +42,4 @@ positionParticles                                          // positions particle
 		max ( 0.08  0.08 0.098);	      // upper corner point of the box 
 	} 
 }
+

tutorials/sphereGranFlow/layeredSiloFilling/settings/settingsDict

@@ -20,7 +20,8 @@ timePrecision   6;			                     // maximum number of digits for time f
 
 g 			 (0 0 -9.8);          // gravity vector (m/s2) 
 
-// save necessary (i.e., required) data on disk
+// 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); 
@@ -32,3 +33,6 @@ writeFormat				ascii;                   // data writting format (ascii or binary
 timersReport 			            Yes;  	      // report timers
 
 timersReportInterval   	           0.01;	      // time interval for reporting timers
+
+
+