tutorials-1 after diameter->distance

tutorials/grainGranFlow/rotatingDrum/settings/particlesDict

@@ -44,8 +44,8 @@ positionParticles
 	
 	orderedInfo
 	{
-		// minimum space between centers of particles
+		// minimum distance between particles centers
-		diameter 0.001;
+		distance 0.001;
 		
 		// number of particles in the simulation 	 	
 		numPoints 50000;

tutorials/postprocessPhasicFlow/segregation/settings/particlesDict

@@ -24,7 +24,7 @@ positionParticles
 		
 	positionOrderedInfo
 	{		
-		diameter 0.005; 	// minimum space between centers of particles
+		distance 0.005; 	// minimum distance between particles centers
 		numPoints 30000; 	// number of particles in the simulation 
 		axisOrder (z x y);  // axis order for filling the space with particles
 	}
@@ -41,7 +41,7 @@ setFields
 	{
 		velocity 		realx3 	(0 0 0); // linear velocity (m/s)
 		acceleration 	realx3 	(0 0 0); // linear acceleration (m/s2)
-		r	Velocity 	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 
 	}
 
@@ -54,6 +54,7 @@ setFields
 			{
 				begin 	0;			// begin index of points
 				end 	29999;		// end index of points
+				number 	10000;	    // number of points to be selected 
 			}
 			fieldValue  // fields that the selector is applied to 
 			{

tutorials/sphereGranFlow/RotaryAirLockValve/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/RotaryAirLockValve/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/RotaryAirLockValve/settings/domainDict

@@ -6,7 +6,9 @@ objectName 	domainDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+
+// Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                                        
 {
     min     (0.397538 0.178212 0.00);
     

tutorials/sphereGranFlow/RotaryAirLockValve/settings/settingsDict

@@ -25,10 +25,12 @@ g               (0 -9.8 0);                 // gravity vector (m/s2)
 includeObjects (diameter mass);
 
 // exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1);
+excludeObjects ();
 
 integrationMethod       AdamsBashforth2;
 
+integrationHistory      off;
+
 writeFormat     ascii;                      // data writting format (ascii or binary)
 
 timersReport    Yes;                        // report timers: Yes or No

tutorials/sphereGranFlow/binarySystemOfParticles/README.md

@@ -47,7 +47,7 @@ positionParticles
     method ordered;         // other options: random or empty
     orderedInfo
     {        
-           diameter     0.005;     // minimum space between centers of particles
+        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
     }

tutorials/sphereGranFlow/binarySystemOfParticles/settings/domainDict

@@ -6,8 +6,8 @@ objectName 	domainDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-// Simulation domain: every particles that goes outside this domain will be deleted
 
+// Simulation domain: every particles that goes outside this domain will be deleted
 globalBox                     
 {
     min     (-0.12 -0.12 0);

tutorials/sphereGranFlow/binarySystemOfParticles/settings/geometryDict

@@ -44,7 +44,6 @@ surfaces
     /*
         This is a plane wall at the rear end of cylinder
     */
-
     wall1
     {
         type         planeWall;                  // other options: cuboidWall and  cylinderWall
@@ -65,7 +64,6 @@ surfaces
     /*
         This is a plane wall at the front end of cylinder
     */
-
     wall2
     {
         type         planeWall;                  // other options: cuboidWall and  cylinderWall 

tutorials/sphereGranFlow/binarySystemOfParticles/settings/particlesDict

@@ -6,6 +6,7 @@ objectName 	particlesDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 setFields
 {
     /*
@@ -54,7 +55,7 @@ positionParticles 				                 // positions particles
 
     orderedInfo
     {       
-		diameter    0.005; 	                     // diameter of particles
+        distance    0.005;                       // minimum distance between particles centers
 
         numPoints   30000;                       // number of particles in the simulation
 

tutorials/sphereGranFlow/binarySystemOfParticles/settings/settingsDict

@@ -21,15 +21,15 @@ timePrecision     6;		                     // maximum number of digits for time
 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     (); 
-excludeObjects     (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
 integrationMethod        AdamsBashforth2;        // integration method
 
+integrationHistory       off;                    // do not keep integration history on disk (saves space)
+
 writeFormat              ascii;                  // data writting format (ascii or binary)
 
 timersReport             Yes;                    // report timers

tutorials/sphereGranFlow/conveyorBelt/caseSetup/particleInsertion

@@ -6,14 +6,14 @@ objectName particleInsertion;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 active           Yes;     // is insertion active -> yes or no
 
 checkForCollision No;     // is checked          -> yes or no
 
 /*
-   one layers of particles are packed 
+   one layer of particles are packed 
 */
-
 layer0
 {  
     timeControl          simulationTime;

tutorials/sphereGranFlow/conveyorBelt/caseSetup/shapes

@@ -6,6 +6,7 @@ objectName 	sphereDict;
 objectType  sphereShape;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 names        (lightSphere heavySphere);          // names of shapes 
 
 diameters                (0.007 0.007);          // diameter of shapes 

tutorials/sphereGranFlow/conveyorBelt/settings/domainDict

@@ -6,7 +6,9 @@ objectName 	domainDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+
+// Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                  
 {
     min (-0.11 -0.11 -0.41);
     
@@ -16,19 +18,15 @@ globalBox                                        // Simulation domain: every par
 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/conveyorBelt/settings/geometryDict

@@ -6,7 +6,9 @@ objectName 	geometryDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-motionModel          conveyorBelt;               // motion model can be rotatingAxis or stationary or vibrating
+
+// motion model can be rotatingAxis or stationary or vibrating
+motionModel          conveyorBelt;               
 
 conveyorBeltInfo
 {
@@ -73,8 +75,3 @@ surfaces
     }
 }
 
-
-
-
-
-

tutorials/sphereGranFlow/conveyorBelt/settings/particlesDict

@@ -6,16 +6,14 @@ objectName 	particlesDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 setFields
 {
 	/*
 	    Default value for fields defined for particles
-
 		These fields should always be defined for simulations with 
-
 		spherical particles.
 	*/
-
 	defaultValue 
 	{
 		velocity 		realx3 	    (0 0 0);     // linear velocity (m/s)
@@ -31,17 +29,8 @@ setFields
 	{}
 }
 
-positionParticles                                // positions particles 
+positionParticles  
 {
-	method                empty;                 // other options: ordered and random 
+	method                empty;  // other options: file, ordered and random 
-
-	regionType              box;                 // other options: cylinder and sphere  
-
-	boxInfo                                      // box region for positioning particles 
-	{
-		min (-0.08 -0.08 0.015);                 // lower corner point of the box 
-
-		max ( 0.08  0.08 0.098);	             // upper corner point of the box 
-	} 
 }
 

tutorials/sphereGranFlow/conveyorBelt/settings/settingsDict

@@ -6,7 +6,8 @@ objectName 	settingsDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-run   layerdSiloFilling;
+
+run        conveyorBelt;
 
 dt              0.00005;                         // time step for integration (s)
 
@@ -21,13 +22,10 @@ timePrecision         6;	                     // maximum number of digits for ti
 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/drum-PeriodicBoundary/README.md

@@ -72,7 +72,7 @@ boundaries
 ## Running the Case 
 The solver for this simulation is `sphereGranFlow`. Enter the following commands in the terminal. Depending on the computational power, it may take a few minutes to a few hours to complete. 
 
-```sh
+```
 geometryPhasicFlow
 particlesPhasicFlow
 sphereGranFlow
@@ -81,6 +81,6 @@ sphereGranFlow
 ## Post Processing 
 After finishing the simulation, you can render the results in ParaView. To convert the results to VTK format, just enter the following command in the terminal. This will convert all the results (particles and geometry) to VTK format and store them in the `VTK/` folder. 
 
-```sh
+```
 pFlowToVTK --binary
 ```

tutorials/sphereGranFlow/drum-PeriodicBoundary/settings/settingsDict

@@ -24,18 +24,12 @@ g               (0 -9.8 0);         // gravity vector (m/s2)
 includeObjects  (diameter);         // save necessary (i.e., required) data on disk
 
 // exclude unnecessary data from saving on disk
-excludeObjects  (rVelocity.dy1
+excludeObjects  (); 
-                 rVelocity.dy2
-                 rVelocity.dy3 
-                 pStructPosition.dy1
-                 pStructPosition.dy2
-                 pStructPosition.dy3 
-                 pStructVelocity.dy1
-                 pStructVelocity.dy2
-                 pStructVelocity.dy3); 
 
 integrationMethod     AdamsBashforth4;  // integration method
 
+integrationHistory    off;              // to save space on disk  
+
 writeFormat           ascii;            // data writting format (ascii or binary)
 
 timersReport          Yes;              // report timers (Yes or No)

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/README.md

@@ -3,7 +3,7 @@
 ## Problem
 A homogenization silo is used to mix particles inside a silo using the circulation of particles. A pneumatic conveying system carries particles from the exit and re-enters them from the top. Here, we use a `periodic` boundary to simulate the action of the pneumatic conveyor system for circulating particles. Particles exiting from the bottom are re-entered from the top using this boundary (`periodic`).
 
-The simulation case setup is essentially similar to the [`layeredSiloFilling`](https://github.com/PhasicFlow/phasicFlow/tree/main/tutorials/sphereGranFlow/layeredSiloFilling) tutorial. There is also another change with regard to `layeredSiloFilling`. The exit gate is opened after the filling phase of the silo (see `settings/geometryDict` for more details).
+The simulation case setup is essentially similar to the [`layeredSiloFilling`](../layeredSiloFilling/) tutorial. There is also another change with regard to `layeredSiloFilling`. The exit gate is opened after the filling phase of the silo (see `settings/geometryDict` for more details).
 
 <div align ="center">
 <img src="./homoSilo.jpeg" style="width: 400px;">

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/caseSetup/interaction

@@ -37,7 +37,6 @@ model
                                  heavyMat-heavyMat    heavyMat-wallMat
                                                       wallMat-wallMat  );
    */
-
    Yeff (1.0e6 1.0e6 1.0e6                       // Young modulus [Pa]
                1.0e6 1.0e6
                      1.0e6);

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/caseSetup/particleInsertion

@@ -109,7 +109,6 @@ layer2
     mixture
     {
         parType1 1; // only parType1
-      
     }
 }
 
@@ -143,7 +142,6 @@ layer3
     mixture
     {
         parType2 1;
-      
     }
 }
 
@@ -176,7 +174,6 @@ layer4
     mixture
     {
         parType1 1;
-      
     }
 }
 
@@ -209,6 +206,5 @@ layer5
     mixture
     {
         parType2 1;
-      
     }
 }

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/domainDict

@@ -38,12 +38,12 @@ boundaries
         type exit;   
     }
 
-	rear
+    rear // z-
     {
         type periodic;      
     }
 
-	front
+    front // z+ 
     {
         type periodic;   
     }

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/geometryDict

@@ -61,7 +61,6 @@ surfaces
     /*
         This is a plane wall at the exit of silo
     */
-
     exitGate
     {
         type        planeWall;                   // other options: cuboidWall and cylinderWall

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/particlesDict

@@ -13,7 +13,6 @@ setFields
         These fields should always be defined for simulations with 
         spherical particles.
     */
-
     defaultValue 
     {
         velocity        realx3      (0 0 0);     // linear velocity (m/s)

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/settingsDict

@@ -25,12 +25,12 @@ g 			    (0 0 -9.8); // gravity vector (m/s2)
 includeObjects (diameter);    
 
 // exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 rVelocity.dy2 rVelocity.dy3 
+excludeObjects (); 
-				pStructPosition.dy1 pStructPosition.dy2 pStructPosition.dy3
-				pStructVelocity.dy1 pStructVelocity.dy2 pStructVelocity.dy3); 
 
 integrationMethod       AdamsBashforth4; // integration method 
 
+integrationHistory      off;       // to save space on disk 
+
 writeFormat             binary;    // data writting format (ascii or binary)
 
 timersReport            Yes;       // report timers

tutorials/sphereGranFlow/layeredSiloFilling/settings/particlesDict

@@ -13,7 +13,6 @@ setFields
 		These fields should always be defined for simulations with 
 		spherical particles.
 	*/
-
 	defaultValue 
 	{
 		velocity 		realx3 	    (0 0 0);     // linear velocity (m/s)

tutorials/sphereGranFlow/layeredSiloFilling/settings/settingsDict

@@ -25,10 +25,12 @@ g               (0 0 -9.8);    // gravity vector (m/s^2)
 includeObjects  (diameter mass);
 
 // exclude unnecessary data from saving on disk
-excludeObjects  (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1);
+excludeObjects  ();
 
 integrationMethod    AdamsBashforth2; // integration method
 
+integrationHistory   off;
+
 writeFormat          ascii;           // data writing format (ascii or binary)
 
 timersReport         Yes;             // report timers

tutorials/sphereGranFlow/rotatingDrumMedium/README.md

@@ -0,0 +1,161 @@
+# Simulating a Medium-Scale Rotating Drum (v-1.0)
+
+## Problem Definition
+
+This tutorial demonstrates the simulation of a medium-sized rotating drum with a diameter of 0.24 m and a length of 0.36 m. The drum is filled with 250,000 spherical glass beads with a diameter of 3 mm. The drum rotates at a constant speed, and the simulation captures the flow behavior and mixing of the particles.
+
+<div align="center">
+<b>
+A view of the rotating drum simulation
+</b>
+</div>
+
+***
+
+## Setting up the Case
+
+PhasicFlow simulation case setup is based on text-based scripts provided in two folders located in the simulation case folder: `settings` and `caseSetup`. All commands should be entered in the terminal while the current working directory is the simulation case folder.
+
+### Creating Particles
+
+In the file `settings/particlesDict`, two dictionaries, `positionParticles` and `setFields`, define how particles are positioned and what field values they have initially.
+
+The `positionParticles` dictionary specifies the ordered positioning method to place 250,000 particles within a cylindrical region:
+
+```C++
+positionParticles
+{
+    method ordered;                // other options: random and empty
+    
+    orderedInfo
+    {
+        distance   0.003;          // minimum distance between particles centers
+        numPoints  250000;         // number of particles in the simulation 
+        axisOrder  (z y x);        // axis order for filling the space with particles
+    }
+
+    regionType cylinder;           // other options: box and sphere  
+    
+    cylinderInfo
+    {
+        p1 (0.0 0.0 0.003);        // begin point of cylinder axis
+        p2 (0.0 0.0 0.357);        // end point of cylinder axis
+        radius     0.117;          // radius of cylinder 
+    }
+}
+```
+
+The `setFields` dictionary defines the initial values for particle fields:
+
+```C++
+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    glassBead; // name of the particle shape 
+    }
+}
+```
+
+To create the particles based on these settings, enter the following command in the terminal:
+
+```
+> particlesPhasicFlow
+```
+
+### Creating Geometry
+
+In the file `settings/geometryDict`, you can find information for creating the rotating drum geometry. The simulation uses the `rotatingAxis` motion model to define rotation around a fixed axis.
+
+The surfaces of the drum are defined in the `surfaces` dictionary, including the cylindrical shell and end walls.
+
+To create the geometry based on these settings, enter the following command in the terminal:
+
+```
+> geometryPhasicFlow
+```
+
+### Defining Properties and Interactions
+
+In the file `caseSetup/shapes`, the particle shape, diameter, and material are defined:
+
+```C++
+names       (glassBead);    // names of shapes 
+diameters       (0.003);    // diameter of shapes 
+materials    (glassMat);    // material names for shapes
+```
+
+In the file `caseSetup/interaction`, the material properties and interaction models are defined:
+
+```C++
+materials     (glassMat wallMat);  // a list of materials names
+densities     (2500.0 2500);       // density of materials [kg/m3]
+
+model
+{
+    contactForceModel    nonLinearLimited;
+    rollingFrictionModel           normal;
+    
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
+
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);          // Young modulus [Pa]
+   
+    Geff (0.8e6  0.8e6  
+                 0.8e6);          // Shear modulus [Pa]
+
+    nu   (0.25   0.25  
+                 0.25);           // Poisson's ratio [-]
+
+    en   (0.97   0.85   
+                 1.00);           // coefficient of normal restitution
+
+    mu   (0.65   0.65   
+                 0.65);           // dynamic friction 
+
+    mur  (0.1    0.1    
+                 0.1);            // rolling friction
+}
+```
+
+The contact search settings are also defined in this file, including the method, update interval, and other parameters.
+
+## Running the Simulation
+
+To run the simulation, follow these steps in order:
+
+1. Create the initial particle fields:
+
+   ```
+   > particlesPhasicFlow
+   ```
+
+2. Create the geometry:
+
+   ```
+   > geometryPhasicFlow
+   ```
+
+3. Start the simulation:
+
+   ```
+   > sphereGranFlow
+   ```
+
+The simulation will run according to the settings defined in `settings/settingsDict`, including the time step, start/end times, and gravity vector.
+
+## Post-Processing
+
+After the simulation is complete, you can visualize the results using ParaView. To convert the simulation results to VTK format, use the following command:
+
+```
+> pFlowToVTK --binary
+```
+
+This will create VTK files in the `VTK/` folder that can be opened in ParaView for visualization and analysis.

tutorials/sphereGranFlow/rotatingDrumMedium/caseSetup/interaction

@@ -6,6 +6,7 @@ objectName interaction;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 materials         (glassMat wallMat);                       // a list of materials names
 
 densities         (2500.0 2500);                            // density of materials [kg/m3]

tutorials/sphereGranFlow/rotatingDrumMedium/caseSetup/particleInsertion

@@ -1,10 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
-objectType dicrionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-active         No;                                      // is checked          -> Yes or No
-

tutorials/sphereGranFlow/rotatingDrumMedium/settings/domainDict

@@ -6,7 +6,9 @@ objectName     domainDict;
 objectType     dictionary;
 fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+
+// Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                                        
 {
     min (-0.12 -0.12 0);
 

tutorials/sphereGranFlow/rotatingDrumMedium/settings/geometryDict

@@ -6,6 +6,7 @@ objectName     geometryDict;
 objectType     dictionary;
 fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
+
 motionModel rotatingAxis;                         // motion model: rotating object around an axis
 
 

tutorials/sphereGranFlow/rotatingDrumMedium/settings/particlesDict

@@ -36,7 +36,7 @@ positionParticles                                    // positions particles
 
     orderedInfo
     {
-        diameter   0.003;                            // minimum space between centers of particles
+        distance   0.003;                            // minimum distance between particles centers
 
         numPoints  250000;                           // number of particles in the simulation 
 

tutorials/sphereGranFlow/rotatingDrumMedium/settings/settingsDict

@@ -23,7 +23,7 @@ g                       (0 -9.8 0);              // gravity vector (m/s2)
 includeObjects (diameter);                       // save necessary (i.e., required) data on disk
 
 // exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+excludeObjects (); 
 
 integrationMethod       AdamsBashforth2;         // integration method 
 

tutorials/sphereGranFlow/rotatingDrumSmall/README.md

@@ -1,35 +1,36 @@
-# Simularing a rotating drum (v-1.0) 
+# Simulating a Rotating Drum (v-1.0)
-## Problem definition 
+
-The problem is to simulate a rotating drum with the diameter 0.24 m and the length 0.1 m rotating at 11.6 rpm. It is filled with 30,000 4-mm spherical particles. The timestep for integration is 0.00001 s.
+## Problem Definition
+
+The problem is to simulate a rotating drum with a diameter of 0.24 m and a length of 0.1 m, rotating at 11.6 rpm. It is filled with 30,000 spherical particles, each with a diameter of 4 mm. The timestep for integration is 0.00001 s. This tutorial demonstrates the basic setup for creating a rotation-based simulation using built-in geometry in PhasicFlow.
+
 <div align="center">
 <b>
-    
+A view of the rotating drum
-A view of rotating drum
 </b>
-<b>
+<div>
-
+<img src="https://github.com/PhasicFlow/phasicFlow/blob/media/media/rotating-drum-s.png" width="600px">
-![](https://github.com/PhasicFlow/phasicFlow/blob/media/media/rotating-drum-s.png)
+</div>
-
+</div>
-</b></div>
 
 ***
 
-## Setting up the case 
+## Setting up the Case 
-PhasicFlow simulation case setup is based on the text-based scripts that we provide in two folders located in the simulation case folder: `settings` and `caseSetup` (You can find the case setup files in the above folders.
-All the commands should be entered in the terminal while the current working directory is the simulation case folder (at the top of the `caseSetup` and `settings`).
 
+PhasicFlow simulation case setup is based on text-based scripts provided in two folders located in the simulation case folder: `settings` and `caseSetup`. All commands should be entered in the terminal while the current working directory is the simulation case folder (at the top level of `caseSetup` and `settings`).
 
-### Creating particles
+### Creating Particles
 
-Open the file  `settings/particlesDict`. Two dictionaries, `positionParticles` and `setFields` position particles and set the field values for the particles. 
+In the file `settings/particlesDict`, two dictionaries, `positionParticles` and `setFields`, position particles and set the field values for the particles.
-In dictionary `positionParticles`, the positioning `method` is `ordered`, which position particles in order in the space defined by `box`. `box` space is defined by two corner points `min` and `max`. In dictionary `orderedInfo`, `numPoints` defines number of particles; `diameter`, the distance between two adjacent particles, and `axisOrder` defines the axis order for filling the space by particles. 
+
+The `positionParticles` dictionary uses the `ordered` method to position particles in a space defined by `box`. The box space is defined by two corner points: `min` and `max`. In the `orderedInfo` sub-dictionary, `numPoints` defines the number of particles (30,000), `distance` defines the spacing between adjacent particles (4 mm), and `axisOrder` defines the axis order for filling the space with particles.
 
 <div align="center"> 
 in <b>settings/particlesDict</b> file
 </div>
 
 ```C++
-positionParticles                                // positions particles 
+positionParticles           
 { 
     method         ordered; // other options: random and empty
 
@@ -37,7 +38,7 @@ positionParticles                                // positions particles
 
     orderedInfo
     {
-        diameter  0.004;                         // minimum space between centers of particles
+        distance  0.004;    // minimum space between centers of particles
 
         numPoints 30000;    // number of particles in the simulation 
 
@@ -54,7 +55,8 @@ positionParticles                                // positions particles
     }
 }
 ```
-In dictionary `setFields`, dictionary `defaultValue` defines the initial value for particle fields (here, `velocity`, `acceleration`, `rotVelocity`, and `shapeName`). Note that `shapeName` field should be consistent with the name of shape that you later set for shapes (here one shape with name `sphere1`).
+
+In the `setFields` dictionary, the `defaultValue` sub-dictionary defines the initial values for particle fields (velocity, acceleration, rotational velocity, and shape name). The shape name field should be consistent with the name defined in the shapes file (here, "sphere1").
 
 <div align="center"> 
 in <b>settings/particlesDict</b> file
@@ -76,17 +78,20 @@ setFields
 
     selectors
     {
-
+        // Selectors can be used to modify properties for specific particle groups
     }
 }
 ```
 
-Enter the following command in the terminal to create the particles and store them in `0` folder.
+To create the particles and store them in the `0` folder, enter the following command:
 
-`> particlesPhasicFlow`
+```
+particlesPhasicFlow
+```
 
-### Creating geometry
+### Creating Geometry
-In file `settings/geometryDict` , you can provide information for creating geometry. Each simulation should have a `motionModel` that defines a model for moving the surfaces in the simulation. `rotatingAxis` model defines a fixed axis which rotates around itself. The dictionary `rotAxis` defines an motion component with `p1` and `p2` as the end points of the axis and `omega` as the rotation speed in rad/s. You can define more than one motion component in a simulation. 
+
+In the file `settings/geometryDict`, you define the motion model and geometry for the simulation. The `rotatingAxis` motion model defines a fixed axis which rotates around itself. The `rotAxis` dictionary specifies the axis endpoints and rotation speed.
 
 <div align="center"> 
 in <b>settings/geometryDict</b> file
@@ -95,7 +100,7 @@ in <b>settings/geometryDict</b> file
 ```C++
 motionModel rotatingAxis; 
 
-rotatingAxisInfo                                 // information for rotatingAxisMotion motion model 
+rotatingAxisInfo 
 {
     rotAxis 
     {
@@ -107,7 +112,11 @@ rotatingAxisInfo                                 // information for rotatingAxis
     }
 }
 ```
-In the dictionary `surfaces` you can define all the surfaces (walls) in the simulation. Two main options are available: built-in geometries in PhasicFlow, and providing surfaces with stl file. Here we use built-in geometries. In `cylinder` dictionary, a cylindrical shell with end radii, `radius1` and `radius2`, axis end points `p1` and `p2`, `material` name `prop1`, `motion` component `rotAxis` is defined. `resolution` sets number of division for the cylinder shell. `wall1` and `wall2` define two plane walls at two ends of cylindrical shell with coplanar corner points `p1`, `p2`, `p3`, and `p4`, `material` name `prop1` and `motion` component `rotAxis`.  
+
+The `surfaces` dictionary defines all the walls in the simulation. This tutorial uses built-in geometries provided by PhasicFlow. The geometry consists of:
+
+1. A `cylinder` dictionary defining a cylindrical shell with end radii (`radius1` and `radius2`), axis endpoints (`p1` and `p2`), material name (`prop1`), and motion component (`rotAxis`).
+2. Two plane walls (`wall1` and `wall2`) at the ends of the cylindrical shell, each defined with four coplanar corner points, the same material name, and the same motion component.
 
 <div align="center"> 
 in <b>settings/geometryDict</b> file
@@ -119,7 +128,6 @@ surfaces
     /*
         A cylinder with begin and end radii 0.12 m and axis points at (0 0 0) and (0 0 0.1)
     */
-
     cylinder
     {
         type cylinderWall;      // type of the wall
@@ -142,7 +150,6 @@ surfaces
     /*
         This is a plane wall at the rear end of cylinder
     */
-
     wall1
     {
         type       planeWall;      // type of the wall
@@ -163,7 +170,6 @@ surfaces
     /*
         This is a plane wall at the front end of cylinder
     */
-
     wall2
     {
         type       planeWall;      // type of the wall
@@ -182,12 +188,16 @@ surfaces
     }
 }
 ```
-Enter the following command in the terminal to create the geometry and store it in `0/geometry` folder.
 
-`> geometryPhasicFlow`
+To create the geometry and store it in the `0/geometry` folder, enter:
 
-### Defining properties and interactions 
+```
-In the file `caseSetup/interaction` , you find properties of materials. `materials` defines a list of material names in the simulation and `densities` sets the corresponding density of each material name. model dictionary defines the interaction model for particle-particle and particle-wall interactions. `contactForceModel` selects the model for mechanical contacts (here nonlinear model with limited tangential displacement) and `rollingFrictionModel` selects the model for calculating rolling friction. Other required prosperities should be defined in this dictionary. 
+geometryPhasicFlow
+```
+
+### Defining Properties and Interactions 
+
+In the file `caseSetup/interaction`, you define properties of materials and their interactions. The `materials` entry lists material names, and `densities` sets the corresponding densities. The `model` dictionary defines the contact force and rolling friction models, along with other required properties.
 
 <div align="center"> 
 in <b>caseSetup/interaction</b> file
@@ -195,37 +205,41 @@ in <b>caseSetup/interaction</b> file
 
 ```C++
 materials                   (prop1);   // a list of materials names
+
 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
+
     mu    (0.3);       // dynamic friction 
+
     mur   (0.1);       // rolling friction      
 }
 ```
 
-Dictionary `contactSearch` sets the methods for particle-particle and particle-wall contact search. `method` specifies the algorithm for finding neighbor list for particle-particle contacts. `updateInterval` sets the number of iterations between each occurance of  updating neighbor list and `sizeRatio` sets the size of enlarged cells (with respect to particle diameter) for finding neighbor list. Larger `sizeRatio` include more particles in the neighbor list and you require to update it less frequent. 
+The `contactSearch` dictionary specifies the algorithm and parameters for finding particle-particle contacts. The `method` determines the broad search algorithm, `updateInterval` sets how often to update the neighbor list, and `sizeRatio` controls the enlarged cell size for finding neighbors.
 
 <div align="center"> 
 in <b>caseSetup/interaction</b> file
 </div>
 
 ```C++
-contactListType   sortedContactList; 
-
 contactSearch
 {
-  
+    method          NBS;  
-    method          NBS;                          // method for broad search 
 
     updateInterval   10;
 
@@ -235,57 +249,25 @@ contactSearch
 
     adjustableBox   Yes;
 } 
-
 ```
 
-In the file `caseSetup/shape`, you can define a list of `names` for shapes (`shapeName` in particle field), a list of diameters for shapes and their `properties` names. 
+In the file `caseSetup/shapes`, you define particle shapes, including their names, diameters, and material properties:
 
 <div align="center"> 
-in <b>caseSetup/shape</b> file
+in <b>caseSetup/shapes</b> file
 </div>
 
 ```C++
 names       (sphere1);    // names of shapes 
+
 diameters     (0.004);    // diameter of shapes 
+
 materials     (prop1);    // material names for shapes
 ```
 
-Other settings for the simulation can be set in file `settings/settingsDict`. 
+### Simulation Domain and Boundaries
 
-<div align="center"> 
+The file `settings/domainDict` defines a rectangular bounding box with boundaries. Particles that exit this box are automatically deleted.
-in <b>settings/settingsDict</b> file
-</div>
-
-```C++
-run   rotatingDrumSmall;
-
-dt              0.00001;                         // time step for integration (s)
-
-startTime             0;                         // start time for simulation 
-
-endTime              10;                         // end time for simulation 
-
-saveInterval        0.1;                         // time interval for saving the simulation
-
-timePrecision         6;                         // maximum number of digits for time folder 
-
-g            (0 -9.8 0);                         // gravity vector (m/s2) 
-
-includeObjects (diameter);                       // save necessary (i.e., required) data on disk
-
-// exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
-
-integrationMethod       AdamsBashforth2;         // integration method 
-
-writeFormat                       ascii;         // data writting format (ascii or binary)
-
-timersReport                        Yes;         // report timers (Yes or No)
-
-timersReportInterval               0.01;         // time interval for reporting timers
-```
-
-The dictionary `settings/domainDict` defines the a rectangular bounding box with two corner points for the simulation. Each particle that gets out of this box, will be deleted automatically. 
 
 <div align="center"> 
 in <b>settings/domainDict</b> file
@@ -334,13 +316,77 @@ boundaries
 }
 ```
 
+### Other Settings
 
-## Running the case 
+Additional parameters for the simulation are set in `settings/settingsDict`, including timestep, start and end times, saving intervals, and gravity:
-The solver for this simulation is `sphereGranFlow`. Enter the following command in the terminal. Depending on the computational power, it may take a few minutes to a few hours to complete. 
 
-`> sphereGranFlow`
+<div align="center"> 
+in <b>settings/settingsDict</b> file
+</div>
 
-## Post processing 
+```C++
-After finishing the simulation, you can render the results in Paraview. To convert the results to VTK format, just enter the following command in the terminal. This will converts all the results (particles and geometry) to VTK format and store them in folder `VTK/`. 
+dt              0.00001;     // time step for integration (s)
 
-`> pFlowToVTK --binary`
+startTime             0;     // start time for simulation 
+
+endTime              10;     // end time for simulation 
+
+saveInterval        0.1;     // time interval for saving the simulation
+
+timePrecision         6;     // maximum number of digits for time folder 
+
+g            (0 -9.8 0);     // gravity vector (m/s2) 
+
+includeObjects (diameter);   // save necessary (i.e., required) data on disk
+
+// exclude unnecessary data from saving on disk
+excludeObjects ();
+
+integrationMethod       AdamsBashforth2;  // integration method
+
+integrationHistory                  off;  // to save space on disk
+
+writeFormat                       ascii;  // data writing format (ascii or binary)
+
+timersReport                        Yes;  // report timers (Yes or No)
+```
+
+## Running the Case 
+
+To execute the simulation, follow these steps in order:
+
+1. Create the geometry:
+
+```
+geometryPhasicFlow
+```
+
+2. Create the initial particle fields:
+
+```
+particlesPhasicFlow
+```
+
+3. Run the simulation:
+
+```
+sphereGranFlow
+```
+
+Depending on your computational resources, the simulation may take from a few minutes to several hours to complete.
+
+## Post Processing 
+
+After the simulation completes, you can visualize the results in ParaView by converting them to VTK format:
+
+```
+pFlowToVTK --binary
+```
+
+This command converts all simulation results (particles and geometry) to VTK format and stores them in a `VTK/` folder. You can then open these files in ParaView for detailed analysis and visualization.
+
+For more specific field output, you can specify fields:
+
+```
+pFlowToVTK --binary --fields diameter velocity id
+```

tutorials/sphereGranFlow/rotatingDrumSmall/caseSetup/interaction

@@ -6,6 +6,7 @@ objectName interaction;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 materials                   (prop1);             // a list of materials names
 
 densities                  (1000.0);             // density of materials [kg/m3]

tutorials/sphereGranFlow/rotatingDrumSmall/caseSetup/particleInsertion

@@ -1,13 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
-objectType dicrionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-active         No;                               // is insertion active -> Yes or No
-
-collisionCheck No;                               // is checked          -> Yes or No
-
-

tutorials/sphereGranFlow/rotatingDrumSmall/settings/domainDict

@@ -6,7 +6,9 @@ objectName 	domainDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+
+// 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 
 
@@ -17,31 +19,31 @@ boundaries
 {
     left
     {
-		type     exit;	                  // other options: periodict, reflective 
+        type     exit;                    // other options: periodic, reflective 
     }
 
     right
     {
-		type     exit;                    // other options: periodict, reflective 
+        type     exit;                    // other options: periodic, reflective 
     }
 
     bottom
     {
-		type     exit;                    // other options: periodict, reflective 
+        type     exit;                    // other options: periodic, reflective 
     }
 
     top
     {
-		type     exit;                    // other options: periodict, reflective 
+        type     exit;                    // other options: periodic, reflective 
     }
 
     rear
     {
-		type     exit;                    // other options: periodict, reflective 
+        type     exit;                    // other options: periodic, reflective 
     }
 
     front
     {
-		type     exit;                    // other options: periodict, reflective 
+        type     exit;                    // other options: periodic, reflective 
     }
 }

tutorials/sphereGranFlow/rotatingDrumSmall/settings/geometryDict

@@ -6,6 +6,7 @@ objectName 	geometryDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 motionModel rotatingAxis; 
 
 rotatingAxisInfo                                 // information for rotatingAxisMotion motion model 
@@ -25,7 +26,6 @@ surfaces
 	/*
 	    A cylinder with begin and end radii 0.12 m and axis points at (0 0 0) and (0 0 0.1)
 	*/
-
 	cylinder
 	{
 		type cylinderWall;                       // type of the wall
@@ -48,7 +48,6 @@ surfaces
 	/*
 		This is a plane wall at the rear end of cylinder
 	*/
-
 	wall1
 	{
 		type       planeWall;			         // type of the wall
@@ -69,7 +68,6 @@ surfaces
 	/*
 		This is a plane wall at the front end of cylinder
 	*/
-
 	wall2
 	{
 		type       planeWall;                    // type of the wall

tutorials/sphereGranFlow/rotatingDrumSmall/settings/particlesDict

@@ -10,12 +10,9 @@ setFields
 {
     /*
         Default value for fields defined for particles
-
         These fields should always be defined for simulations with 
-
         spherical particles.
     */
-
     defaultValue 
     {
         velocity        realx3  (0 0 0);         // linear velocity (m/s)
@@ -41,7 +38,7 @@ positionParticles                                // positions particles
 
     orderedInfo
     {
-		diameter  0.004; 						 // minimum space between centers of particles
+        distance  0.004;                         // minimum distance between particles centers
 
         numPoints 30000;                         // number of particles in the simulation 
 

tutorials/sphereGranFlow/rotatingDrumSmall/settings/settingsDict

@@ -6,6 +6,7 @@ objectName 	settingsDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 run   rotatingDrumSmall;
 
 dt              0.00001;                         // time step for integration (s)
@@ -27,6 +28,8 @@ excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1);
 
 integrationMethod       AdamsBashforth2;         // integration method
 
+integrationHistory                  off; 
+
 writeFormat                       ascii;         // data writting format (ascii or binary)
 
 timersReport                        Yes;         // report timers (Yes or No)

tutorials/sphereGranFlow/toteBlender/settings/particlesDict

@@ -38,7 +38,7 @@ positionParticles
 
     orderedInfo
     {
-        diameter    0.005;   // minimum space between centers of particles
+        distance    0.005;   // minimum distance between particles centers
                  
         numPoints   24000;   // number of particles in the simulation