bug correction for the time when empty is used

binarySystemOfParticles is Updated.

solvers/sphereGranFlow/sphereGranFlow.cpp

@@ -74,7 +74,7 @@ pFlow::initialize_pFlowProcessors();
 
 	do 
 	{
-		
+		//Ping;
 		if(! sphInsertion.insertParticles( 
 			Control.time().currentIter(),
 			Control.time().currentTime(),
@@ -84,27 +84,31 @@ pFlow::initialize_pFlowProcessors();
 			"particle insertion failed in sphereDFlow solver.\n";
 			return 1;
 		}
-		 
+		
 		// set force to zero
 		surfGeometry.beforeIteration();
 
 		// set force to zero, predict, particle deletion and etc. 
 		sphParticles.beforeIteration();
-
+		//Ping;
 		sphInteraction.beforeIteration();
 		
-		sphInteraction.iterate();	
-		
+		sphInteraction.iterate();
+			
 		surfGeometry.iterate();
 
+		//Ping;
 		sphParticles.iterate();
-
+		
+		//Ping;
 		sphInteraction.afterIteration();
 
+		//Ping;
 		surfGeometry.afterIteration();
 
+		//Ping;
 		sphParticles.afterIteration();
-				
+		//Ping;	
 
 	}while(Control++);
 

src/Particles/globalDamping/globalDamping.cpp

@@ -35,10 +35,14 @@ pFlow::globalDamping::globalDamping(const systemControl& control)
     performDamping_ = !equal(dampingFactor_, static_cast<real>(1.0));
 
     if( performDamping_ )
-		REPORT(2)<<"Global damping "<<Yellow_Text("is active")<<
-		" and damping factor is "<<dampingFactor_<<END_REPORT;
-	else
-		REPORT(2)<<"Global damping "<<Yellow_Text("is not active")<<"."<<END_REPORT;
+    {
+      REPORT(2)<<"Global damping "<<Yellow_Text("is active")<<
+		  " and damping factor is "<<dampingFactor_<<END_REPORT;
+    }
+		else
+		{
+      REPORT(2)<<"Global damping "<<Yellow_Text("is not active")<<"."<<END_REPORT;
+    }
 
 }
 

src/phasicFlow/smartPointers/uniquePtr.hpp

@@ -27,6 +27,7 @@ Licence:
 
 #include "pFlowMacros.hpp"
 #include "error.hpp"
+#include "iOstream.hpp"
 
 // just for preventing the use of std namespace and adding some minor functionalities
 

tutorials/sphereGranFlow/binarySystemOfParticles/README.md

@@ -28,8 +28,8 @@ in <b>caseSetup/sphereShape</b> file
 
 ```C++
 names        (smallSphere largeSphere); // names of shapes 
-diameters    (0.003     0.005);    // diameter of shapes (m)
-materials    (prop1  prop1);       // material names for shapes 
+diameters                (0.003 0.005); // diameter of shapes (m)
+materials               (prop1  prop1); // material names for shapes 
 ```
 ### Positioning and initial mixture 
 
@@ -44,18 +44,17 @@ in <b>settings/particlesDict</b> file
 // positions particles 
 positionParticles
 {
-    method ordered;     // other options: random or empty
-
+    method ordered;         // other options: random or empty
     orderedInfo
     {        
-        diameter 0.005;     // minimum space between centers of particles
-        numPoints 30000;    // number of particles in the simulation 
+           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 
+    cylinder                    // cylinder region for positioning particles 
     {
         p1 (0.0 0.0 0.003);     // begin point of cylinder axis (m m m)
         p2 (0.0 0.0 0.097);     // end point of cylinder axis (m m m)
@@ -76,9 +75,9 @@ setFields
 {
     /*
         Default value for fields defined for particles
-    These fields should always be defined for simulations with 
-    spherical particles.
-*/
+        These fields should always be defined for simulations with 
+        spherical particles.
+    */
 
     defaultValue 
     {
@@ -87,20 +86,21 @@ setFields
         rotVelocity     realx3     (0 0 0); // rotational velocity (rad/s)
         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 
-                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 
             {
                 /*
                     sets shapeName of the selected points to largeSphere
@@ -139,4 +139,4 @@ Options:
   --setFields-only            Exectue the setFields part only. Read the pointStructure from time folder and setFields and save the result in the same time folder.
 ```
 
-so, with flag `--setFields-only`, you can execute the `setFields` part of `particlesDict`. Now suppose that you have a simulation case which proceeded up to 2 seconds and for any reason you want to change some field value at time 3 s and continue the simulation from 3 s. To this end, you need to change `startTime` in settings dictionary to 3, execute `particlesPhasicFlow --setFields-only`, and start the simulation. 
+so, with flag `--setFields-only`, you can execute the `setFields` part of `particlesDict`. Now suppose that you have a simulation case which proceeded up to 2 seconds and for any reason you want to change some field value at time 3 s and continue the simulation from 3 s. To this end, you need to change `startTime` in settings dictionary to 3, execute `particlesPhasicFlow --setFields-only`, and start the simulation. 

tutorials/sphereGranFlow/binarySystemOfParticles/caseSetup/interaction

@@ -6,9 +6,9 @@ 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;
 
@@ -38,14 +38,14 @@ model
 
    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/settings/geometryDict

@@ -26,19 +26,19 @@ surfaces
 	{
 		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 
 	}
 
 	/*

tutorials/sphereGranFlow/binarySystemOfParticles/settings/particlesDict

@@ -29,20 +29,20 @@ setFields
 	{
 		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 
 			{
-				shapeName 	word    largeSphere; // sets shapeName of the selected points to largeSphere
+				shapeName 	word largeSphere;    // sets shapeName of the selected points to largeSphere
 			}
 		}
 	}
@@ -50,13 +50,13 @@ setFields
 
 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
 	}
@@ -69,6 +69,6 @@ positionParticles 				                 // positions particles
 
 		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/conveyorBelt/caseSetup/interaction

@@ -16,13 +16,13 @@ contactSearch
 {
    method         NBS;                           // method for broad search particle-particle
    
-   updateInterval 10;
+   updateInterval  10;
 
    sizeRatio      1.1;
 
-   cellExtent     0.55;
+   cellExtent    0.55;
 
-   adjustableBox  No;
+   adjustableBox   No;
 } 
 
 model
@@ -46,25 +46,25 @@ model
                0.8e6 0.8e6
                      0.8e6);
 
-   nu    (0.25 0.25  0.25                        // Poisson's ratio [-]
-               0.25  0.25
-                     0.25);
+   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
-             0.97    0.85
-                     1.00);
+   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 
-             1.0  1.0
-                  1.0);
+   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 
-              0.65 0.35
-                   0.35);
+   mu    (0.65   0.65 0.35                       // dynamic friction 
+                 0.65 0.35
+                      0.35);
 
-   mur (0.1  0.1 0.1                             // rolling friction 
-             0.1 0.1
-                 0.1);       
+   mur       (0.1  0.1 0.1                       // rolling friction 
+                   0.1 0.1
+                       0.1);       
 }
 
 

tutorials/sphereGranFlow/conveyorBelt/settings/geometryDict

@@ -6,7 +6,7 @@ objectName 	geometryDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-motionModel            conveyorBelt;               // motion model can be rotatingAxis or stationary or vibrating
+motionModel          conveyorBelt;               // motion model can be rotatingAxis or stationary or vibrating
 
 conveyorBeltInfo
 {
@@ -54,17 +54,22 @@ surfaces
 
 	belt
 	{
-		type 	 stlWall;  	// type of the wall
-		file 	 belt.stl;	// file name in stl folder		
-		material wallMat;   // material name of this wall
-		motion 	 conveyorBelt1;		// motion component name 
+		type 	          stlWall;  	         // type of the wall
+
+		file 	         belt.stl;	             // file name in stl folder	
+
+		material          wallMat;               // material name of this wall
+
+		motion 	    conveyorBelt1;		         // motion component name 
 	}
 
 	box
 	{
-		type 	 stlWall;  	// type of the wall
-		file 	 box.stl;	// file name in stl folder		
-		material wallMat;   // material name of this wall
+		type 	         stlWall;  	             // type of the wall
+
+		file 	         box.stl;	             // file name in stl folder
+
+		material         wallMat;                // material name of this wall
 	}
 }
 

utilities/particlesPhasicFlow/empty/empty.cpp

@@ -30,7 +30,7 @@ pFlow::empty::empty(
 	positionParticles(control, dict),
 	position_
 	(
-		"empty",maxNumberOfParticles(), 0, RESERVE()
+		"empty",1, 0, RESERVE()
 	)
 {
 }

utilities/particlesPhasicFlow/positionOrdered/positionOrdered.cpp

@@ -146,8 +146,8 @@ pFlow::positionOrdered::positionOrdered
 	position_
 	(
 		"positionOrdered", 
-		max(maxNumberOfParticles(), numPoints_), 
-		numPoints_ ,
+		numPoints_, 
+		numPoints_,
 		RESERVE()
 	)
 {

utilities/particlesPhasicFlow/positionParticles/positionParticles.cpp

@@ -32,45 +32,10 @@ pFlow::realx3Vector pFlow::positionParticles::sortByMortonCode(
 		uint64 index;
 	};
 
-	/*realx3 minP = min(position);
-	realx3 maxP = max(position);
-	real cellsize = maxDiameter();
-	cells<uint64> allCells( box(minP, maxP), cellsize);
-
-	Vector<indexMorton> indMor(position.size(),RESERVE());
-
-	indMor.clear();
-
-	uint64 ind=0;
-	for(const auto& p:position)
-	{
-		auto cellInd = allCells.pointIndex(p);
-		indMor.push_back( 
-			{ xyzToMortonCode64(cellInd.x(), cellInd.y(), cellInd.z()),
-			ind++});
-	}
-
-	INFORMATION<<"Performing morton sorting."<<END_INFO;
-	std::sort(
-		indMor.begin(),
-		indMor.end(),
-		[]( const indexMorton &lhs, const indexMorton &rhs){
-			return lhs.morton < rhs.morton; } );
-
-	realx3Vector sortedPos(position.capacity(), RESERVE());
-	sortedPos.clear();
-
-
-	for(auto& ind:indMor)
-	{
-		sortedPos.push_back( position[ind.index] );
-	}*/
-
     WARNING<<"Morton sorting is inactive!"<<END_WARNING;
 	return position;
 }
 
-
 pFlow::positionParticles::positionParticles
 (
 	systemControl& control,
@@ -78,12 +43,8 @@ pFlow::positionParticles::positionParticles
 )
 :
 	regionType_(dict.getValOrSet<word>("regionType", "domain")),
-	maxNumberOfParticles_(dict.getValOrSet(
-		"maxNumberOfParticles", 
-		static_cast<uint32>(10000))),
 	mortonSorting_(dict.getValOrSet("mortonSorting", Logical("Yes")))
 {
-
 	if( regionType_ != "domain" )	
 	{
 		pRegion_ = peakableRegion::create(
@@ -92,7 +53,7 @@ pFlow::positionParticles::positionParticles
 	}	
 	else
 	{
-		fileDictionary domainDict
+		fileDictionary domainDictionary
 		(
 			objectFile
 			{
@@ -103,12 +64,10 @@ pFlow::positionParticles::positionParticles
 			},
 			&control.settings()
 		);
-		pRegion_ = peakableRegion::create(regionType_,domainDict.subDict("globalBox"));
+		pRegion_ = peakableRegion::create("box", domainDictionary.subDict("globalBox"));
 	}
-	
 }
 
-
 pFlow::realx3Vector pFlow::positionParticles::getFinalPosition()
 {
 	if(mortonSorting_)
@@ -130,10 +89,8 @@ pFlow::uniquePtr<pFlow::positionParticles>
     const dictionary & dict
 )
 {
-
 	word method = dict.getVal<word>("method");
 
-
 	if( dictionaryvCtorSelector_.search(method) )
 	{
 		return dictionaryvCtorSelector_[method] (control, dict);

utilities/particlesPhasicFlow/positionParticles/positionParticles.hpp

@@ -40,12 +40,8 @@ private:
 
 	word 			regionType_;
 
-	uint32  		maxNumberOfParticles_ = 10000;
-
 	Logical 		mortonSorting_;
 
-	
-
 	realx3Vector sortByMortonCode(const realx3Vector& position)const;
 
 protected:
@@ -83,12 +79,6 @@ public:
 		return mortonSorting_();
 	} 
 
-	inline
-	auto maxNumberOfParticles()const
-	{
-		return maxNumberOfParticles_;
-	}
-
 	virtual uint32 numPoints()const = 0;
 
 	virtual uint32 size()const = 0;

utilities/particlesPhasicFlow/positionRandom/positionRandom.cpp

@@ -122,14 +122,14 @@ pFlow::positionRandom::positionRandom
 	position_
 	(
 		"position",
-		maxNumberOfParticles(),
+		1,
 		0,
 		RESERVE()
 	),
 	diameters_
 	(
 		"diameters",
-		maxNumberOfParticles(),
+		1,
 		0,
 		RESERVE()
 	)