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------------------------------------------------------------
revno: 3804
committer: Anton Gladky <gladky.anton@xxxxxxxxx>
timestamp: Tue 2016-03-08 10:18:20 +0100
message:
  vtkExporter: increase number of leading zeros to 8
  
  Minor formatting fixes
modified:
  pkg/dem/Polyhedra.cpp
  pkg/dem/Polyhedra.hpp
  pkg/dem/Polyhedra_Ig2.cpp
  pkg/dem/Polyhedra_Ig2.hpp
  py/export.py


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=== modified file 'pkg/dem/Polyhedra.cpp'
--- pkg/dem/Polyhedra.cpp	2014-10-22 10:13:18 +0000
+++ pkg/dem/Polyhedra.cpp	2016-03-08 09:18:20 +0000
@@ -17,7 +17,7 @@
 	/* some code in cpp (this file): */ 
 	#ifdef YADE_OPENGL
 		(Gl1_Polyhedra) (Gl1_PolyhedraGeom) (Gl1_PolyhedraPhys)
-	#endif	
+	#endif
 	);
 
 //*********************************************************************************
@@ -56,7 +56,7 @@
 	v.clear();
 	for (Polyhedron::Vertex_iterator vIter = P.vertices_begin(); vIter != P.vertices_end(); ++vIter, i++){
 		v.push_back(Vector3r(vIter->point().x(),vIter->point().y(),vIter->point().z()));
-	}	
+	}
 
 	//list surface triangles for plotting
 	faceTri.clear();
@@ -82,7 +82,7 @@
 		seed = rand();
 		Initialize();
 	}
-        Vector3r translation((-1)*centroid);
+	Vector3r translation((-1)*centroid);
 	
 	//set centroid to be [0,0,0]
 	for(int i=0;i<N;i++) {
@@ -93,10 +93,10 @@
 	Vector3r origin(0,0,0);
 
 	//move and rotate also the CGAL structure Polyhedron
-	Transformation t_trans(1.,0.,0.,translation[0],0.,1.,0.,translation[1],0.,0.,1.,translation[2],1.);		
-	std::transform( P.points_begin(), P.points_end(), P.points_begin(), t_trans);	
+	Transformation t_trans(1.,0.,0.,translation[0],0.,1.,0.,translation[1],0.,0.,1.,translation[2],1.);
+	std::transform( P.points_begin(), P.points_end(), P.points_begin(), t_trans);
 
-	//compute inertia	
+	//compute inertia
 	Real vtet;
 	Vector3r ctet;
 	Matrix3r Itet1, Itet2;
@@ -111,7 +111,7 @@
 			-ctet[0]*ctet[1], ctet[0]*ctet[0]+ctet[2]*ctet[2], -ctet[2]*ctet[1],
 			-ctet[0]*ctet[2], -ctet[2]*ctet[1], ctet[1]*ctet[1]+ctet[0]*ctet[0];
 		inertia_tensor = inertia_tensor + Itet1 + Itet2*vtet; 
-	}	
+	}
 
 	if(std::abs(inertia_tensor(0,1))+std::abs(inertia_tensor(0,2))+std::abs(inertia_tensor(1,2)) < 1E-13){
 		// no need to rotate, inertia already diagonal
@@ -142,9 +142,9 @@
 		Vector3r third = (I_rot.col(0)).cross(I_rot.col(1));
 		I_rot(0,2) = third[0];
 		I_rot(1,2) = third[1];
-		I_rot(2,2) = third[2];	
-		
-					
+		I_rot(2,2) = third[2];
+		
+		
 		inertia = Vector3r(I_new(0,0),I_new(1,1),I_new(2,2));
 		orientation = Quaternionr(I_rot); 
 		//rotate the voronoi cell so that x - is maximal inertia axis and z - is minimal inertia axis
@@ -152,7 +152,7 @@
 		for(int i=0; i< (int) v.size();i++) {
 			v[i] =  orientation.conjugate()*v[i];
 		}
-			
+		
 		//rotate also the CGAL structure Polyhedron
 		Matrix3r rot_mat = (orientation.conjugate()).toRotationMatrix();
 		Transformation t_rot(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2),rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),1.);	
@@ -167,12 +167,12 @@
 /* Generator of randomly shaped polyhedron based on Voronoi tessellation*/
 
 void Polyhedra::GenerateRandomGeometry(){
-	srand(seed);	
+	srand(seed);
 
 	vector<CGALpoint> nuclei;
 	nuclei.push_back(CGALpoint(5.,5.,5.));
 	CGALpoint trial;
-	int iter = 0; 
+	unsigned int iter = 0; 
 	bool isOK;
 	//fill box 5x5x5 with randomly located nuclei with restricted minimal mutual distance 0.75 which gives approximate mean mutual distance 1;
 	Real dist_min2 = 0.75*0.75;
@@ -184,32 +184,29 @@
 			isOK = pow(nuclei[i].x()-trial.x(),2)+pow(nuclei[i].y()-trial.y(),2)+pow(nuclei[i].z()-trial.z(),2) > dist_min2;
 			if (!isOK) break;
 		}
-
 		if(isOK){
 			iter = 0;
 			nuclei.push_back(trial);
-		}				
-	}	
-	
-	
-	//perform Voronoi tessellation	
-        nuclei.erase(nuclei.begin());
+		}
+	}
+	
+	//perform Voronoi tessellation
+	nuclei.erase(nuclei.begin());
 	Triangulation dt(nuclei.begin(), nuclei.end());
 	Triangulation::Vertex_handle zero_point = dt.insert(CGALpoint(5.,5.,5.));
 	v.clear();
-        std::vector<Triangulation::Cell_handle>  ch_cells;
-    	dt.incident_cells(zero_point,std::back_inserter(ch_cells));
-	for(std::vector<Triangulation::Cell_handle>::iterator ci = ch_cells.begin(); ci !=ch_cells.end(); ++ci){
-		v.push_back(FromCGALPoint(dt.dual(*ci))-Vector3r(5.,5.,5.));				
+	std::vector<Triangulation::Cell_handle>  ch_cells;
+ 	dt.incident_cells(zero_point,std::back_inserter(ch_cells));
+	for(auto ci = ch_cells.begin(); ci !=ch_cells.end(); ++ci){
+		v.push_back(FromCGALPoint(dt.dual(*ci))-Vector3r(5.,5.,5.));
 	}
 
-
 	//resize and rotate the voronoi cell
 	Quaternionr Rot(Real(rand())/RAND_MAX,Real(rand())/RAND_MAX,Real(rand())/RAND_MAX,Real(rand())/RAND_MAX);
 	Rot.normalize();
 	for(int i=0; i< (int) v.size();i++) {
 		v[i] = Rot*(Vector3r(v[i][0]*size[0],v[i][1]*size[1],v[i][2]*size[2]));
-	}	
+	}
 	
 	//to avoid patological cases (that should not be present, but CGAL works somehow unpredicable)
 	if (v.size() < 8) {

=== modified file 'pkg/dem/Polyhedra.hpp'
--- pkg/dem/Polyhedra.hpp	2015-06-06 12:45:20 +0000
+++ pkg/dem/Polyhedra.hpp	2016-03-08 09:18:20 +0000
@@ -104,7 +104,7 @@
 			.def("GetSurfaceTriangulation",&Polyhedra::GetSurfaceTriangulation,"triangulation of facets (for plotting)")
 			.def("GetSurfaces",&Polyhedra::GetSurfaces,"get indices of surfaces' vertices (for postprocessing)")
 			.def("setVertices",&Polyhedra::setVertices,"set vertices and update receiver")
-		);		
+		);
 		REGISTER_CLASS_INDEX(Polyhedra,Shape);
 };
 REGISTER_SERIALIZABLE(Polyhedra);

=== modified file 'pkg/dem/Polyhedra_Ig2.cpp'
--- pkg/dem/Polyhedra_Ig2.cpp	2016-03-07 08:38:44 +0000
+++ pkg/dem/Polyhedra_Ig2.cpp	2016-03-08 09:18:20 +0000
@@ -396,58 +396,4 @@
 	return true;
 }
 
-/*
-bool Ig2_Sphere_Polyhedra_PolyhedraGeom::go(const shared_ptr<Shape>& shape1,const shared_ptr<Shape>& shape2,const State& state1,const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr<Interaction>& interaction){
-
-	const Se3r& se31=state1.se3; 
-	const Se3r& se32=state2.se3;
-	Polyhedra* B = static_cast<Polyhedra*>(shape2.get());
-	const Real& r=shape1->cast<Sphere>().radius;
-
-	//cout << "Sphere x Polyhedra" << endl;
-
-	bool isNew = !interaction->geom;
-
-	//move and rotate 1st the CGAL structure Polyhedron
-	Matrix3r rot_mat = (se32.orientation).toRotationMatrix();
-	Vector3r trans_vec = se32.position;
-	Transformation t_rot_trans(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2), trans_vec[0],rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1],rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.);
-	Polyhedron PB = B->GetPolyhedron();
-	std::transform( PB.points_begin(), PB.points_end(), PB.points_begin(), t_rot_trans);
-	std::transform( PB.facets_begin(), PB.facets_end(), PB.planes_begin(),Plane_equation());	
-	
-	shared_ptr<PolyhedraGeom> bang;
-	if (isNew) {
-		// new interaction
-		bang=shared_ptr<PolyhedraGeom>(new PolyhedraGeom());
-		bang->isShearNew = true;
-		interaction->geom = bang;
-	}else{	
-		// use data from old interaction
-  		bang=YADE_PTR_CAST<PolyhedraGeom>(interaction->geom);
-	}
-
-	//volume and centroid of intersection
-	Real volume, area;
-        CGALvector normalCGAL;
-	CGALpoint centroidCGAL=ToCGALPoint(se32.position);
-	Sphere_Polyhedron_intersection(PB, r, ToCGALPoint(se31.position), centroidCGAL,  volume, normalCGAL, area);
- 	if(isnan(volume) || volume<=1E-25 || volume > B->GetVolume()) {bang->equivalentPenetrationDepth=0; return true;}
-	Vector3r centroid = FromCGALPoint(centroidCGAL);
-	Vector3r normal = FromCGALVector(normalCGAL);
-
-	
-
-	// store calculated stuff in bang; some is redundant
-	bang->equivalentCrossSection=area;
-	bang->contactPoint=centroid;
-	bang->penetrationVolume=volume;
-	bang->equivalentPenetrationDepth=volume/area;
-	bang->precompute(state1,state2,scene,interaction,normal,bang->isShearNew,shift2);
-	bang->normal=normal;
-
-	return true;	
-}
-*/
-
 #endif // YADE_CGAL

=== modified file 'pkg/dem/Polyhedra_Ig2.hpp'
--- pkg/dem/Polyhedra_Ig2.hpp	2014-10-22 10:13:18 +0000
+++ pkg/dem/Polyhedra_Ig2.hpp	2016-03-08 09:18:20 +0000
@@ -72,20 +72,4 @@
 REGISTER_SERIALIZABLE(Ig2_Sphere_Polyhedra_ScGeom);
 
 //***************************************************************************
-/*! Create Polyhedra (collision geometry) from colliding Sphere & Polyhedra. */
-/*
-class Ig2_Sphere_Polyhedra_PolyhedraGeom: public IGeomFunctor
-{
-	public:
-		virtual ~Ig2_Sphere_Polyhedra_PolyhedraGeom(){};
-		virtual bool go(const shared_ptr<Shape>& shape1, const shared_ptr<Shape>& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr<Interaction>& c);
-		FUNCTOR2D(Sphere,Polyhedra);
-		DEFINE_FUNCTOR_ORDER_2D(Sphere,Polyhedra);
-		YADE_CLASS_BASE_DOC(Ig2_Sphere_Polyhedra_PolyhedraGeom,IGeomFunctor,"Create/update geometry of collision between Sphere and Polyhedra");	
-		DECLARE_LOGGER;	
-	private:		
-};
-REGISTER_SERIALIZABLE(Ig2_Sphere_Polyhedra_PolyhedraGeom);
-*/
-
 #endif // YADE_CGAL

=== modified file 'py/export.py'
--- py/export.py	2014-12-09 23:14:45 +0000
+++ py/export.py	2016-03-08 09:18:20 +0000
@@ -326,7 +326,7 @@
 		piece.appendChild(cell_data)
 
 		# Write to file and exit
-		outFile = open(self.baseName+'%04d'%self.snapCount+'.vtu', 'w')
+		outFile = open(self.baseName+'%08d'%self.snapCount+'.vtu', 'w')
 #		xml.dom.ext.PrettyPrint(doc, file)
 		doc.writexml(outFile, newl='\n')
 		outFile.close()
@@ -414,7 +414,7 @@
 		if not bodies: return
 		nBodies = len(bodies)
 		# output file
-		fName = self.baseName+'-spheres-%04d'%(numLabel if numLabel else self.spheresSnapCount)+'.vtk'
+		fName = self.baseName+'-spheres-%08d'%(numLabel if numLabel else self.spheresSnapCount)+'.vtk'
 		outFile = open(fName, 'w')
 		# head
 		outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,nBodies))
@@ -463,7 +463,7 @@
 		if not bodies: return
 		nBodies = len(bodies)
 		# output file
-		fName = self.baseName+'-facets-%04d'%(numLabel if numLabel else self.facetsSnapCount)+'.vtk'
+		fName = self.baseName+'-facets-%08d'%(numLabel if numLabel else self.facetsSnapCount)+'.vtk'
 		outFile = open(fName, 'w')
 		# head
 		outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,3*nBodies))
@@ -543,7 +543,7 @@
 			nodes[e[1]] = pt2
 			nodes[e[2]] = pt3
 		# output file
-		fName = self.baseName+'-facets-%04d'%(numLabel if numLabel else self.facetsSnapCount)+'.vtk'
+		fName = self.baseName+'-facets-%08d'%(numLabel if numLabel else self.facetsSnapCount)+'.vtk'
 		outFile = open(fName, 'w')
 		# head
 		outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,len(nodes)))
@@ -592,7 +592,7 @@
 			return
 		nIntrs = len(intrs)
 		# output file
-		fName = self.baseName+'-intrs-%04d'%(numLabel if numLabel else self.intrsSnapCount)+'.vtk'
+		fName = self.baseName+'-intrs-%08d'%(numLabel if numLabel else self.intrsSnapCount)+'.vtk'
 		outFile = open(fName, 'w')
 		# head
 		outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,2*nIntrs))
@@ -713,7 +713,7 @@
 			return
 		nIntrs = len(intrs)
 		# output file
-		fName = self.baseName+'-cps-%04d'%(numLabel if numLabel else self.contactPointsSnapCount)+'.vtk'
+		fName = self.baseName+'-cps-%08d'%(numLabel if numLabel else self.contactPointsSnapCount)+'.vtk'
 		outFile = open(fName, 'w')
 		# head
 		outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,nIntrs))
@@ -774,7 +774,7 @@
 			self._warn("exportPeriodicCell: scene is not periodic, no export...")
 			return
 		hSize = O.cell.hSize
-		fName = self.baseName+'-periCell-%04d'%(numLabel if numLabel else self.intrsSnapCount)+'.vtk'
+		fName = self.baseName+'-periCell-%08d'%(numLabel if numLabel else self.intrsSnapCount)+'.vtk'
 		outFile = open(fName, 'w')
 		outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET UNSTRUCTURED_GRID\nPOINTS 8 double\n"%(comment))
 		vertices = [
@@ -820,7 +820,7 @@
 			bodyFaces.append(ff)
 		# output file
 		nFaces = sum(len(f) for f in bodyFaces)
-		fName = self.baseName+'-polyhedra-%04d'%(numLabel if numLabel else self.polyhedraSnapCount)+'.vtk'
+		fName = self.baseName+'-polyhedra-%08d'%(numLabel if numLabel else self.polyhedraSnapCount)+'.vtk'
 		outFile = open(fName, 'w')
 		# head
 		outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,nVertices))