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[Branch ~yade-pkg/yade/git-trunk] Rev 3684: Revert previous commit.

 

------------------------------------------------------------
revno: 3684
committer: Anton Gladky <gladky.anton@xxxxxxxxx>
timestamp: Mon 2015-06-15 08:33:01 +0200
message:
  Revert previous commit.
  
  Sometimes the following error occurs:
  
  FATAL /home/gladk/dem/yade/trunk/core/ThreadRunner.cpp:30 run: Exception
  occured:
  boost: mutex lock failed in pthread_mutex_lock: Invalid argument
modified:
  pkg/common/InsertionSortCollider.cpp
  pkg/common/InsertionSortCollider.hpp
  pkg/dem/GeneralIntegratorInsertionSortCollider.cpp


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=== modified file 'pkg/common/InsertionSortCollider.cpp'
--- pkg/common/InsertionSortCollider.cpp	2015-06-13 07:40:38 +0000
+++ pkg/common/InsertionSortCollider.cpp	2015-06-15 06:33:01 +0000
@@ -30,28 +30,22 @@
 	assert(!periodic);
 	assert(v.size==(long)v.vec.size());
 	for(long i=1; i<v.size; i++){
-		const Bounds viInit=v[i];
-		long j=i-1;
-		/* cache hasBB; otherwise 1% overall performance hit */ const bool viInitBB=viInit.hasBB;
-		const bool isMin=viInit.isMin;
+		const Bounds viInit=v[i]; long j=i-1; /* cache hasBB; otherwise 1% overall performance hit */ const bool viInitBB=viInit.flags.hasBB;
+		const bool isMin=viInit.flags.isMin; 
 
 		while(j>=0 && v[j]>viInit){
 			v[j+1]=v[j];
 			#ifdef PISC_DEBUG
 				if(watchIds(v[j].id,viInit.id)) cerr<<"Swapping #"<<v[j].id<<"  with #"<<viInit.id<<" ("<<setprecision(80)<<v[j].coord<<">"<<setprecision(80)<<viInit.coord<<" along axis "<<v.axis<<")"<<endl;
-				if(v[j].id==viInit.id){
-					cerr<<"Inversion of body #"<<v[j].id<<" with itself, "<<v[j].isMin<<" & "<<
-								viInit.isMin<<", isGreater "<<(v[j]>viInit)<<", "<<(v[j].coord>viInit.coord)<<endl;
-								j--;
-								continue;
-				}
+				if(v[j].id==viInit.id){ cerr<<"Inversion of body #"<<v[j].id<<" with itself, "<<v[j].flags.isMin<<" & "<<viInit.flags.isMin<<", isGreater "<<(v[j]>viInit)<<", "<<(v[j].coord>viInit.coord)<<endl; j--; continue; }
 			#endif
 			// no collisions without bounding boxes
 			// also, do not collide body with itself; it sometimes happens for facets aligned perpendicular to an axis, for reasons that are not very clear
 			// see https://bugs.launchpad.net/yade/+bug/669095
 			// skip bounds with same isMin flags, since inversion doesn't imply anything in that case  
-			if(isMin && !v[j].isMin && doCollide && viInitBB && v[j].hasBB && (viInit.id!=v[j].id)) {
-				handleBoundInversion(viInit.id,v[j].id,interactions,scene);
+			if(isMin && !v[j].flags.isMin && doCollide && viInitBB && v[j].flags.hasBB && (viInit.id!=v[j].id)) {
+				/*if (isMin)*/ handleBoundInversion(viInit.id,v[j].id,interactions,scene);
+// 				else handleBoundSplit(viInit.id,v[j].id,interactions,scene);
 			}
 			j--;
 		}
@@ -95,13 +89,11 @@
 	for (unsigned k=0; k<nChunks;k++) {
 		int threadNum = omp_get_thread_num();
 		for(long i=chunks[k]+1; i<chunks[k+1]; i++){
-			const Bounds viInit=v[i];
-			long j=i-1;
-			const bool viInitBB=viInit.hasBB;
-			const bool isMin=viInit.isMin;
+			const Bounds viInit=v[i]; long j=i-1; const bool viInitBB=viInit.flags.hasBB;
+			const bool isMin=viInit.flags.isMin; 
 			while(j>=chunks[k] && v[j]>viInit){
 				v[j+1]=v[j];
-				if(isMin && !v[j].isMin && doCollide && viInitBB && v[j].hasBB && (viInit.id!=v[j].id)) {
+				if(isMin && !v[j].flags.isMin && doCollide && viInitBB && v[j].flags.hasBB && (viInit.id!=v[j].id)) {
 					const Body::id_t& id1 = v[j].id; const Body::id_t& id2 = viInit.id; 
 					if (spatialOverlap(id1,id2) && Collider::mayCollide(Body::byId(id1,scene).get(),Body::byId(id2,scene).get()) && !interactions->found(id1,id2))
 						newInteractions[threadNum].push_back(std::pair<Body::id_t,Body::id_t>(v[j].id,viInit.id));
@@ -123,14 +115,12 @@
 		long halfChunkEnd = long(i+chunkSize*0.5);
 		for(; i<halfChunkEnd; i++){
 			if (!(v[i]<v[i-1])) break; //contiguous chunks now connected consistently
-			const Bounds viInit=v[i];
-			long j=i-1;
-			/* cache hasBB; otherwise 1% overall performance hit */ const bool viInitBB=viInit.hasBB;
-			const bool isMin=viInit.isMin;
+			const Bounds viInit=v[i]; long j=i-1; /* cache hasBB; otherwise 1% overall performance hit */ const bool viInitBB=viInit.flags.hasBB;
+			const bool isMin=viInit.flags.isMin; 
 
 			while(j>=halfChunkStart && viInit<v[j]){
 				v[j+1]=v[j];
-				if(isMin && !v[j].isMin && doCollide && viInitBB && v[j].hasBB && (viInit.id!=v[j].id)) {
+				if(isMin && !v[j].flags.isMin && doCollide && viInitBB && v[j].flags.hasBB && (viInit.id!=v[j].id)) {
 					const Body::id_t& id1 = v[j].id; const Body::id_t& id2 = viInit.id;
 					//FIXME: do we need the check with found(id1,id2) here? It is checked again below...
 					if (spatialOverlap(id1,id2) && Collider::mayCollide(Body::byId(id1,scene).get(),Body::byId(id2,scene).get()) && !interactions->found(id1,id2))
@@ -160,7 +150,7 @@
 			it=BB[0].vec.begin(),et=BB[0].vec.end(); it < et; ++it)
 	{		
 		if (it->coord > bv.max[0]) break;
-		if (!it->isMin || !it->hasBB) continue;
+		if (!it->flags.isMin || !it->flags.hasBB) continue;
 		int offset = 3*it->id;
 		const shared_ptr<Body>& b=Body::byId(it->id,scene);
 		if(!b || !b->bound) continue;
@@ -303,16 +293,15 @@
 					const shared_ptr<Bound>& bv=b->bound;
 					// coordinate is min/max if has bounding volume, otherwise both are the position. Add periodic shift so that we are inside the cell
 					// watch out for the parentheses around ?: within ?: (there was unwanted conversion of the Reals to bools!)
-					BBji.coord=((BBji.hasBB=((bool)bv)) ? (BBji.isMin ? bv->min[j] : bv->max[j]) : (b->state->pos[j])) - (periodic ? BBj.cellDim*BBji.period : 0.);
+					BBji.coord=((BBji.flags.hasBB=((bool)bv)) ? (BBji.flags.isMin ? bv->min[j] : bv->max[j]) : (b->state->pos[j])) - (periodic ? BBj.cellDim*BBji.period : 0.);
 					// if initializing periodic, shift coords & record the period into BBj[i].period
 					if(doInitSort && periodic) BBji.coord=cellWrap(BBji.coord,0,BBj.cellDim,BBji.period);
 					// for each body, copy its minima and maxima, for quick checks of overlaps later
 					//bounds have been all updated when j==0, we can safely copy them here when j==1
-					if (BBji.isMin && j==1 &&bv) {
-						 memcpy(&minima[3*id],&bv->min,3*sizeof(Real));
-						 memcpy(&maxima[3*id],&bv->max,3*sizeof(Real));
-					}
-				} else { BBj[i].hasBB=false; /* for vanished body, keep the coordinate as-is, to minimize inversions. */ }
+					if (BBji.flags.isMin && j==1 &&bv) {
+						 memcpy(&minima[3*id],&bv->min,3*sizeof(Real)); memcpy(&maxima[3*id],&bv->max,3*sizeof(Real)); 
+					}					
+				} else { BBj[i].flags.hasBB=false; /* for vanished body, keep the coordinate as-is, to minimize inversions. */ }
 			}
 		}
 
@@ -363,13 +352,13 @@
 				for(long i=0; i<2*nBodies; i++){
 					// start from the lower bound (i.e. skipping upper bounds)
 					// skip bodies without bbox, because they don't collide
-					if(!(V[i].isMin && V[i].hasBB)) continue;
+					if(!(V[i].flags.isMin && V[i].flags.hasBB)) continue;
 					const Body::id_t& iid=V[i].id;
 					// go up until we meet the upper bound
 					for(long j=i+1; /* handle case 2. of swapped min/max */ j<2*nBodies && V[j].id!=iid; j++){
 						const Body::id_t& jid=V[j].id;
 						// take 2 of the same condition (only handle collision [min_i..max_i]+min_j, not [min_i..max_i]+min_i (symmetric)
-						if(!(V[j].isMin && V[j].hasBB)) continue;
+						if(!(V[j].flags.isMin && V[j].flags.hasBB)) continue;
 						if (spatialOverlap(iid,jid) && Collider::mayCollide(Body::byId(iid,scene).get(),Body::byId(jid,scene).get()) ){
 						#ifdef YADE_OPENMP
 							unsigned int threadNum = omp_get_thread_num();
@@ -389,13 +378,13 @@
 				#endif
 			} else { // periodic case: see comments above
 				for(long i=0; i<2*nBodies; i++){
-					if(!(V[i].isMin && V[i].hasBB)) continue;
+					if(!(V[i].flags.isMin && V[i].flags.hasBB)) continue;
 					const Body::id_t& iid=V[i].id;
 					long cnt=0;
 					// we might wrap over the periodic boundary here; that's why the condition is different from the aperiodic case
 					for(long j=V.norm(i+1); V[j].id!=iid; j=V.norm(j+1)){
 						const Body::id_t& jid=V[j].id;
-						if(!(V[j].isMin && V[j].hasBB)) continue;
+						if(!(V[j].flags.isMin && V[j].flags.hasBB)) continue;
 						handleBoundInversionPeri(iid,jid,interactions,scene);
 						if(cnt++>2*(long)nBodies){ LOG_FATAL("Uninterrupted loop in the initial sort?"); throw std::logic_error("loop??"); }
 					}
@@ -435,11 +424,8 @@
 		if(v[i_1].coord<=iCmpCoord) continue;
 		// vi is the copy that will travel down the list, while other elts go up
 		// if will be placed in the list only at the end, to avoid extra copying
-		int j=i_1;
-		Bounds vi=v[i];
-		const bool viHasBB=vi.hasBB;
-		const bool isMin=v[i].isMin;
-		 
+		int j=i_1; Bounds vi=v[i];  const bool viHasBB=vi.flags.hasBB;
+		const bool isMin=v[i].flags.isMin; 
 		while(v[j].coord>vi.coord + /* wrap for elt just below split */ (v.norm(j+1)==loIdx ? v.cellDim : 0)){
 			long j1=v.norm(j+1);
 			// OK, now if many bodies move at the same pace through the cell and at one point, there is inversion,
@@ -455,8 +441,14 @@
 			// inversions close the the split need special care
 			if(j==loIdx && vi.coord<0) { vi.period-=1; vi.coord+=v.cellDim; loIdx=v.norm(loIdx+1); }
 			else if(j1==loIdx) { vNew.period+=1; vNew.coord-=v.cellDim; loIdx=v.norm(loIdx-1); }
-			if(isMin && !v[j].isMin && (doCollide && viHasBB && v[j].hasBB)){
+			if(isMin && !v[j].flags.isMin && (doCollide && viHasBB && v[j].flags.hasBB)){
 				// see https://bugs.launchpad.net/yade/+bug/669095 and similar problem in aperiodic insertionSort
+				#if 0
+				if(vi.id==vNew.id){
+					LOG_FATAL("Inversion of body's #"<<vi.id<<" boundary with its other boundary, "<<v[j].coord<<" meets "<<vi.coord);
+					throw runtime_error(__FILE__ ": Body's boundary metting its opposite boundary.");
+				}
+				#endif
 				if((vi.id!=vNew.id)) handleBoundInversionPeri(vi.id,vNew.id,interactions,scene);
 			}
 			j=v.norm(j-1);
@@ -545,81 +537,6 @@
 	return true;
 }
 
-inline bool InsertionSortCollider::spatialOverlap(const Body::id_t& id1, const Body::id_t& id2) const {
-	assert(!periodic);
-	return	(minima[3*id1+0]<=maxima[3*id2+0]) && (maxima[3*id1+0]>=minima[3*id2+0]) &&
-					(minima[3*id1+1]<=maxima[3*id2+1]) && (maxima[3*id1+1]>=minima[3*id2+1]) &&
-					(minima[3*id1+2]<=maxima[3*id2+2]) && (maxima[3*id1+2]>=minima[3*id2+2]);
-}
-
-bool InsertionSortCollider::shouldBeErased(Body::id_t id1, Body::id_t id2, Scene* rb) const {
-	if(!periodic) {
-		return !spatialOverlap(id1,id2);
-	} else {
-		Vector3i periods;
-		return !spatialOverlapPeri(id1,id2,rb,periods);
-	}
-}
-
-void InsertionSortCollider::invalidatePersistentData() {
-	for(int i=0; i<3; i++) {
-		BB[i].vec.clear();
-		BB[i].size=0;
-	}
-}
-
-bool InsertionSortCollider::Bounds::operator<(const Bounds& b) const {
-	/* handle special case of zero-width bodies, which could otherwise get min/max swapped in the unstable std::sort */
-	if(id==b.id && coord==b.coord) return isMin;
-	return coord<b.coord;
-}
-
-bool InsertionSortCollider::Bounds::operator>(const Bounds& b) const {
-	if(id==b.id && coord==b.coord) return !isMin;
-	return coord>b.coord;
-}
-
-#ifdef PISC_DEBUG
-bool InsertionSortCollider::Bounds::watchIds(Body::id_t id1,Body::id_t id2) const {
-	return (watch1<0 &&(watch2==id1||watch2==id2))||
-				 (watch2<0 && (watch1==id1||watch1==id2))||
-				 (watch1==id1 && watch2==id2)||
-				 (watch1==id2 && watch2==id1);
-}
-#endif
-
-void InsertionSortCollider::VecBounds::updatePeriodicity(Scene* scene){
-	assert(scene->isPeriodic);
-	assert(axis>=0 && axis <=2);
-	cellDim=scene->cell->getSize()[axis];
-}
-
-long InsertionSortCollider::VecBounds::norm(long i) const {
-	if(i<0) i+=size;
-	long ret=i%size;
-	assert(ret>=0 && ret<size);
-	return ret;
-}
-
-void InsertionSortCollider::VecBounds::dump(ostream& os) {
-	string ret;
-	for(size_t i=0; i<vec.size(); i++) {
-		os<<((long)i==loIdx?"@@ ":"")<<vec[i].coord<<"(id="<<vec[i].id
-			<<","<<(vec[i].isMin?"min":"max")<<",p"<<vec[i].period<<") ";
-	}
-	os<<endl;
-}
-
-InsertionSortCollider::Bounds& InsertionSortCollider::VecBounds::operator[](long idx) {
-	assert(idx<size && idx>=0);
-	return vec[idx];
-}
-
-const InsertionSortCollider::Bounds& InsertionSortCollider::VecBounds::operator[](long idx) const {
-	assert(idx<size && idx>=0);
-	return vec[idx];
-}
-
 boost::python::tuple InsertionSortCollider::dumpBounds(){
   boost::python::list bl[3]; // 3 bound lists, inserted into the tuple at the end
 	for(int axis=0; axis<3; axis++){
@@ -627,11 +544,11 @@
 		if(periodic){
 			for(long i=0; i<V.size; i++){
 				long ii=V.norm(i); // start from the period boundary
-				bl[axis].append(boost::python::make_tuple(V[ii].coord,(V[ii].isMin?-1:1)*V[ii].id,V[ii].period));
+				bl[axis].append(boost::python::make_tuple(V[ii].coord,(V[ii].flags.isMin?-1:1)*V[ii].id,V[ii].period));
 			}
 		} else {
 			for(long i=0; i<V.size; i++){
-				bl[axis].append(boost::python::make_tuple(V[i].coord,(V[i].isMin?-1:1)*V[i].id));
+				bl[axis].append(boost::python::make_tuple(V[i].coord,(V[i].flags.isMin?-1:1)*V[i].id));
 			}
 		}
 	}

=== modified file 'pkg/common/InsertionSortCollider.hpp'
--- pkg/common/InsertionSortCollider.hpp	2015-06-13 07:40:38 +0000
+++ pkg/common/InsertionSortCollider.hpp	2015-06-15 06:33:01 +0000
@@ -86,24 +86,30 @@
 
 	friend class GeneralIntegratorInsertionSortCollider;
 
-	// struct for storing bounds of bodies
+	//! struct for storing bounds of bodies
 	struct Bounds{
-		// coordinate along the given sortAxis
+		//! coordinate along the given sortAxis
 		Real coord;
 		//! id of the body this bound belongs to
 		Body::id_t id;
-		// periodic cell coordinate
+		//! periodic cell coordinate
 		int period;
-		// is it the minimum (true) or maximum (false) bound?
-		bool hasBB=true;
-		bool isMin=true;
-		Bounds(Real coord_, Body::id_t id_, bool _isMin): coord(coord_), id(id_), period(0), isMin(_isMin){};
-		bool operator<(const Bounds& b) const;
-		bool operator>(const Bounds& b) const;
+		//! is it the minimum (true) or maximum (false) bound?
+		struct{ unsigned hasBB:1; unsigned isMin:1; } flags;
+		Bounds(Real coord_, Body::id_t id_, bool isMin): coord(coord_), id(id_), period(0){ flags.isMin=isMin; }
+		bool operator<(const Bounds& b) const {
+			/* handle special case of zero-width bodies, which could otherwise get min/max swapped in the unstable std::sort */
+			if(id==b.id && coord==b.coord) return flags.isMin;
+			return coord<b.coord;
+		}
+		bool operator>(const Bounds& b) const {
+			if(id==b.id && coord==b.coord) return !flags.isMin;
+			return coord>b.coord;
+		}
 	};
 	#ifdef PISC_DEBUG
 		int watch1, watch2;
-		bool watchIds(Body::id_t,Body::id_t) const;
+		bool watchIds(Body::id_t id1,Body::id_t id2) const { return (watch1<0 &&(watch2==id1||watch2==id2))||(watch2<0 && (watch1==id1||watch1==id2))||(watch1==id1 && watch2==id2)||(watch1==id2 && watch2==id1); }
 	#endif
 		// we need this to find out about current maxVelocitySq
 		shared_ptr<NewtonIntegrator> newton;
@@ -119,32 +125,37 @@
 		long size;
 		// index of the lowest coordinate element, before which the container wraps
 		long loIdx;
-		Bounds& operator[](long);
-		const Bounds& operator[](long idx) const;
+		Bounds& operator[](long idx){ assert(idx<size && idx>=0); return vec[idx]; }
+		const Bounds& operator[](long idx) const { assert(idx<size && idx>=0); return vec[idx]; }
 		// update number of bodies, periodic properties and size from Scene
-		void updatePeriodicity(Scene*);
+		void updatePeriodicity(Scene* scene){
+			assert(scene->isPeriodic);
+			assert(axis>=0 && axis <=2);
+			cellDim=scene->cell->getSize()[axis];
+		}
 		// normalize given index to the right range (wraps around)
-		long norm(long) const;
+		long norm(long i) const { if(i<0) i+=size; long ret=i%size; assert(ret>=0 && ret<size); return ret;}
 		VecBounds(): axis(-1), size(0), loIdx(0){}
-		void dump(ostream&);
+		void dump(ostream& os){ string ret; for(size_t i=0; i<vec.size(); i++) os<<((long)i==loIdx?"@@ ":"")<<vec[i].coord<<"(id="<<vec[i].id<<","<<(vec[i].flags.isMin?"min":"max")<<",p"<<vec[i].period<<") "; os<<endl;}
 	};
 	private:
-	// storage for bounds
+	//! storage for bounds
 	VecBounds BB[3];
-	// storage for bb maxima and minima
+	//! storage for bb maxima and minima
 	std::vector<Real> maxima, minima;
-	// Whether the Scene was periodic (to detect the change, which shouldn't happen, but shouldn't crash us either)
+	//! Whether the Scene was periodic (to detect the change, which shouldn't happen, but shouldn't crash us either)
 	bool periodic;
 
 	// return python representation of the BB struct, as ([...],[...],[...]).
   boost::python::tuple dumpBounds();
 
-	/* sorting routine; insertion sort is very fast for strongly pre-sorted lists, which is our case
-     http://en.wikipedia.org/wiki/Insertion_sort has the algorithm and other details
+	/*! sorting routine; insertion sort is very fast for strongly pre-sorted lists, which is our case
+  	    http://en.wikipedia.org/wiki/Insertion_sort has the algorithm and other details
 	*/
 	void insertionSort(VecBounds& v,InteractionContainer*,Scene*,bool doCollide=true);
 	void insertionSortParallel(VecBounds& v,InteractionContainer*,Scene*,bool doCollide=true);
 	void handleBoundInversion(Body::id_t,Body::id_t,InteractionContainer*,Scene*);
+// 	bool spatialOverlap(Body::id_t,Body::id_t) const;
 
 	// periodic variants
 	void insertionSortPeri(VecBounds& v,InteractionContainer*,Scene*,bool doCollide=true);
@@ -152,18 +163,27 @@
 	void handleBoundSplit(Body::id_t,Body::id_t,InteractionContainer*,Scene*);
 	
 	bool spatialOverlapPeri(Body::id_t,Body::id_t,Scene*,Vector3i&) const;
-	bool spatialOverlap(const Body::id_t& id1, const Body::id_t& id2) const;
+	inline bool spatialOverlap(const Body::id_t& id1, const Body::id_t& id2) const {
+	assert(!periodic);
+	return	(minima[3*id1+0]<=maxima[3*id2+0]) && (maxima[3*id1+0]>=minima[3*id2+0]) &&
+		(minima[3*id1+1]<=maxima[3*id2+1]) && (maxima[3*id1+1]>=minima[3*id2+1]) &&
+		(minima[3*id1+2]<=maxima[3*id2+2]) && (maxima[3*id1+2]>=minima[3*id2+2]);
+	}
 	
 	static Real cellWrap(const Real, const Real, const Real, int&);
 	static Real cellWrapRel(const Real, const Real, const Real);
 
+
 	public:
-	// Predicate called from loop within InteractionContainer::erasePending
-	bool shouldBeErased(Body::id_t, Body::id_t, Scene*) const;
+	//! Predicate called from loop within InteractionContainer::erasePending
+	bool shouldBeErased(Body::id_t id1, Body::id_t id2, Scene* rb) const {
+		if(!periodic) return !spatialOverlap(id1,id2);
+		else { Vector3i periods; return !spatialOverlapPeri(id1,id2,rb,periods); }
+	}
 	virtual bool isActivated();
 
 	// force reinitialization at next run
-	virtual void invalidatePersistentData();
+	virtual void invalidatePersistentData(){ for(int i=0; i<3; i++){ BB[i].vec.clear(); BB[i].size=0; }}
 
 	vector<Body::id_t> probeBoundingVolume(const Bound&);
 

=== modified file 'pkg/dem/GeneralIntegratorInsertionSortCollider.cpp'
--- pkg/dem/GeneralIntegratorInsertionSortCollider.cpp	2015-06-13 07:40:38 +0000
+++ pkg/dem/GeneralIntegratorInsertionSortCollider.cpp	2015-06-15 06:33:01 +0000
@@ -141,9 +141,9 @@
 					// coordinate is min/max if has bounding volume, otherwise both are the position. Add periodic shift so that we are inside the cell
 					// watch out for the parentheses around ?: within ?: (there was unwanted conversion of the Reals to bools!)
 					
-					BBj[i].coord=((BBj[i].hasBB=((bool)bv)) ? (BBj[i].isMin ? bv->min[j] : bv->max[j]) : (b->state->pos[j])) - (periodic ? BBj.cellDim*BBj[i].period : 0.);
+					BBj[i].coord=((BBj[i].flags.hasBB=((bool)bv)) ? (BBj[i].flags.isMin ? bv->min[j] : bv->max[j]) : (b->state->pos[j])) - (periodic ? BBj.cellDim*BBj[i].period : 0.);
 					
-				} else { BBj[i].hasBB=false; /* for vanished body, keep the coordinate as-is, to minimize inversions. */ }
+				} else { BBj[i].flags.hasBB=false; /* for vanished body, keep the coordinate as-is, to minimize inversions. */ }
 				// if initializing periodic, shift coords & record the period into BBj[i].period
 				if(doInitSort && periodic) {
 					BBj[i].coord=cellWrap(BBj[i].coord,0,BBj.cellDim,BBj[i].period);
@@ -195,13 +195,13 @@
 				for(long i=0; i<2*nBodies; i++){
 					// start from the lower bound (i.e. skipping upper bounds)
 					// skip bodies without bbox, because they don't collide
-					if(!(V[i].isMin && V[i].hasBB)) continue;
+					if(!(V[i].flags.isMin && V[i].flags.hasBB)) continue;
 					const Body::id_t& iid=V[i].id;
 					// go up until we meet the upper bound
 					for(long j=i+1; /* handle case 2. of swapped min/max */ j<2*nBodies && V[j].id!=iid; j++){
 						const Body::id_t& jid=V[j].id;
 						// take 2 of the same condition (only handle collision [min_i..max_i]+min_j, not [min_i..max_i]+min_i (symmetric)
-						if(!V[j].isMin) continue;
+						if(!V[j].flags.isMin) continue;
 						/* abuse the same function here; since it does spatial overlap check first, it is OK to use it */
 						handleBoundInversion(iid,jid,interactions,scene);
 						assert(j<2*nBodies-1);
@@ -209,13 +209,13 @@
 				}
 			} else { // periodic case: see comments above
 				for(long i=0; i<2*nBodies; i++){
-					if(!(V[i].isMin && V[i].hasBB)) continue;
+					if(!(V[i].flags.isMin && V[i].flags.hasBB)) continue;
 					const Body::id_t& iid=V[i].id;
 					long cnt=0;
 					// we might wrap over the periodic boundary here; that's why the condition is different from the aperiodic case
 					for(long j=V.norm(i+1); V[j].id!=iid; j=V.norm(j+1)){
 						const Body::id_t& jid=V[j].id;
-						if(!V[j].isMin) continue;
+						if(!V[j].flags.isMin) continue;
 						handleBoundInversionPeri(iid,jid,interactions,scene);
 						if(cnt++>2*(long)nBodies){ LOG_FATAL("Uninterrupted loop in the initial sort?"); throw std::logic_error("loop??"); }
 					}