// 2009 © Václav Šmilauer <eudoxos@arcig.cz>
// 2013 © Bruno Chareyre <bruno.chareyre@grenoble-inp.fr>

#include "InsertionSortCollider.hpp"
#include <lib/high-precision/Constants.hpp>
#include <core/Dispatching.hpp>
#include <core/Interaction.hpp>
#include <core/InteractionContainer.hpp>
#include <core/Scene.hpp>
#include <pkg/common/Sphere.hpp>

#include <boost/static_assert.hpp>
#ifdef YADE_OPENMP
#include <omp.h>
#endif

namespace yade { // Cannot have #include directive inside.

using math::max;
using math::min; // using inside .cpp file is ok.

YADE_PLUGIN((InsertionSortCollider))
CREATE_LOGGER(InsertionSortCollider);


// called by the insertion sort if 2 bodies swapped their bounds in such a way that a new overlap may appear
void InsertionSortCollider::handleBoundInversion(Body::id_t id1, Body::id_t id2, InteractionContainer* interactions, Scene*)
{
	assert(!periodic);
	assert(id1 != id2);
#ifdef YADE_MPI //Note #0: this #ifdef is painfull, there many others needed hereafter (see #1), compilation without MPI will fail atm
	if (spatialOverlap(id1, id2) && Collider::mayCollide(Body::byId(id1, scene).get(), Body::byId(id2, scene).get(), scene->subdomain)
	    && !interactions->found(id1, id2))
#else
	if (spatialOverlap(id1, id2) && Collider::mayCollide(Body::byId(id1, scene).get(), Body::byId(id2, scene).get()) && !interactions->found(id1, id2))
#endif
		interactions->insert(shared_ptr<Interaction>(new Interaction(id1, id2)));
}

void InsertionSortCollider::insertionSort(VecBounds& v, InteractionContainer* interactions, Scene*, bool doCollide)
{
	assert(!periodic);
	//assert(v.size()==v.vec.size());
	for (size_t 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.flags.hasBB;
		const bool   isMin    = viInit.flags.isMin;

		while (j >= 0 && v[j] > viInit) {
			v[j + 1] = v[j];
			// 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 (old site, fixed bug) 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].flags.isMin && doCollide && viInitBB && v[j].flags.hasBB && (viInit.id != v[j].id)) {
				if (viInit.id < v[j].id) handleBoundInversion(viInit.id, v[j].id, interactions, scene);
				else
					handleBoundInversion(v[j].id, viInit.id, interactions, scene);
				/*if (isMin)*/
				// 				else handleBoundSplit(viInit.id,v[j].id,interactions,scene);
			}
			j--;
		}
		v[j + 1] = viInit;
	}
}

#ifdef YADE_OPENMP
//Parallel version, only for non-periodic case at the moment (feel free to implement for the periodic case...)
void InsertionSortCollider::insertionSortParallel(VecBounds& v, InteractionContainer* interactions, Scene*, bool doCollide)
{
	assert(!periodic);
	///escape parallel sort if 1/ single thread or 2/ not at least 10 bounds per-thread
	if ((ompThreads <= 1) or (v.size() < size_t(10 * ompThreads))) return insertionSort(v, interactions, scene, doCollide);

	Real chunksVerlet = 4 * verletDist; //is 2* the theoretical requirement?
	if (chunksVerlet <= 0) { LOG_ERROR("Parallel insertion sort needs verletDist>0"); }

	///chunks defines subsets of the bounds lists, we make sure they are not too small wrt. verlet dist.
	std::vector<Body::id_t> chunks;
	unsigned                nChunks   = ompThreads;
	unsigned                chunkSize = unsigned(v.size() / nChunks) + 1;
	for (unsigned n = 0; n < nChunks; n++)
		chunks.push_back(n * chunkSize);
	chunks.push_back(v.size());
	while (nChunks > 1) {
		bool changeChunks = false;
		for (unsigned n = 1; n < nChunks; n++)
			if (chunksVerlet > (v[chunks[n]].coord - v[chunks[n - 1]].coord)) changeChunks = true;
		if (!changeChunks) break;
		nChunks--;
		chunkSize = unsigned(v.size() / nChunks) + 1;
		chunks.clear();
		for (unsigned n = 0; n < nChunks; n++)
			chunks.push_back(n * chunkSize);
		chunks.push_back(v.size());
	}

	///Define per-thread containers bufferizing the actual insertion of new interactions, since inserting is not thread-safe
	std::vector<std::vector<std::pair<Body::id_t, Body::id_t>>> newInteractions;
	newInteractions.resize(ompThreads, std::vector<std::pair<Body::id_t, Body::id_t>>());
	for (int kk = 0; kk < ompThreads; kk++)
		newInteractions[kk].reserve(long(chunkSize * 0.3));

/// First sort, independant in each chunk
#pragma omp parallel for schedule(dynamic, 1) num_threads(ompThreads > 0 ? min(ompThreads, omp_get_max_threads()) : omp_get_max_threads())
	for (unsigned k = 0; k < nChunks; k++) {
		int threadNum = omp_get_thread_num();
		for (auto i = chunks[k] + 1; i < chunks[k + 1]; i++) {
			const Bounds viInit = v[i];
			auto         j      = i - 1;
			if (not(j >= chunks[k] && v[j] > viInit)) continue; //else we need to assign v[j+1] after the 'while'
			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].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;
//(see #0 if compilation fails)
#ifdef YADE_MPI
					if (spatialOverlap(id1, id2)
					    && Collider::mayCollide(Body::byId(id1, scene).get(), Body::byId(id2, scene).get(), scene->subdomain)
					    && !interactions->found(id1, id2))
#else
					if (spatialOverlap(id1, id2) && Collider::mayCollide(Body::byId(id1, scene).get(), Body::byId(id2, scene).get())
					    && !interactions->found(id1, id2))
#endif

						newInteractions[threadNum].push_back(std::pair<Body::id_t, Body::id_t>(v[j].id, viInit.id));
				}
				j--;
			}
			v[j + 1] = viInit;
		}
	}
	///In the second sort, the chunks are connected consistently.
	///If sorting requires to move a bound past half-chunk, the algorithm is not thread safe,
	/// if it happens we run the 1-thread sort at the end
	bool parallelFailed = false;
#pragma omp parallel for schedule(dynamic, 1) num_threads(ompThreads > 0 ? min(ompThreads, omp_get_max_threads()) : omp_get_max_threads())
	for (unsigned k = 1; k < nChunks; k++) {
		int  threadNum      = omp_get_thread_num();
		long i              = chunks[k];
		long halfChunkStart = long(i - chunkSize * 0.5);
		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.flags.hasBB;
			const bool   isMin    = viInit.flags.isMin;

			while (j >= halfChunkStart && viInit < v[j]) {
				v[j + 1] = v[j];
				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...
#ifdef YADE_MPI
					if (spatialOverlap(id1, id2)
					    && Collider::mayCollide(Body::byId(id1, scene).get(), Body::byId(id2, scene).get(), scene->subdomain)
					    && !interactions->found(id1, id2))
#else
					if (spatialOverlap(id1, id2) && Collider::mayCollide(Body::byId(id1, scene).get(), Body::byId(id2, scene).get())
					    && !interactions->found(id1, id2))
#endif
						newInteractions[threadNum].push_back(std::pair<Body::id_t, Body::id_t>(v[j].id, viInit.id));
				}
				j--;
			}
			v[j + 1] = viInit;
			if (j < halfChunkStart) parallelFailed = true;
		}
		if (i >= halfChunkEnd) parallelFailed = true;
	}
	/// Now insert interactions sequentially
	for (int n = 0; n < ompThreads; n++)
		for (size_t k = 0, kend = newInteractions[n].size(); k < kend; k++)
			/*if (!interactions->found(newInteractions[n][k].first,newInteractions[n][k].second))*/ //Not needed, already checked above
			if (newInteractions[n][k].first < newInteractions[n][k].second)
				interactions->insert(shared_ptr<Interaction>(new Interaction(newInteractions[n][k].first, newInteractions[n][k].second)));
			else
				interactions->insert(shared_ptr<Interaction>(new Interaction(newInteractions[n][k].second, newInteractions[n][k].first)));
	/// If some bounds traversed more than a half-chunk, we complete colliding with the sequential sort
	if (parallelFailed) return insertionSort(v, interactions, scene, doCollide);
}
#endif

vector<Body::id_t> InsertionSortCollider::probeBoundingVolume(const Bound& bv)
{
	if (periodic) { throw invalid_argument("InsertionSortCollider::probeBoundingVolume: handling periodic boundary not implemented."); }
	vector<Body::id_t> ret;
	for (vector<Bounds>::const_iterator it = BB[0].cbegin(), et = BB[0].cend(); it < et; ++it) {
		if (it->coord > bv.max[0]) break;
		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;
		const Real& sweepLength = b->bound->sweepLength;
		Vector3r    disp        = b->state->pos - b->bound->refPos;
		if (!(maxima[offset] - sweepLength + disp[0] < bv.min[0] || minima[offset] + sweepLength + disp[0] > bv.max[0]
		      || minima[offset + 1] + sweepLength + disp[1] > bv.max[1] || maxima[offset + 1] - sweepLength + disp[1] < bv.min[1]
		      || minima[offset + 2] + sweepLength + disp[2] > bv.max[2] || maxima[offset + 2] - sweepLength + disp[2] < bv.min[2])) {
			ret.push_back(it->id);
		}
	}
	return ret;
}
// STRIDE
bool InsertionSortCollider::isActivated()
{
	// activated if number of bodies changes (hence need to refresh collision information)
	// or the time of scheduled run already came, or we were never scheduled yet
	if (!strideActive) { return true; }
	if (!newton) { return true; }
	fastestBodyMaxDist = newton->maxVelocitySq;
	if (fastestBodyMaxDist >= 1 || fastestBodyMaxDist == 0) { return true; }
	if (BB[0].size() != 2 * scene->bodies->size() and not scene->bodies->useRedirection) { return true; }
	if (scene->interactions->dirty) { return true; }
	if (scene->doSort) { return true; }
	return false;
}

void InsertionSortCollider::action()
{
#ifdef ISC_TIMING
	timingDeltas->start();
#endif
	numAction++;
	const size_t nBodies                     = scene->bodies->size();
	keepListsShort                           = scene->bodies->useRedirection;
	InteractionContainer* interactions       = scene->interactions.get();
	scene->interactions->iterColliderLastRun = -1;
	scene->doSort                            = false;
#ifdef YADE_OPENMP
	if (ompThreads <= 0) ompThreads = omp_get_max_threads();
#endif
	// periodicity changed, force reinit
	if (scene->isPeriodic != periodic) {
		for (int i = 0; i < 3; i++) {
			BB[i].clear();
		}
		periodic = scene->isPeriodic;
	}
	// pre-conditions
	// adjust storage size
	bool doInitSort = false;
	if (doSort) {
		doInitSort = true;
		doSort     = false;
	}
	// ### Prepare lists of bounds. First approach: Bounds are from id=0 to id=nBodies, possibly with many null bounds after body erase
	if (not keepListsShort) {
		if (BB[0].size() != 2 * nBodies) {
			// store previous size
			size_t BBsize = BB[0].size();
			LOG_DEBUG("Resize bounds containers from " << BBsize << " to " << nBodies * 2 << ", will std::sort.");
			// bodies deleted; clear the container completely, and do as if all bodies were added (rather slow…)
			// future possibility: insertion sort with such operator that deleted bodies would all go to the end, then just trim bounds
			if (2 * nBodies < BBsize) {
				for (int i = 0; i < 3; i++)
					BB[i].clear();
			}
			// more than 20% new bodies, do initial sort again
			if (BBsize == 0 || ((2 * nBodies - BBsize) / double(BBsize)) > 0.2) doInitSort = true;
			assert((BBsize % 2) == 0);
			for (int i = 0; i < 3; i++) {
				BB[i].reserve(2 * nBodies);
				// add lower and upper bounds; coord is not important, will be updated from bb shortly
				for (size_t id = BBsize / 2; id < nBodies; id++) {
					BB[i].push_back(Bounds(0, id, /*isMin=*/true));
					BB[i].push_back(Bounds(0, id, /*isMin=*/false));
				}
			}
		}

		// ### Second approach with using body redirection: Bounds sizes match the number of real bodies in the scene
	} else if (not scene->bodies->checkedByCollider) {
		scene->bodies->updateRealBodies();
		vector<Body::id_t>&       insrts  = scene->bodies->insertedBodies;
		const vector<Body::id_t>& erased  = scene->bodies->erasedBodies;
		size_t                    nInsert = insrts.size();
		size_t                    nErased = erased.size();
		size_t                    nReal   = scene->bodies->realBodies.size();
		size_t                    BBsize  = BB[0].size();

		// BBsize==0 if collider runs for the first time, 1/ at iteration 0, or 2/ at iteration N after loading scene.
		// In both cases it should be safe to insert all real bodies from scratch, hence the copy below.
		// It will simply ignore any sequence of insert/erase that could have happen before collider execution
		// Next collision detections will effectively insert/erase incrementaly after this initialisation
		if (BBsize == 0) {
			insrts  = scene->bodies->realBodies;
			nInsert = nReal;
		}

		// Handle erased bodies
		int countNoBound = 0;
		if (nErased > 0) {
			for (const auto& id : erased)
				if (3 * (id + 1) <= (int)minima.size())
					minima[3 * id] = Mathr::MAX_REAL; // invalidate data so we can check what was erased in next loop and remove the bounds


			size_t idxTarget = 0;
			for (size_t i = 0; i < 3; i++) {
				idxTarget      = 0;
				VecBounds& BBi = BB[i];
				// move all bounds to the beginning of the vector
				for (size_t idx = 0; idx < BBsize; idx++) {
					const Body::id_t& id = BBi[idx].id;
					if (Body::byId(id, scene) /*and Body::byId(id, scene)->isBounded()*/
					    and (3 * (id + 1) > (int)minima.size() or minima[3 * id] != Mathr::MAX_REAL)) {
						if (idxTarget < idx) BBi[idxTarget] = BBi[idx];
						idxTarget++;
					} else {
						if (i == 0 and Body::byId(id, scene) and not Body::byId(id, scene)->isBounded()) countNoBound++;
						continue;
					}
				}
				if (idxTarget < BBi.size()) BBi.resize(idxTarget);
				else
					break; // if first coordinate is unchanged no need to check the two others
			}
		}

		// Now handle inserted bodies
		if (not smartInsertErase) { // else we handle newly inserted ones at the end
			if (BB[0].size() == 0 or nInsert / double(BB[0].size()) > 0.05) doInitSort = true;
			std::sort(insrts.begin(), insrts.end()); // so we can identify duplicates more easily in case of multiple insert/erase with same id

			for (int i = 0; i < 3; i++) {
				for (size_t idx = 0; idx < nInsert; idx++) {
					if (idx > 0 and insrts[idx] == insrts[idx - 1]) continue; // skip duplicate
					if (Body::byId(insrts[idx], scene)
					    and Body::byId(insrts[idx], scene)->isBounded()) { //could have been inserted then erased
						BB[i].push_back(Bounds(0, insrts[idx], /*isMin=*/true));
						BB[i].push_back(Bounds(0, insrts[idx], /*isMin=*/false));
					}
				}
			}
		}
	}
	scene->bodies->checkedByCollider = true; // bounds lists and bodies list are in sync

	if (minima.size() != (size_t)3 * nBodies) {
		minima.resize(3 * nBodies);
		maxima.resize(3 * nBodies);
	}

	//Increase the size of force container.
	scene->forces.addMaxId(scene->bodies->size());

	// update periodicity
	assert(BB[0].axis == 0);
	assert(BB[1].axis == 1);
	assert(BB[2].axis == 2);
	if (periodic) {
		for (int i = 0; i < 3; i++)
			BB[i].updatePeriodicity(scene);
		invSizes = Vector3r(1. / scene->cell->getSize()[0], 1. / scene->cell->getSize()[1], 1. / scene->cell->getSize()[2]);
	}

	if (verletDist < 0) {
		Real minR = std::numeric_limits<Real>::infinity();
		for (const auto& b : *scene->bodies) {
			if (!b || !b->shape) continue;
			Sphere* s = dynamic_cast<Sphere*>(b->shape.get());
			if (!s) continue;
			minR = min(s->radius, minR);
		}
		if (math::isinf(minR))
			LOG_WARN("verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive "
			         "verletDist in your script.");
		// if no spheres, disable stride
		verletDist = math::isinf(minR) ? 0 : math::abs(verletDist) * minR;
	}
	// if interactions are dirty, force reinitialization
	if (scene->interactions->dirty) {
		doInitSort                 = true;
		scene->interactions->dirty = false;
	}

	// update bounds via boundDispatcher
	boundDispatcher->scene              = scene;
	boundDispatcher->sweepDist          = verletDist;
	boundDispatcher->minSweepDistFactor = minSweepDistFactor;
	boundDispatcher->targetInterv       = targetInterv;
	boundDispatcher->updatingDispFactor = updatingDispFactor;
	boundDispatcher->action();
	ISC_CHECKPOINT("boundDispatcher");

	// STRIDE
	if (verletDist > 0) {
		// get NewtonIntegrator, to ask for the maximum velocity value
		if (!newton) {
			FOREACH(shared_ptr<Engine> & e, scene->engines)
			{
				newton = YADE_PTR_DYN_CAST<NewtonIntegrator>(e);
				if (newton) break;
			}
			if (!newton) { throw runtime_error("InsertionSortCollider.verletDist>0, but unable to locate NewtonIntegrator within O.engines."); }
		}
	}
	// STRIDE
	// get us ready for strides, if they were deactivated
	if (verletDist > 0) strideActive = true;
	if (strideActive) {
		assert(verletDist > 0);
		assert(YADE_PTR_DYN_CAST<NewtonIntegrator>(newton));
		assert(strideActive);
		assert(newton->maxVelocitySq >= 0);
		newton->updatingDispFactor = updatingDispFactor;
	} else
		boundDispatcher->sweepDist = 0;

	ISC_CHECKPOINT("bound");
	// copy bounds along given axis into our arrays
	const size_t   nBounds = BB[0].size();
	const Vector3r maxVect(Mathr::MAX_REAL, Mathr::MAX_REAL, Mathr::MAX_REAL);
	// 	#pragma omp parallel for schedule(guided) num_threads(ompThreads>0 ? min(ompThreads,omp_get_max_threads()) : omp_get_max_threads())
	for (int j = 0; j < 3; j++) {
		// 		const long cacheIter = scene->iter;
		VecBounds& BBj = BB[j];
		for (size_t i = 0; i < nBounds; i++) {
			Bounds&                 BBji = BBj[i];
			const Body::id_t        id   = BBji.id;
			const shared_ptr<Body>& b    = Body::byId(id, scene);
			if (b) {
				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!)
				// FIXME: the Mathr::MAX_REAL trick will not work very well for periodic BCs.
				BBji.coord = ((BBji.flags.hasBB = ((bool)bv)) ? (BBji.flags.isMin ? bv->min[j] : bv->max[j])
				                                              : (keepListsShort ? Mathr::MAX_REAL : 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 (YADE_REAL_BIT <= 64)
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wpragmas"
// this is to remove warning about manipulating raw memory
#pragma GCC diagnostic ignored "-Wclass-memaccess"
				if (bv) {
					if (BBji.flags.isMin && j == 1) memcpy(&minima[3 * id], &bv->min, 3 * sizeof(Real));
					memcpy(&maxima[3 * id], &bv->max, 3 * sizeof(Real));
				} else if (keepListsShort) {
					memcpy(&minima[3 * id], &maxVect, 3 * sizeof(Real));
					memcpy(&maxima[3 * id], &maxVect, 3 * sizeof(Real));
				}
#pragma GCC diagnostic pop
#else
				if (bv) {
					if (BBji.flags.isMin && j == 1) {
						minima[3 * id]     = bv->min[0];
						minima[3 * id + 1] = bv->min[1];
						minima[3 * id + 2] = bv->min[2];
					}
					maxima[3 * id]     = bv->max[0];
					maxima[3 * id + 1] = bv->max[1];
					maxima[3 * id + 2] = bv->max[2];
				} else if (keepListsShort) {
					minima[3 * id]     = maxVect[0];
					minima[3 * id + 1] = maxVect[1];
					minima[3 * id + 2] = maxVect[2];
					maxima[3 * id]     = maxVect[0];
					maxima[3 * id + 1] = maxVect[1];
					maxima[3 * id + 2] = maxVect[2];
				}
#endif
			} else {
				BBj[i].flags.hasBB = false; /* for vanished body, keep the coordinate as-is, to minimize inversions. */
#ifdef YADE_MPI
				if (keepListsShort) LOG_ERROR("Shouldn't happen " << id << " in " << scene->subdomain);
#endif
			}
		}
	}
	ISC_CHECKPOINT("copy");
	// remove interactions which have disconnected bounds and are not real (will run parallel if YADE_OPENMP)
	interactions->conditionalyEraseNonReal(*this, scene);

	ISC_CHECKPOINT("erase");
	// sort
	// the regular case
	if (!doInitSort && !sortThenCollide) {
		/* each inversion in insertionSort calls may add interaction */
		//1000 bodies is heuristic minimum above which parallel sort is called
		if (!periodic)
			for (int i = 0; i < 3; i++)
#ifdef YADE_OPENMP
			{
				if (ompThreads <= 1 || nBodies < 1000 || verletDist == 0) insertionSort(BB[i], interactions, scene);
				else
					insertionSortParallel(BB[i], interactions, scene);
			}
#else

			{
				insertionSort(BB[i], interactions, scene);
			}
#endif
		else
			for (int i = 0; i < 3; i++)
				insertionSortPeri(BB[i], interactions, scene);

		if (keepListsShort and smartInsertErase
		    and scene->bodies->insertedBodies.size() > 0) { // Do the init sort on new bodies only, Precondition: initial bounds list is sorted
			for (const auto& id1 : scene->bodies->insertedBodies) {
				const shared_ptr<Body>& b = Body::byId(id1, scene);
				if (b and b->isBounded()) {
					for (const auto& id2 : probeBoundingVolume(*(b->bound))) { // Probe interactions with new body
						if (Collider::mayCollide(
						            Body::byId(id1, scene).get(),
						            Body::byId(id2, scene).get()
#ifdef YADE_MPI
						                    ,
						            scene->subdomain
#endif
						            )
						    and !interactions->found(id1, id2))
							interactions->insert(shared_ptr<Interaction>(new Interaction(id1, id2)));
					}
					// then insert bounds in the right place so that they remain sorted
					for (int i = 0; i < 3; i++) {
						auto bMin = Bounds(b->bound->min[i], id1, /*isMin=*/true);
						auto bMax = Bounds(b->bound->max[i], id1, /*isMin=*/false);
						auto it   = std::lower_bound(BB[i].begin(), BB[i].end(), bMin);
						it        = BB[i].insert(it, bMin);
						it        = std::lower_bound(it, BB[i].end(), bMax);
						BB[i].insert(it, bMax);
					}
				}
			}
		}
	}
	// create initial interactions (much slower)
	else {
		if (doInitSort) {
			// the initial sort is in independent in 3 dimensions, may be run in parallel; it seems that there is no time gain running in parallel, though
			// important to reset loInx for periodic simulation (!!)
			// 				#pragma omp parallel for schedule(dynamic,1) num_threads(min(ompThreads,3))
			for (int i = 0; i < 3; i++) {
				BB[i].loIdx = 0;
				BB[i].sort();
			}
			numReinit++;
		} else { // sortThenCollide
			if (!periodic)
				for (int i = 0; i < 3; i++)
					insertionSort(BB[i], interactions, scene, false);
			else
				for (int i = 0; i < 3; i++)
					insertionSortPeri(BB[i], interactions, scene, false);
		}

		// traverse the container along requested axis and find overlaps
		assert(sortAxis == 0 || sortAxis == 1 || sortAxis == 2);
		VecBounds& V = BB[sortAxis];
		findOverlaps(V);
	}
	scene->bodies->insertedBodies.clear();
	scene->bodies->erasedBodies.clear();
	ISC_CHECKPOINT("sort&collide");
}


void InsertionSortCollider::findOverlaps(VecBounds& V)
{
	InteractionContainer* interactions = scene->interactions.get();
	// go through potential aabb collisions, create interactions as necessary
	if (!periodic) {
#ifdef YADE_OPENMP
		std::vector<std::vector<std::pair<Body::id_t, Body::id_t>>> newInts;
		newInts.resize(ompThreads, std::vector<std::pair<Body::id_t, Body::id_t>>());
		for (int kk = 0; kk < ompThreads; kk++)
#pragma omp parallel for schedule(guided, 200) num_threads(ompThreads)
#endif
			for (size_t i = 0; i < V.size(); i++) {
				// start from the lower bound (i.e. skipping upper bounds)
				// skip bodies without bbox, because they don't collide
				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 (size_t j = i + 1; /* handle case 2. of swapped min/max */ j < V.size() && 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].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_MPI
					                    ,
					            scene->subdomain
#endif
					            )) {
#ifdef YADE_OPENMP
						unsigned int threadNum = omp_get_thread_num();
						newInts[threadNum].push_back(std::pair<Body::id_t, Body::id_t>(iid, jid));
#else
					if (!interactions->found(iid, jid)) {
						if (iid < jid) interactions->insert(shared_ptr<Interaction>(new Interaction(iid, jid)));
						else
							interactions->insert(shared_ptr<Interaction>(new Interaction(jid, iid)));
					}
#endif
					}
				}
			}
//go through newly created candidates sequentially, duplicates coming from different threads may exist so we check existence with found()
#ifdef YADE_OPENMP
		for (int n = 0; n < ompThreads; n++)
			for (size_t k = 0, kend = newInts[n].size(); k < kend; k++)
				if (!interactions->found(newInts[n][k].first, newInts[n][k].second)) {
					if (newInts[n][k].first < newInts[n][k].second)
						interactions->insert(shared_ptr<Interaction>(new Interaction(newInts[n][k].first, newInts[n][k].second)));
					else
						interactions->insert(shared_ptr<Interaction>(new Interaction(newInts[n][k].second, newInts[n][k].first)));
				}
#endif
	} else { // periodic case: see comments above
		for (size_t i = 0; i < V.size(); i++) {
			if (!(V[i].flags.isMin && V[i].flags.hasBB)) continue;
			const Body::id_t& iid = V[i].id;
			// 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].flags.isMin && V[j].flags.hasBB)) continue;
				if (iid < jid) handleBoundInversionPeri(iid, jid, interactions, scene);
				else
					handleBoundInversionPeri(jid, iid, interactions, scene);
			}
		}
	}
}


// return floating value wrapped between x0 and x1 and saving period number to period
Real InsertionSortCollider::cellWrap(const Real x, const Real x0, const Real x1, int& period)
{
	Real xNorm = (x - x0) / (x1 - x0);
	period     = (int)floor(xNorm); // some people say this is very slow; probably optimized by gcc, however (google suggests)
	return x0 + (xNorm - period) * (x1 - x0);
}

// return coordinate wrapped to 0…x1, relative to x0; don't care about period
Real InsertionSortCollider::cellWrapRel(const Real x, const Real x0, const Real x1)
{
	Real xNorm = (x - x0) / (x1 - x0);
	return (xNorm - floor(xNorm)) * (x1 - x0);
}

//NOTE: possible improvements:
// 1) (not only periodic) keep a mask defining overlaps in directions 1,2,3, and compare the sum instead of checking overlap in three directions everytime there is an inversion. (maybe not possible? does it need a N² table?!!)
// 2) use norm() only when needed (first and last elements, mainly, can be treated as special cases)
void InsertionSortCollider::insertionSortPeri(VecBounds& v, InteractionContainer* interactions, Scene*, bool doCollide)
{
	assert(periodic);
	size_t&       loIdx = v.loIdx;
	const size_t& size  = v.size();

	// The condition in next "for" loop would segfault if size=0, escape here and warn
	if (BB[0].size() == 0) {
		LOG_WARN("no bounds where found, empty scene? Turn collider off if nothing to collide, else please report bug");
		return;
	}

	/* We have to visit each bound at least once (first condition), but this is not enough. The correct ordering in the begining of the list needs a second pass to connect begin and end consistently (the second condition). Strictly the second condition should include "+ (v.norm(j+1)==loIdx ? v.cellDim : 0)" but it is ok as is since the shift is added inside the loop. */
	for (size_t _i = 0; (_i < size) || (v[v.norm(_i)].coord < v[v.norm(_i - 1)].coord); _i++) {
		const size_t i   = v.norm(_i); //FIXME: useless, and many others can probably be removed
		const size_t i_1 = v.norm(i - 1);
		//switch period of (i) if the coord is below the lower edge cooridnate-wise and just above the split
		if (i == loIdx && v[i].coord < 0) {
			v[i].period -= 1;
			v[i].coord += v.cellDim;
			loIdx = v.norm(loIdx + 1);
		}
		// coordinate of v[i] used to check inversions
		// if crossing the split, adjust by cellDim;
		// if we get below the loIdx however, the v[i].coord will have been adjusted already, no need to do that here
		const Real iCmpCoord = v[i].coord + (i == loIdx ? v.cellDim : 0);
		// no inversion
		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
		size_t     j       = i_1;
		Bounds     vi      = v[i];
		const bool viHasBB = vi.flags.hasBB;
		const bool isMin   = v[i].flags.isMin;

		//For the first pass, the bounds are not travelling down past v[0] (j<_i above prevents that), otherwise we would not know which part of the list has been correctly sorted. Only after the first pass, we sort end vs. begining of the list.
		while ((j < _i) and v[j].coord > (vi.coord + /* wrap for elt just below split */ (v.norm(j + 1) == loIdx ? v.cellDim : 0))) {
			size_t 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,
			// this can happen without any side-effects
			if (false && v[j].coord > 2 * v.cellDim) {
				// this condition is not strictly necessary, but the loop of insertionSort would have to run more times.
				// Since size of particle is required to be < .5*cellDim, this would mean simulation explosion anyway
				LOG_FATAL("Body #" << v[j].id << " going faster than 1 cell in one step? Not handled.");
				throw runtime_error(__FILE__ ": body moving too fast (skipped 1 cell).");
			}
			Bounds& vNew(v[j1]); // elt at j+1 being overwritten by the one at j and adjusted
			vNew = v[j];
			// inversions close to 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].flags.isMin && (doCollide && viHasBB && v[j].flags.hasBB))
				if (vi.id != vNew.id) {
					if (vi.id < vNew.id) handleBoundInversionPeri(vi.id, vNew.id, interactions, scene);
					else
						handleBoundInversionPeri(vNew.id, vi.id, interactions, scene);
				}
			j = v.norm(j - 1);
		}
		v[v.norm(j + 1)] = vi;
	}
	//Keep coord's in [0,cellDim] by clamping the largest values
	for (size_t i = v.norm(loIdx - 1); v[i].coord > v.cellDim; i = v.norm(--i)) {
		v[i].period += 1;
		v[i].coord -= v.cellDim;
		loIdx = i;
	}
}

// called by the insertion sort if 2 bodies swapped their bounds
void InsertionSortCollider::handleBoundInversionPeri(Body::id_t id1, Body::id_t id2, InteractionContainer* interactions, Scene*)
{
	assert(periodic);
	if (interactions->found(id1, id2)) return; // we want to _create_ new ones, we don't care about existing ones
	Vector3i periods(Vector3i::Zero());
	bool     overlap = spatialOverlapPeri(id1, id2, scene, periods);
	if (overlap
	    && Collider::mayCollide(
	            Body::byId(id1, scene).get(),
	            Body::byId(id2, scene).get()
#ifdef YADE_MPI
	                    ,
	            scene->subdomain
#endif
	            )) {
		shared_ptr<Interaction> newI = shared_ptr<Interaction>(new Interaction(id1, id2));
		newI->cellDist               = periods;
		interactions->insert(newI);
	}
}

/* Performance hint
	================

	Since this function is called (most the time) from insertionSort,
	we actually already know what is the overlap status in that one dimension, including
	periodicity information; both values could be passed down as a parameters, avoiding 1 of 3 loops here.
	We do some floats math here, so the speedup could noticeable; doesn't concertn the non-periodic variant,
	where it is only plain comparisons taking place.
*/
//! return true if bodies bb overlap in all 3 dimensions
bool InsertionSortCollider::spatialOverlapPeri(Body::id_t id1, Body::id_t id2, Scene* scene2, Vector3i& periods) const
{
	// scene shadows a member ‘yade::InsertionSortCollider::scene’
	assert(periodic);
	assert(id1 != id2); // programming error, or weird bodies (too large?)
	for (int axis = 0; axis < 3; axis++) {
		Real dim = scene2->cell->getSize()[axis];
		// LOG_DEBUG("dim["<<axis<<"]="<<dim);
		// too big bodies
		if (!allowBiggerThanPeriod) {
			assert(maxima[3 * id1 + axis] - minima[3 * id1 + axis] < .99 * dim);
			assert(maxima[3 * id2 + axis] - minima[3 * id2 + axis] < .99 * dim);
		}
		// define normalized positions relative to id1->max, and with +1 shift for id1->min so that body1's bounds cover an interval [shiftedMin; 1] at the end of a b1-centric period
		Real lmin       = (minima[3 * id2 + axis] - maxima[3 * id1 + axis]) * invSizes[axis];
		Real lmax       = (maxima[3 * id2 + axis] - maxima[3 * id1 + axis]) * invSizes[axis];
		Real shiftedMin = (minima[3 * id1 + axis] - maxima[3 * id1 + axis]) * invSizes[axis] + 1.;

#ifdef YADE_MPI
		bool subDoverlap      = (Body::byId(id1, scene2)->getIsSubdomain() || Body::byId(id2, scene2)->getIsSubdomain());
		bool fluidBodyOverLap = (Body::byId(id1, scene2)->getIsFluidDomainBbox() || Body::byId(id2, scene2)->getIsFluidDomainBbox());
		if (((lmax - lmin) > 0.5 || shiftedMin < 0) && !(subDoverlap or fluidBodyOverLap)) {
#else
		if ((lmax - lmin) > 0.5 || shiftedMin < 0) {
#endif
			if (allowBiggerThanPeriod) {
				periods[axis] = 0;
				continue;
			} else {
				LOG_FATAL(
				        "Body #" << ((lmax - lmin) > 0.5 ? id2 : id1) << " spans over half of the cell size " << dim << " (axis=" << axis
				                 << ", see flags allowBiggerThanPeriod and Cell.flipFlippable)");
				throw runtime_error(__FILE__ ": Body larger than half of the cell size encountered.");
			}
		}
		int period1 = int(math::floor(lmax));

		//overlap around zero, on the "+" side
		if ((lmin - period1) <= overlapTolerance) {
			periods[axis] = -period1;
			continue;
		}
		//overlap around 1, on the "-" sides
		if ((lmax - period1 + overlapTolerance) >= shiftedMin) {
			periods[axis] = -period1 - 1;
			continue;
		}
		// none of the above, exit
		return false;
	}
	return true;
}

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++) {
		VecBounds& V = BB[axis];
		if (periodic) {
			for (size_t 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].flags.isMin ? -1 : 1) * V[ii].id, V[ii].period));
			}
		} else {
			for (size_t i = 0; i < V.size(); i++) {
				bl[axis].append(boost::python::make_tuple(V[i].coord, (V[i].flags.isMin ? -1 : 1) * V[i].id));
			}
		}
	}
	return boost::python::make_tuple(bl[0], bl[1], bl[2]);
}

void InsertionSortCollider::VecBounds::updatePeriodicity(Scene* scene)
{
	assert(scene->isPeriodic);
	assert(axis >= 0 && axis <= 2);
	cellDim = scene->cell->getSize()[axis];
}

} // namespace yade
