LogicHandler.h

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#pragma once
#include <atomic>
#include <limits>
#include <memory>
#include <optional>
#include <tuple>
#include <type_traits>
#include <vector>
 
#include "autopas/LogicHandlerInfo.h"
#include "autopas/cells/FullParticleCell.h"
#include "autopas/containers/TraversalInterface.h"
#include "autopas/iterators/ContainerIterator.h"
#include "autopas/options/IteratorBehavior.h"
#include "autopas/tuning/AutoTuner.h"
#include "autopas/tuning/Configuration.h"
#include "autopas/tuning/selectors/ContainerSelector.h"
#include "autopas/tuning/selectors/ContainerSelectorInfo.h"
#include "autopas/tuning/selectors/TraversalSelector.h"
#include "autopas/utils/NumParticlesEstimator.h"
#include "autopas/utils/StaticCellSelector.h"
#include "autopas/utils/StaticContainerSelector.h"
#include "autopas/utils/Timer.h"
#include "autopas/utils/WrapOpenMP.h"
#include "autopas/utils/logging/FLOPLogger.h"
#include "autopas/utils/logging/IterationLogger.h"
#include "autopas/utils/logging/IterationMeasurements.h"
#include "autopas/utils/logging/LiveInfoLogger.h"
#include "autopas/utils/logging/Logger.h"
#include "autopas/utils/markParticleAsDeleted.h"
 
namespace autopas {
 
template <typename Particle_T>
class LogicHandler {
 public:
  LogicHandler(std::unordered_map<InteractionTypeOption::Value, std::unique_ptr<AutoTuner>> &autotuners,
               const LogicHandlerInfo &logicHandlerInfo, unsigned int rebuildFrequency, const std::string &outputSuffix)
      : _autoTunerRefs(autotuners),
        _logicHandlerInfo(logicHandlerInfo),
        _neighborListRebuildFrequency{rebuildFrequency},
        _particleBuffer(autopas_get_max_threads()),
        _haloParticleBuffer(autopas_get_max_threads()),
        _containerSelector(logicHandlerInfo.boxMin, logicHandlerInfo.boxMax, logicHandlerInfo.cutoff),
        _verletClusterSize(logicHandlerInfo.verletClusterSize),
        _sortingThreshold(logicHandlerInfo.sortingThreshold),
        _iterationLogger(outputSuffix, std::any_of(autotuners.begin(), autotuners.end(),
                                                   [](const auto &tuner) { return tuner.second->canMeasureEnergy(); })),
        _flopLogger(outputSuffix),
        _liveInfoLogger(outputSuffix),
        _bufferLocks(std::max(2, autopas::autopas_get_max_threads())) {
    using namespace autopas::utils::ArrayMath::literals;
    // Initialize AutoPas with tuners for given interaction types
    for (const auto &[interactionType, tuner] : autotuners) {
      _interactionTypes.insert(interactionType);
 
      const auto configuration = tuner->getCurrentConfig();
      // initialize the container and make sure it is valid
      const ContainerSelectorInfo containerSelectorInfo{configuration.cellSizeFactor, _logicHandlerInfo.verletSkin,
                                                        _neighborListRebuildFrequency, _verletClusterSize,
                                                        configuration.loadEstimator};
      _containerSelector.selectContainer(configuration.container, containerSelectorInfo);
      checkMinimalSize();
    }
 
    // initialize locks needed for remainder traversal
    const auto interactionLength = logicHandlerInfo.cutoff + logicHandlerInfo.verletSkin;
    const auto interactionLengthInv = 1. / interactionLength;
    const auto boxLengthWithHalo = logicHandlerInfo.boxMax - logicHandlerInfo.boxMin + (2 * interactionLength);
    initSpacialLocks(boxLengthWithHalo, interactionLengthInv);
    for (auto &lockPtr : _bufferLocks) {
      lockPtr = std::make_unique<std::mutex>();
    }
  }
 
  autopas::ParticleContainerInterface<Particle_T> &getContainer() { return _containerSelector.getCurrentContainer(); }
 
  [[nodiscard]] std::vector<Particle_T> collectLeavingParticlesFromBuffer(bool insertOwnedParticlesToContainer) {
    const auto &boxMin = _containerSelector.getCurrentContainer().getBoxMin();
    const auto &boxMax = _containerSelector.getCurrentContainer().getBoxMax();
    std::vector<Particle_T> leavingBufferParticles{};
    for (auto &cell : _particleBuffer) {
      auto &buffer = cell._particles;
      if (insertOwnedParticlesToContainer) {
        // Can't be const because we potentially modify ownership before re-adding
        for (auto &p : buffer) {
          if (p.isDummy()) {
            continue;
          }
          if (utils::inBox(p.getR(), boxMin, boxMax)) {
            p.setOwnershipState(OwnershipState::owned);
            _containerSelector.getCurrentContainer().addParticle(p);
          } else {
            leavingBufferParticles.push_back(p);
          }
        }
        buffer.clear();
      } else {
        for (auto iter = buffer.begin(); iter < buffer.end();) {
          auto &p = *iter;
 
          auto fastRemoveP = [&]() {
            // Fast remove of particle, i.e., swap with last entry && pop.
            std::swap(p, buffer.back());
            buffer.pop_back();
            // Do not increment the iter afterward!
          };
          if (p.isDummy()) {
            // We remove dummies!
            fastRemoveP();
            // In case we swapped a dummy here, don't increment the iterator and do another iteration to check again.
            continue;
          }
          // if p was a dummy a new particle might now be at the memory location of p so we need to check that.
          // We also just might have deleted the last particle in the buffer in that case the inBox check is meaningless
          if (not buffer.empty() and utils::notInBox(p.getR(), boxMin, boxMax)) {
            leavingBufferParticles.push_back(p);
            fastRemoveP();
          } else {
            ++iter;
          }
        }
      }
    }
    return leavingBufferParticles;
  }
 
  [[nodiscard]] std::vector<Particle_T> updateContainer() {
#ifdef AUTOPAS_ENABLE_DYNAMIC_CONTAINERS
    this->checkNeighborListsInvalidDoDynamicRebuild();
#endif
    bool doDataStructureUpdate = not neighborListsAreValid();
 
    if (_functorCalls > 0) {
      // Bump iteration counters for all autotuners
      for (const auto &[interactionType, autoTuner] : _autoTunerRefs) {
        const bool needsToWait = checkTuningStates(interactionType);
        // Called before bumpIterationCounters as it would return false after that.
        if (autoTuner->inLastTuningIteration()) {
          _iterationAtEndOfLastTuningPhase = _iteration;
        }
        autoTuner->bumpIterationCounters(needsToWait);
      }
 
      // We will do a rebuild in this timestep
      if (not _neighborListsAreValid.load(std::memory_order_relaxed)) {
        _stepsSinceLastListRebuild = 0;
      }
      ++_stepsSinceLastListRebuild;
      _containerSelector.getCurrentContainer().setStepsSinceLastRebuild(_stepsSinceLastListRebuild);
      ++_iteration;
    }
 
    // The next call also adds particles to the container if doDataStructureUpdate is true.
    auto leavingBufferParticles = collectLeavingParticlesFromBuffer(doDataStructureUpdate);
 
    AutoPasLog(TRACE, "Initiating container update.");
    auto leavingParticles = _containerSelector.getCurrentContainer().updateContainer(not doDataStructureUpdate);
    leavingParticles.insert(leavingParticles.end(), leavingBufferParticles.begin(), leavingBufferParticles.end());
 
    // Substract the amount of leaving particles from the number of owned particles.
    _numParticlesOwned.fetch_sub(leavingParticles.size(), std::memory_order_relaxed);
    // updateContainer deletes all halo particles.
    std::for_each(_haloParticleBuffer.begin(), _haloParticleBuffer.end(), [](auto &buffer) { buffer.clear(); });
    _numParticlesHalo.store(0, std::memory_order_relaxed);
    return leavingParticles;
  }
 
  std::vector<Particle_T> resizeBox(const std::array<double, 3> &boxMin, const std::array<double, 3> &boxMax) {
    using namespace autopas::utils::ArrayMath::literals;
    const auto &oldMin = _containerSelector.getCurrentContainer().getBoxMin();
    const auto &oldMax = _containerSelector.getCurrentContainer().getBoxMax();
 
    // if nothing changed do nothing
    if (oldMin == boxMin and oldMax == boxMax) {
      return {};
    }
 
    // sanity check that new size is actually positive
    for (size_t i = 0; i < boxMin.size(); ++i) {
      if (boxMin[i] >= boxMax[i]) {
        utils::ExceptionHandler::exception(
            "New box size in dimension {} is not positive!\nboxMin[{}] = {}\nboxMax[{}] = {}", i, i, boxMin[i], i,
            boxMax[i]);
      }
    }
 
    // warn if domain changes too drastically
    const auto newLength = boxMax - boxMin;
    const auto oldLength = oldMax - oldMin;
    const auto relDiffLength = newLength / oldLength;
    for (size_t i = 0; i < newLength.size(); ++i) {
      // warning threshold is set arbitrary and up for change if needed
      if (relDiffLength[i] > 1.3 or relDiffLength[i] < 0.7) {
        AutoPasLog(WARN,
                   "LogicHandler.resize(): Domain size changed drastically in dimension {}! Gathered AutoTuning "
                   "information might not be applicable anymore!\n"
                   "Size old box : {}\n"
                   "Size new box : {}\n"
                   "Relative diff: {}",
                   i, utils::ArrayUtils::to_string(oldLength), utils::ArrayUtils::to_string(newLength),
                   utils::ArrayUtils::to_string(relDiffLength));
      }
    }
 
    // check all particles
    std::vector<Particle_T> particlesNowOutside;
    for (auto pIter = _containerSelector.getCurrentContainer().begin(); pIter.isValid(); ++pIter) {
      // make sure only owned ones are present
      if (not pIter->isOwned()) {
        utils::ExceptionHandler::exception(
            "LogicHandler::resizeBox() encountered non owned particle. "
            "When calling resizeBox() these should be already deleted. "
            "This could be solved by calling updateContainer() before resizeBox().");
      }
      // owned particles that are now outside are removed from the container and returned
      if (not utils::inBox(pIter->getR(), boxMin, boxMax)) {
        particlesNowOutside.push_back(*pIter);
        decreaseParticleCounter(*pIter);
        internal::markParticleAsDeleted(*pIter);
      }
    }
 
    // actually resize the container
    _containerSelector.resizeBox(boxMin, boxMax);
    // The container might have changed sufficiently enough so that we need more or less spacial locks
    const auto boxLength = boxMax - boxMin;
    const auto interactionLengthInv = 1. / (_containerSelector.getCurrentContainer().getInteractionLength());
    initSpacialLocks(boxLength, interactionLengthInv);
 
    // Set this flag, s.t., the container is rebuilt!
    _neighborListsAreValid.store(false, std::memory_order_relaxed);
 
    return particlesNowOutside;
  }
 
  void reserve(size_t numParticles) {
    const auto &container = _containerSelector.getCurrentContainer();
    const auto numParticlesHaloEstimate = autopas::utils::NumParticlesEstimator::estimateNumHalosUniform(
        numParticles, container.getBoxMin(), container.getBoxMax(), container.getInteractionLength());
    reserve(numParticles, numParticlesHaloEstimate);
  }
 
  void reserve(size_t numParticles, size_t numHaloParticles) {
    const auto numHaloParticlesPerBuffer = numHaloParticles / _haloParticleBuffer.size();
    for (auto &buffer : _haloParticleBuffer) {
      buffer.reserve(numHaloParticlesPerBuffer);
    }
    // there is currently no good heuristic for this buffer so reuse the one for halos.
    for (auto &buffer : _particleBuffer) {
      buffer.reserve(numHaloParticlesPerBuffer);
    }
 
    _containerSelector.getCurrentContainer().reserve(numParticles, numHaloParticles);
  }
 
  void addParticle(const Particle_T &p) {
    // first check that the particle actually belongs in the container
    const auto &boxMin = _containerSelector.getCurrentContainer().getBoxMin();
    const auto &boxMax = _containerSelector.getCurrentContainer().getBoxMax();
    if (utils::notInBox(p.getR(), boxMin, boxMax)) {
      autopas::utils::ExceptionHandler::exception(
          "LogicHandler: Trying to add a particle that is not in the bounding box.\n"
          "Box Min {}\n"
          "Box Max {}\n"
          "{}",
          boxMin, boxMax, p.toString());
    }
    Particle_T particleCopy = p;
    particleCopy.setOwnershipState(OwnershipState::owned);
    if (not _neighborListsAreValid.load(std::memory_order_relaxed)) {
      // Container has to (about to) be invalid to be able to add Particles!
      _containerSelector.getCurrentContainer().template addParticle<false>(particleCopy);
    } else {
      // If the container is valid, we add it to the particle buffer.
      _particleBuffer[autopas_get_thread_num()].addParticle(particleCopy);
    }
    _numParticlesOwned.fetch_add(1, std::memory_order_relaxed);
  }
 
  void addHaloParticle(const Particle_T &haloParticle) {
    auto &container = _containerSelector.getCurrentContainer();
    const auto &boxMin = container.getBoxMin();
    const auto &boxMax = container.getBoxMax();
    Particle_T haloParticleCopy = haloParticle;
    if (utils::inBox(haloParticleCopy.getR(), boxMin, boxMax)) {
      autopas::utils::ExceptionHandler::exception(
          "LogicHandler: Trying to add a halo particle that is not outside the box of the container.\n"
          "Box Min {}\n"
          "Box Max {}\n"
          "{}",
          utils::ArrayUtils::to_string(boxMin), utils::ArrayUtils::to_string(boxMax), haloParticleCopy.toString());
    }
    haloParticleCopy.setOwnershipState(OwnershipState::halo);
    if (not _neighborListsAreValid.load(std::memory_order_relaxed)) {
      // If the neighbor lists are not valid, we can add the particle.
      container.template addHaloParticle</* checkInBox */ false>(haloParticleCopy);
    } else {
      // Check if we can update an existing halo(dummy) particle.
      bool updated = container.updateHaloParticle(haloParticleCopy);
      if (not updated) {
        // If we couldn't find an existing particle, add it to the halo particle buffer.
        _haloParticleBuffer[autopas_get_thread_num()].addParticle(haloParticleCopy);
      }
    }
    _numParticlesHalo.fetch_add(1, std::memory_order_relaxed);
  }
 
  void deleteAllParticles() {
    _neighborListsAreValid.store(false, std::memory_order_relaxed);
    _containerSelector.getCurrentContainer().deleteAllParticles();
    std::for_each(_particleBuffer.begin(), _particleBuffer.end(), [](auto &buffer) { buffer.clear(); });
    std::for_each(_haloParticleBuffer.begin(), _haloParticleBuffer.end(), [](auto &buffer) { buffer.clear(); });
    // all particles are gone -> reset counters.
    _numParticlesOwned.store(0, std::memory_order_relaxed);
    _numParticlesHalo.store(0, std::memory_order_relaxed);
  }
 
  std::tuple<bool, bool> deleteParticleFromBuffers(Particle_T &particle) {
    // find the buffer the particle belongs to
    auto &bufferCollection = particle.isOwned() ? _particleBuffer : _haloParticleBuffer;
    for (auto &cell : bufferCollection) {
      auto &buffer = cell._particles;
      // if the address of the particle is between start and end of the buffer it is in this buffer
      if (not buffer.empty() and &(buffer.front()) <= &particle and &particle <= &(buffer.back())) {
        const bool isRearParticle = &particle == &buffer.back();
        // swap-delete
        particle = buffer.back();
        buffer.pop_back();
        return {true, not isRearParticle};
      }
    }
    return {false, true};
  }
 
  void decreaseParticleCounter(Particle_T &particle) {
    if (particle.isOwned()) {
      _numParticlesOwned.fetch_sub(1, std::memory_order_relaxed);
    } else {
      _numParticlesHalo.fetch_sub(1, std::memory_order_relaxed);
    }
  }
 
  template <class Functor>
  bool computeInteractionsPipeline(Functor *functor, const InteractionTypeOption &interactionType);
 
  template <class Iterator>
  typename Iterator::ParticleVecType gatherAdditionalVectors(IteratorBehavior behavior) {
    typename Iterator::ParticleVecType additionalVectors;
    if (not(behavior & IteratorBehavior::containerOnly)) {
      additionalVectors.reserve(static_cast<bool>(behavior & IteratorBehavior::owned) * _particleBuffer.size() +
                                static_cast<bool>(behavior & IteratorBehavior::halo) * _haloParticleBuffer.size());
      if (behavior & IteratorBehavior::owned) {
        for (auto &buffer : _particleBuffer) {
          // Don't insert empty buffers. This also means that we won't pick up particles added during iterating if they
          // go to the buffers. But since we wouldn't pick them up if they go into the container to a cell that the
          // iterators already passed this is unsupported anyways.
          if (not buffer.isEmpty()) {
            additionalVectors.push_back(&(buffer._particles));
          }
        }
      }
      if (behavior & IteratorBehavior::halo) {
        for (auto &buffer : _haloParticleBuffer) {
          if (not buffer.isEmpty()) {
            additionalVectors.push_back(&(buffer._particles));
          }
        }
      }
    }
    return additionalVectors;
  }
 
  autopas::ContainerIterator<Particle_T, true, false> begin(IteratorBehavior behavior) {
    auto additionalVectors = gatherAdditionalVectors<ContainerIterator<Particle_T, true, false>>(behavior);
    return _containerSelector.getCurrentContainer().begin(behavior, &additionalVectors);
  }
 
  autopas::ContainerIterator<Particle_T, false, false> begin(IteratorBehavior behavior) const {
    auto additionalVectors =
        const_cast<LogicHandler *>(this)->gatherAdditionalVectors<ContainerIterator<Particle_T, false, false>>(
            behavior);
    return _containerSelector.getCurrentContainer().begin(behavior, &additionalVectors);
  }
 
  autopas::ContainerIterator<Particle_T, true, true> getRegionIterator(const std::array<double, 3> &lowerCorner,
                                                                       const std::array<double, 3> &higherCorner,
                                                                       IteratorBehavior behavior) {
    // sanity check: Most of our stuff depends on `inBox` which does not handle lowerCorner > higherCorner well.
    for (size_t d = 0; d < 3; ++d) {
      if (lowerCorner[d] > higherCorner[d]) {
        autopas::utils::ExceptionHandler::exception(
            "Requesting region Iterator where the upper corner is lower than the lower corner!\n"
            "Lower corner: {}\n"
            "Upper corner: {}",
            lowerCorner, higherCorner);
      }
    }
 
    auto additionalVectors = gatherAdditionalVectors<ContainerIterator<Particle_T, true, true>>(behavior);
    return _containerSelector.getCurrentContainer().getRegionIterator(lowerCorner, higherCorner, behavior,
                                                                      &additionalVectors);
  }
 
  autopas::ContainerIterator<Particle_T, false, true> getRegionIterator(const std::array<double, 3> &lowerCorner,
                                                                        const std::array<double, 3> &higherCorner,
                                                                        IteratorBehavior behavior) const {
    // sanity check: Most of our stuff depends on `inBox` which does not handle lowerCorner > higherCorner well.
    for (size_t d = 0; d < 3; ++d) {
      if (lowerCorner[d] > higherCorner[d]) {
        autopas::utils::ExceptionHandler::exception(
            "Requesting region Iterator where the upper corner is lower than the lower corner!\n"
            "Lower corner: {}\n"
            "Upper corner: {}",
            lowerCorner, higherCorner);
      }
    }
 
    auto additionalVectors =
        const_cast<LogicHandler *>(this)->gatherAdditionalVectors<ContainerIterator<Particle_T, false, true>>(behavior);
    return std::as_const(_containerSelector)
        .getCurrentContainer()
        .getRegionIterator(lowerCorner, higherCorner, behavior, &additionalVectors);
  }
 
  [[nodiscard]] unsigned long getNumberOfParticlesOwned() const { return _numParticlesOwned; }
 
  [[nodiscard]] unsigned long getNumberOfParticlesHalo() const { return _numParticlesHalo; }
 
  bool checkTuningStates(const InteractionTypeOption &interactionType) {
    // Goes over all pairs in _autoTunerRefs and returns true as soon as one is `inTuningPhase()`.
    // The tuner associated with the given interaction type is ignored.
    return std::any_of(std::begin(_autoTunerRefs), std::end(_autoTunerRefs), [&](const auto &entry) {
      return not(entry.first == interactionType) and entry.second->inTuningPhase();
    });
  }
 
  template <class Functor>
  [[nodiscard]] std::tuple<std::optional<std::unique_ptr<TraversalInterface>>, bool> isConfigurationApplicable(
      const Configuration &conf, Functor &functor, const InteractionTypeOption &interactionType);
 
  void setParticleBuffers(const std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                          const std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers);
 
  std::tuple<const std::vector<FullParticleCell<Particle_T>> &, const std::vector<FullParticleCell<Particle_T>> &>
  getParticleBuffers() const;
 
  [[nodiscard]] double getMeanRebuildFrequency(bool considerOnlyLastNonTuningPhase = false) const {
#ifdef AUTOPAS_ENABLE_DYNAMIC_CONTAINERS
    const auto numRebuilds = considerOnlyLastNonTuningPhase ? _numRebuildsInNonTuningPhase : _numRebuilds;
    // The total number of iterations is iteration + 1
    const auto iterationCount =
        considerOnlyLastNonTuningPhase ? _iteration - _iterationAtEndOfLastTuningPhase : _iteration + 1;
    if (numRebuilds == 0) {
      return static_cast<double>(_neighborListRebuildFrequency);
    } else {
      return static_cast<double>(iterationCount) / numRebuilds;
    }
#else
    return static_cast<double>(_neighborListRebuildFrequency);
#endif
  }
 
  bool getNeighborListsInvalidDoDynamicRebuild();
 
  void checkNeighborListsInvalidDoDynamicRebuild();
 
  void resetNeighborListsInvalidDoDynamicRebuild();
 
  bool neighborListsAreValid();
 
 private:
  void initSpacialLocks(const std::array<double, 3> &boxLength, double interactionLengthInv) {
    using namespace autopas::utils::ArrayMath::literals;
    using autopas::utils::ArrayMath::ceil;
    using autopas::utils::ArrayUtils::static_cast_copy_array;
 
    // The maximum number of spatial locks is capped at 1e6.
    // This limit is chosen more or less arbitrary. It is big enough so that our regular MD simulations
    // fall well within it and small enough so that no memory issues arise.
    // There were no rigorous tests for an optimal number of locks.
    // Without this cap, very large domains (or tiny cutoffs) would generate an insane number of locks,
    // that could blow up the memory.
    constexpr size_t maxNumSpacialLocks{1000000};
 
    // One lock per interaction length or less if this would generate too many.
    const std::array<size_t, 3> locksPerDim = [&]() {
      // First naively calculate the number of locks if we simply take the desired cell length.
      // Ceil because both decisions are possible, and we are generous gods.
      const std::array<size_t, 3> locksPerDimNaive =
          static_cast_copy_array<size_t>(ceil(boxLength * interactionLengthInv));
      const auto totalLocksNaive =
          std::accumulate(locksPerDimNaive.begin(), locksPerDimNaive.end(), 1ul, std::multiplies<>());
      // If the number of locks is within the limits everything is fine and we can return.
      if (totalLocksNaive <= maxNumSpacialLocks) {
        return locksPerDimNaive;
      } else {
        // If the number of locks grows too large, calculate the locks per dimension proportionally to the side lengths.
        // Calculate side length relative to dimension 0.
        const std::array<double, 3> boxSideProportions = {
            1.,
            boxLength[0] / boxLength[1],
            boxLength[0] / boxLength[2],
        };
        // With this, calculate the number of locks the first dimension should receive.
        const auto prodProportions =
            std::accumulate(boxSideProportions.begin(), boxSideProportions.end(), 1., std::multiplies<>());
        // Needs floor, otherwise we exceed the limit.
        const auto locksInFirstDimFloat = std::floor(std::cbrt(maxNumSpacialLocks * prodProportions));
        // From this and the proportions relative to the first dimension, we can calculate the remaining number of locks
        const std::array<size_t, 3> locksPerDimLimited = {
            static_cast<size_t>(locksInFirstDimFloat),  // omitted div by 1
            static_cast<size_t>(locksInFirstDimFloat / boxSideProportions[1]),
            static_cast<size_t>(locksInFirstDimFloat / boxSideProportions[2]),
        };
        return locksPerDimLimited;
      }
    }();
    _spacialLocks.resize(locksPerDim[0]);
    for (auto &lockVecVec : _spacialLocks) {
      lockVecVec.resize(locksPerDim[1]);
      for (auto &lockVec : lockVecVec) {
        lockVec.resize(locksPerDim[2]);
        for (auto &lockPtr : lockVec) {
          if (not lockPtr) {
            lockPtr = std::make_unique<std::mutex>();
          }
        }
      }
    }
  }
 
  template <class Functor>
  std::tuple<Configuration, std::unique_ptr<TraversalInterface>, bool> selectConfiguration(
      Functor &functor, const InteractionTypeOption &interactionType);
 
  template <class Functor>
  IterationMeasurements computeInteractions(Functor &functor, TraversalInterface &traversal);
 
  template <class Functor>
  void computeRemainderInteractions(Functor &functor, bool newton3, bool useSoA);
 
  template <bool newton3, class ContainerType, class PairwiseFunctor>
  void computeRemainderInteractions2B(PairwiseFunctor *f, ContainerType &container,
                                      std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                      std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers, bool useSoA);
 
  template <bool newton3, class ContainerType, class PairwiseFunctor>
  void remainderHelperBufferContainerAoS(PairwiseFunctor *f, ContainerType &container,
                                         std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                         std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers);
 
  template <bool newton3, class PairwiseFunctor>
  void remainderHelperBufferBuffer(PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                   bool useSoA);
 
  template <bool newton3, class PairwiseFunctor>
  void remainderHelperBufferBufferAoS(PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers);
 
  template <bool newton3, class PairwiseFunctor>
  void remainderHelperBufferBufferSoA(PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers);
 
  template <class PairwiseFunctor>
  void remainderHelperBufferHaloBuffer(PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                       std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers, bool useSoA);
 
  template <class PairwiseFunctor>
  void remainderHelperBufferHaloBufferAoS(PairwiseFunctor *f,
                                          std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                          std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers);
 
  template <class PairwiseFunctor>
  void remainderHelperBufferHaloBufferSoA(PairwiseFunctor *f,
                                          std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                          std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers);
 
  template <bool newton3, class ContainerType, class TriwiseFunctor>
  void computeRemainderInteractions3B(TriwiseFunctor *f, ContainerType &container,
                                      std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                      std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers);
 
  size_t collectBufferParticles(std::vector<Particle_T *> &bufferParticles,
                                std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers);
 
  template <class TriwiseFunctor>
  void remainderHelper3bBufferBufferBufferAoS(const std::vector<Particle_T *> &bufferParticles,
                                              size_t numOwnedBufferParticles, TriwiseFunctor *f);
 
  template <class ContainerType, class TriwiseFunctor>
  void remainderHelper3bBufferBufferContainerAoS(const std::vector<Particle_T *> &bufferParticles,
                                                 size_t numOwnedBufferParticles, ContainerType &container,
                                                 TriwiseFunctor *f);
 
  template <bool newton3, class ContainerType, class TriwiseFunctor>
  void remainderHelper3bBufferContainerContainerAoS(const std::vector<Particle_T *> &bufferParticles,
                                                    size_t numOwnedBufferParticles, ContainerType &container,
                                                    TriwiseFunctor *f);
 
  void checkMinimalSize() const;
 
  const LogicHandlerInfo _logicHandlerInfo;
  unsigned int _neighborListRebuildFrequency;
 
  unsigned int _verletClusterSize;
 
  size_t _numRebuilds{0};
 
  size_t _numRebuildsInNonTuningPhase{0};
 
  size_t _sortingThreshold;
 
  std::unordered_map<InteractionTypeOption::Value, std::unique_ptr<autopas::AutoTuner>> &_autoTunerRefs;
 
  std::set<InteractionTypeOption> _interactionTypes{};
 
  std::atomic<bool> _neighborListsAreValid{false};
 
  unsigned int _stepsSinceLastListRebuild{0};
 
  unsigned int _functorCalls{0};
 
  unsigned int _iteration{0};
 
  unsigned int _iterationAtEndOfLastTuningPhase{0};
 
  std::atomic<size_t> _numParticlesOwned{0ul};
 
  std::atomic<size_t> _numParticlesHalo{0ul};
 
  std::vector<FullParticleCell<Particle_T>> _particleBuffer;
 
  std::vector<FullParticleCell<Particle_T>> _haloParticleBuffer;
 
  ContainerSelector<Particle_T> _containerSelector;
 
  std::vector<std::vector<std::vector<std::unique_ptr<std::mutex>>>> _spacialLocks;
 
  std::vector<std::unique_ptr<std::mutex>> _bufferLocks;
 
  IterationLogger _iterationLogger;
 
  bool _neighborListInvalidDoDynamicRebuild{false};
 
  void updateRebuildPositions();
 
  LiveInfoLogger _liveInfoLogger;
 
  FLOPLogger _flopLogger;
};
 
template <typename Particle_T>
void LogicHandler<Particle_T>::updateRebuildPositions() {
#ifdef AUTOPAS_ENABLE_DYNAMIC_CONTAINERS
  // The owned particles in buffer are ignored because they do not rely on the structure of the particle containers,
  // e.g. neighbour list, and these are iterated over using the region iterator. Movement of particles in buffer doesn't
  // require a rebuild of neighbor lists.
  AUTOPAS_OPENMP(parallel)
  for (auto iter = this->begin(IteratorBehavior::owned | IteratorBehavior::containerOnly); iter.isValid(); ++iter) {
    iter->resetRAtRebuild();
  }
#endif
}
 
template <typename Particle_T>
void LogicHandler<Particle_T>::checkMinimalSize() const {
  const auto &container = _containerSelector.getCurrentContainer();
  // check boxSize at least cutoff + skin
  for (unsigned int dim = 0; dim < 3; ++dim) {
    if (container.getBoxMax()[dim] - container.getBoxMin()[dim] < container.getInteractionLength()) {
      autopas::utils::ExceptionHandler::exception(
          "Box (boxMin[{}]={} and boxMax[{}]={}) is too small.\nHas to be at least cutoff({}) + skin({}) = {}.", dim,
          container.getBoxMin()[dim], dim, container.getBoxMax()[dim], container.getCutoff(), container.getVerletSkin(),
          container.getCutoff() + container.getVerletSkin());
    }
  }
}
 
template <typename Particle_T>
bool LogicHandler<Particle_T>::getNeighborListsInvalidDoDynamicRebuild() {
  return _neighborListInvalidDoDynamicRebuild;
}
 
template <typename Particle_T>
bool LogicHandler<Particle_T>::neighborListsAreValid() {
  // Implement rebuild indicator as function, so it is only evaluated when needed.
  const auto needRebuild = [&](const InteractionTypeOption &interactionOption) {
    return _interactionTypes.count(interactionOption) != 0 and
           _autoTunerRefs[interactionOption]->willRebuildNeighborLists();
  };
 
  if (_stepsSinceLastListRebuild >= _neighborListRebuildFrequency
#ifdef AUTOPAS_ENABLE_DYNAMIC_CONTAINERS
      or getNeighborListsInvalidDoDynamicRebuild()
#endif
      or needRebuild(InteractionTypeOption::pairwise) or needRebuild(InteractionTypeOption::triwise)) {
    _neighborListsAreValid.store(false, std::memory_order_relaxed);
  }
 
  return _neighborListsAreValid.load(std::memory_order_relaxed);
}
 
template <typename Particle_T>
void LogicHandler<Particle_T>::checkNeighborListsInvalidDoDynamicRebuild() {
#ifdef AUTOPAS_ENABLE_DYNAMIC_CONTAINERS
  const auto skin = getContainer().getVerletSkin();
  // (skin/2)^2
  const auto halfSkinSquare = skin * skin * 0.25;
  // The owned particles in buffer are ignored because they do not rely on the structure of the particle containers,
  // e.g. neighbour list, and these are iterated over using the region iterator. Movement of particles in buffer doesn't
  // require a rebuild of neighbor lists.
  AUTOPAS_OPENMP(parallel reduction(or : _neighborListInvalidDoDynamicRebuild))
  for (auto iter = this->begin(IteratorBehavior::owned | IteratorBehavior::containerOnly); iter.isValid(); ++iter) {
    const auto distance = iter->calculateDisplacementSinceRebuild();
    const double distanceSquare = utils::ArrayMath::dot(distance, distance);
 
    _neighborListInvalidDoDynamicRebuild |= distanceSquare >= halfSkinSquare;
  }
#endif
}
 
template <typename Particle_T>
void LogicHandler<Particle_T>::resetNeighborListsInvalidDoDynamicRebuild() {
  _neighborListInvalidDoDynamicRebuild = false;
}
 
template <typename Particle_T>
void LogicHandler<Particle_T>::setParticleBuffers(
    const std::vector<FullParticleCell<Particle_T>> &particleBuffers,
    const std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers) {
  auto exchangeBuffer = [](const auto &newBuffers, auto &oldBuffers, auto &particleCounter) {
    // sanity check
    if (oldBuffers.size() < newBuffers.size()) {
      autopas::utils::ExceptionHandler::exception(
          "The number of new buffers ({}) is larger than number of existing buffers ({})!", newBuffers.size(),
          oldBuffers.size());
    }
 
    // we will clear the old buffers so subtract the particles from the counters.
    const auto numParticlesInOldBuffers =
        std::transform_reduce(oldBuffers.begin(), std::next(oldBuffers.begin(), newBuffers.size()), 0, std::plus<>(),
                              [](const auto &cell) { return cell.size(); });
    particleCounter.fetch_sub(numParticlesInOldBuffers, std::memory_order_relaxed);
 
    // clear the old buffers and copy the content of the new buffers over.
    size_t numParticlesInNewBuffers = 0;
    for (size_t i = 0; i < newBuffers.size(); ++i) {
      oldBuffers[i].clear();
      for (const auto &p : newBuffers[i]) {
        ++numParticlesInNewBuffers;
        oldBuffers[i].addParticle(p);
      }
    }
    // update the counters.
    particleCounter.fetch_add(numParticlesInNewBuffers, std::memory_order_relaxed);
  };
 
  exchangeBuffer(particleBuffers, _particleBuffer, _numParticlesOwned);
  exchangeBuffer(haloParticleBuffers, _haloParticleBuffer, _numParticlesHalo);
}
 
template <typename Particle_T>
std::tuple<const std::vector<FullParticleCell<Particle_T>> &, const std::vector<FullParticleCell<Particle_T>> &>
LogicHandler<Particle_T>::getParticleBuffers() const {
  return {_particleBuffer, _haloParticleBuffer};
}
 
template <typename Particle_T>
template <class Functor>
IterationMeasurements LogicHandler<Particle_T>::computeInteractions(Functor &functor, TraversalInterface &traversal) {
  // Helper to derive the Functor type at compile time
  constexpr auto interactionType = [] {
    if (utils::isPairwiseFunctor<Functor>()) {
      return InteractionTypeOption::pairwise;
    } else if (utils::isTriwiseFunctor<Functor>()) {
      return InteractionTypeOption::triwise;
    } else {
      utils::ExceptionHandler::exception(
          "LogicHandler::computeInteractions(): Functor is not valid. Only pairwise and triwise functors are "
          "supported. "
          "Please use a functor derived from "
          "PairwiseFunctor or TriwiseFunctor.");
    }
  }();
 
  auto &autoTuner = *_autoTunerRefs[interactionType];
  auto &container = _containerSelector.getCurrentContainer();
#ifdef AUTOPAS_ENABLE_DYNAMIC_CONTAINERS
  if (autoTuner.inFirstTuningIteration()) {
    autoTuner.setRebuildFrequency(getMeanRebuildFrequency(/* considerOnlyLastNonTuningPhase */ true));
    _numRebuildsInNonTuningPhase = 0;
  }
#endif
  autopas::utils::Timer timerTotal;
  autopas::utils::Timer timerRebuild;
  autopas::utils::Timer timerComputeInteractions;
  autopas::utils::Timer timerComputeRemainder;
 
  const bool energyMeasurementsPossible = autoTuner.resetEnergy();
 
  timerTotal.start();
  functor.initTraversal();
 
  // if lists are not valid -> rebuild;
  if (not _neighborListsAreValid.load(std::memory_order_relaxed)) {
    timerRebuild.start();
#ifdef AUTOPAS_ENABLE_DYNAMIC_CONTAINERS
    this->updateRebuildPositions();
#endif
    container.rebuildNeighborLists(&traversal);
#ifdef AUTOPAS_ENABLE_DYNAMIC_CONTAINERS
    this->resetNeighborListsInvalidDoDynamicRebuild();
    _numRebuilds++;
    if (not autoTuner.inTuningPhase()) {
      _numRebuildsInNonTuningPhase++;
    }
#endif
    timerRebuild.stop();
    _neighborListsAreValid.store(true, std::memory_order_relaxed);
  }
 
  timerComputeInteractions.start();
  container.computeInteractions(&traversal);
  timerComputeInteractions.stop();
 
  timerComputeRemainder.start();
  const bool newton3 = autoTuner.getCurrentConfig().newton3;
  const auto dataLayout = autoTuner.getCurrentConfig().dataLayout;
  computeRemainderInteractions(functor, newton3, dataLayout);
  timerComputeRemainder.stop();
 
  functor.endTraversal(newton3);
 
  const auto [energyWatts, energyJoules, energyDeltaT, energyTotal] = autoTuner.sampleEnergy();
  timerTotal.stop();
 
  constexpr auto nanD = std::numeric_limits<double>::quiet_NaN();
  constexpr auto nanL = std::numeric_limits<long>::quiet_NaN();
  return {timerComputeInteractions.getTotalTime(),
          timerComputeRemainder.getTotalTime(),
          timerRebuild.getTotalTime(),
          timerTotal.getTotalTime(),
          energyMeasurementsPossible,
          energyMeasurementsPossible ? energyWatts : nanD,
          energyMeasurementsPossible ? energyJoules : nanD,
          energyMeasurementsPossible ? energyDeltaT : nanD,
          energyMeasurementsPossible ? energyTotal : nanL};
}
 
template <typename Particle_T>
template <class Functor>
void LogicHandler<Particle_T>::computeRemainderInteractions(Functor &functor, bool newton3, bool useSoA) {
  auto &container = _containerSelector.getCurrentContainer();
 
  withStaticContainerType(container, [&](auto &actualContainerType) {
    if constexpr (utils::isPairwiseFunctor<Functor>()) {
      if (newton3) {
        computeRemainderInteractions2B<true>(&functor, actualContainerType, _particleBuffer, _haloParticleBuffer,
                                             useSoA);
      } else {
        computeRemainderInteractions2B<false>(&functor, actualContainerType, _particleBuffer, _haloParticleBuffer,
                                              useSoA);
      }
    } else if constexpr (utils::isTriwiseFunctor<Functor>()) {
      if (newton3) {
        computeRemainderInteractions3B<true>(&functor, actualContainerType, _particleBuffer, _haloParticleBuffer);
      } else {
        computeRemainderInteractions3B<false>(&functor, actualContainerType, _particleBuffer, _haloParticleBuffer);
      }
    }
  });
}
 
template <class Particle_T>
template <bool newton3, class ContainerType, class PairwiseFunctor>
void LogicHandler<Particle_T>::computeRemainderInteractions2B(
    PairwiseFunctor *f, ContainerType &container, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
    std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers, bool useSoA) {
  // Sanity check. If this is violated feel free to add some logic here that adapts the number of locks.
  if (_bufferLocks.size() < particleBuffers.size()) {
    utils::ExceptionHandler::exception("Not enough locks for non-halo buffers! Num Locks: {}, Buffers: {}",
                                       _bufferLocks.size(), particleBuffers.size());
  }
 
  // Balance buffers. This makes processing them with static scheduling quite efficient.
  // Also, if particles were not inserted in parallel, this enables us to process them in parallel now.
  // Cost is at max O(2N) worst O(N) per buffer collection and negligible compared to interacting them.
  auto cellToVec = [](auto &cell) -> std::vector<Particle_T> & { return cell._particles; };
  utils::ArrayUtils::balanceVectors(particleBuffers, cellToVec);
  utils::ArrayUtils::balanceVectors(haloParticleBuffers, cellToVec);
 
  // The following part performs the main remainder traversal. The actual calculation is done in 4 steps carried out
  // in three helper functions.
 
  // only activate time measurements if it will actually be logged
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  autopas::utils::Timer timerBufferContainer;
  autopas::utils::Timer timerPBufferPBuffer;
  autopas::utils::Timer timerPBufferHBuffer;
  autopas::utils::Timer timerBufferSoAConversion;
 
  timerBufferContainer.start();
#endif
  // steps 1 & 2.
  // particleBuffer with all particles close in container
  // and haloParticleBuffer with owned, close particles in container.
  // This is always AoS-based because the container particles are found with region iterators,
  // which don't have an SoA interface.
  remainderHelperBufferContainerAoS<newton3>(f, container, particleBuffers, haloParticleBuffers);
 
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  timerBufferContainer.stop();
  timerBufferSoAConversion.start();
#endif
  if (useSoA) {
    // All (halo-)buffer interactions shall happen vectorized, hence, load all buffer data into SoAs
    for (auto &buffer : particleBuffers) {
      f->SoALoader(buffer, buffer._particleSoABuffer, 0, /*skipSoAResize*/ false);
    }
    for (auto &buffer : haloParticleBuffers) {
      f->SoALoader(buffer, buffer._particleSoABuffer, 0, /*skipSoAResize*/ false);
    }
  }
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  timerBufferSoAConversion.stop();
  timerPBufferPBuffer.start();
#endif
 
  // step 3. particleBuffer with itself and all other buffers
  remainderHelperBufferBuffer<newton3>(f, particleBuffers, useSoA);
 
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  timerPBufferPBuffer.stop();
  timerPBufferHBuffer.start();
#endif
 
  // step 4. particleBuffer with haloParticleBuffer
  remainderHelperBufferHaloBuffer(f, particleBuffers, haloParticleBuffers, useSoA);
 
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  timerPBufferHBuffer.stop();
#endif
 
  // unpack particle SoAs. Halo data is not interesting
  if (useSoA) {
    for (auto &buffer : particleBuffers) {
      f->SoAExtractor(buffer, buffer._particleSoABuffer, 0);
    }
  }
 
  AutoPasLog(TRACE, "Timer Buffers <-> Container  (1+2): {}", timerBufferContainer.getTotalTime());
  AutoPasLog(TRACE, "Timer PBuffers<-> PBuffer    (  3): {}", timerPBufferPBuffer.getTotalTime());
  AutoPasLog(TRACE, "Timer PBuffers<-> HBuffer    (  4): {}", timerPBufferHBuffer.getTotalTime());
  AutoPasLog(TRACE, "Timer Load and extract SoA buffers: {}", timerBufferSoAConversion.getTotalTime());
 
  // Note: haloParticleBuffer with itself is NOT needed, as interactions between halo particles are unneeded!
}
 
template <class Particle_T>
template <bool newton3, class ContainerType, class PairwiseFunctor>
void LogicHandler<Particle_T>::remainderHelperBufferContainerAoS(
    PairwiseFunctor *f, ContainerType &container, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
    std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers) {
  using autopas::utils::ArrayUtils::static_cast_copy_array;
  using namespace autopas::utils::ArrayMath::literals;
 
  // Bunch of shorthands
  const auto cutoff = container.getCutoff();
  const auto interactionLength = container.getInteractionLength();
  const auto interactionLengthInv = 1. / interactionLength;
  const auto haloBoxMin = container.getBoxMin() - interactionLength;
  const auto totalBoxLengthInv = 1. / (container.getBoxMax() + interactionLength - haloBoxMin);
  const std::array<size_t, 3> spacialLocksPerDim{
      _spacialLocks.size(),
      _spacialLocks[0].size(),
      _spacialLocks[0][0].size(),
  };
 
  // Helper function to obtain the lock responsible for a given position.
  // Implemented as lambda because it can reuse a lot of information that is known in this context.
  const auto getSpacialLock = [&](const std::array<double, 3> &pos) -> std::mutex & {
    const auto posDistFromLowerCorner = pos - haloBoxMin;
    const auto relativePos = posDistFromLowerCorner * totalBoxLengthInv;
    // Lock coordinates are the position scaled by the number of locks
    const auto lockCoords =
        static_cast_copy_array<size_t>(static_cast_copy_array<double>(spacialLocksPerDim) * relativePos);
    return *_spacialLocks[lockCoords[0]][lockCoords[1]][lockCoords[2]];
  };
 
  // one halo and particle buffer pair per thread
  AUTOPAS_OPENMP(parallel for schedule(static, 1) default(shared))
  for (int bufferId = 0; bufferId < particleBuffers.size(); ++bufferId) {
    auto &particleBuffer = particleBuffers[bufferId];
    auto &haloParticleBuffer = haloParticleBuffers[bufferId];
    // 1. particleBuffer with all close particles in container
    for (auto &&p1 : particleBuffer) {
      const auto pos = p1.getR();
      const auto min = pos - cutoff;
      const auto max = pos + cutoff;
      container.forEachInRegion(
          [&](auto &p2) {
            if constexpr (newton3) {
              const std::lock_guard<std::mutex> lock(getSpacialLock(p2.getR()));
              f->AoSFunctor(p1, p2, true);
            } else {
              f->AoSFunctor(p1, p2, false);
              // no need to calculate force enacted on a halo
              if (not p2.isHalo()) {
                const std::lock_guard<std::mutex> lock(getSpacialLock(p2.getR()));
                f->AoSFunctor(p2, p1, false);
              }
            }
          },
          min, max, IteratorBehavior::ownedOrHalo);
    }
 
    // 2. haloParticleBuffer with owned, close particles in container
    for (auto &&p1halo : haloParticleBuffer) {
      const auto pos = p1halo.getR();
      const auto min = pos - cutoff;
      const auto max = pos + cutoff;
      container.forEachInRegion(
          [&](auto &p2) {
            // No need to apply anything to p1halo
            //   -> AoSFunctor(p1, p2, false) not needed as it neither adds force nor Upot (potential energy)
            //   -> newton3 argument needed for correct globals
            const std::lock_guard<std::mutex> lock(getSpacialLock(p2.getR()));
            f->AoSFunctor(p2, p1halo, newton3);
          },
          min, max, IteratorBehavior::owned);
    }
  }
}
 
template <class Particle_T>
template <bool newton3, class PairwiseFunctor>
void LogicHandler<Particle_T>::remainderHelperBufferBuffer(PairwiseFunctor *f,
                                                           std::vector<FullParticleCell<Particle_T>> &particleBuffers,
                                                           bool useSoA) {
  if (useSoA) {
    remainderHelperBufferBufferSoA<newton3>(f, particleBuffers);
  } else {
    remainderHelperBufferBufferAoS<newton3>(f, particleBuffers);
  }
}
 
template <class Particle_T>
template <bool newton3, class PairwiseFunctor>
void LogicHandler<Particle_T>::remainderHelperBufferBufferAoS(
    PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers) {
  // For all interactions between different buffers we turn newton3 always off,
  // which ensures that only one thread at a time is writing to a buffer.
  // This saves expensive locks.
 
  // We can not use collapse here without locks, otherwise races would occur.
  AUTOPAS_OPENMP(parallel for)
  for (size_t bufferIdxI = 0; bufferIdxI < particleBuffers.size(); ++bufferIdxI) {
    for (size_t bufferIdxJOffset = 0; bufferIdxJOffset < particleBuffers.size(); ++bufferIdxJOffset) {
      // Let each bufferI use a different starting point for bufferJ to minimize false sharing
      const auto bufferIdxJ = (bufferIdxI + bufferIdxJOffset) % particleBuffers.size();
 
      // interact the two buffers
      if (bufferIdxI == bufferIdxJ) {
        // CASE Same buffer
        // Only use Newton3 if it is allowed, and we are working on only one buffer. This avoids data races.
        const bool useNewton3 = newton3;
        auto &bufferRef = particleBuffers[bufferIdxI];
        const auto bufferSize = bufferRef.size();
        for (auto i = 0; i < bufferSize; ++i) {
          auto &p1 = bufferRef[i];
          // If Newton3 is disabled run over the whole buffer, otherwise only what is ahead
          for (auto j = useNewton3 ? i + 1 : 0; j < bufferSize; ++j) {
            if (i == j) {
              continue;
            }
            auto &p2 = bufferRef[j];
            f->AoSFunctor(p1, p2, useNewton3);
          }
        }
      } else {
        // CASE: Two buffers
        for (auto &p1 : particleBuffers[bufferIdxI]) {
          for (auto &p2 : particleBuffers[bufferIdxJ]) {
            f->AoSFunctor(p1, p2, false);
          }
        }
      }
    }
  }
}
 
template <class Particle_T>
template <bool newton3, class PairwiseFunctor>
void LogicHandler<Particle_T>::remainderHelperBufferBufferSoA(
    PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers) {
  // we can not use collapse here without locks, otherwise races would occur.
  AUTOPAS_OPENMP(parallel for)
  for (size_t i = 0; i < particleBuffers.size(); ++i) {
    for (size_t jj = 0; jj < particleBuffers.size(); ++jj) {
      auto *particleBufferSoAA = &particleBuffers[i]._particleSoABuffer;
      // instead of starting every (parallel) iteration i at j == 0 offset them by i to minimize waiting times at locks
      const auto j = (i + jj) % particleBuffers.size();
      if (i == j) {
        // For buffer interactions where bufferA == bufferB we can always enable newton3 if it is allowed.
        f->SoAFunctorSingle(*particleBufferSoAA, newton3);
      } else {
        // For all interactions between different buffers we turn newton3 always off,
        // which ensures that only one thread at a time is writing to a buffer. This saves expensive locks.
        auto *particleBufferSoAB = &particleBuffers[j]._particleSoABuffer;
        f->SoAFunctorPair(*particleBufferSoAA, *particleBufferSoAB, false);
      }
    }
  }
}
 
template <class Particle_T>
template <class PairwiseFunctor>
void LogicHandler<Particle_T>::remainderHelperBufferHaloBuffer(
    PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
    std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers, bool useSoA) {
  if (useSoA) {
    remainderHelperBufferHaloBufferSoA<PairwiseFunctor>(f, particleBuffers, haloParticleBuffers);
  } else {
    remainderHelperBufferHaloBufferAoS<PairwiseFunctor>(f, particleBuffers, haloParticleBuffers);
  }
}
 
template <class Particle_T>
template <class PairwiseFunctor>
void LogicHandler<Particle_T>::remainderHelperBufferHaloBufferAoS(
    PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
    std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers) {
  // Here, phase / color based parallelism turned out to be more efficient than tasks
  AUTOPAS_OPENMP(parallel)
  for (int interactionOffset = 0; interactionOffset < haloParticleBuffers.size(); ++interactionOffset) {
    AUTOPAS_OPENMP(for)
    for (size_t i = 0; i < particleBuffers.size(); ++i) {
      auto &particleBuffer = particleBuffers[i];
      auto &haloBuffer = haloParticleBuffers[(i + interactionOffset) % haloParticleBuffers.size()];
 
      for (auto &p1 : particleBuffer) {
        for (auto &p2 : haloBuffer) {
          f->AoSFunctor(p1, p2, false);
        }
      }
    }
  }
}
 
template <class Particle_T>
template <class PairwiseFunctor>
void LogicHandler<Particle_T>::remainderHelperBufferHaloBufferSoA(
    PairwiseFunctor *f, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
    std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers) {
  // Here, phase / color based parallelism turned out to be more efficient than tasks
  AUTOPAS_OPENMP(parallel)
  for (int interactionOffset = 0; interactionOffset < haloParticleBuffers.size(); ++interactionOffset) {
    AUTOPAS_OPENMP(for)
    for (size_t i = 0; i < particleBuffers.size(); ++i) {
      auto &particleBufferSoA = particleBuffers[i]._particleSoABuffer;
      auto &haloBufferSoA =
          haloParticleBuffers[(i + interactionOffset) % haloParticleBuffers.size()]._particleSoABuffer;
      f->SoAFunctorPair(particleBufferSoA, haloBufferSoA, false);
    }
  }
}
 
template <class Particle_T>
template <bool newton3, class ContainerType, class TriwiseFunctor>
void LogicHandler<Particle_T>::computeRemainderInteractions3B(
    TriwiseFunctor *f, ContainerType &container, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
    std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers) {
  // Vector to collect pointers to all buffer particles
  std::vector<Particle_T *> bufferParticles;
  const auto numOwnedBufferParticles = collectBufferParticles(bufferParticles, particleBuffers, haloParticleBuffers);
 
  // The following part performs the main remainder traversal.
 
  // only activate time measurements if it will actually be logged
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  autopas::utils::Timer timerBufferBufferBuffer;
  autopas::utils::Timer timerBufferBufferContainer;
  autopas::utils::Timer timerBufferContainerContainer;
  timerBufferBufferBuffer.start();
#endif
 
  // Step 1: Triwise interactions of all particles in the buffers (owned and halo)
  remainderHelper3bBufferBufferBufferAoS(bufferParticles, numOwnedBufferParticles, f);
 
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  timerBufferBufferBuffer.stop();
  timerBufferBufferContainer.start();
#endif
 
  // Step 2: Triwise interactions of 2 buffer particles with 1 container particle
  remainderHelper3bBufferBufferContainerAoS(bufferParticles, numOwnedBufferParticles, container, f);
 
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  timerBufferBufferContainer.stop();
  timerBufferContainerContainer.start();
#endif
 
  // Step 3: Triwise interactions of 1 buffer particle and 2 container particles
  remainderHelper3bBufferContainerContainerAoS<newton3>(bufferParticles, numOwnedBufferParticles, container, f);
 
#if SPDLOG_ACTIVE_LEVEL <= SPDLOG_LEVEL_TRACE
  timerBufferContainerContainer.stop();
#endif
 
  AutoPasLog(TRACE, "Timer Buffer <-> Buffer <-> Buffer       : {}", timerBufferBufferBuffer.getTotalTime());
  AutoPasLog(TRACE, "Timer Buffer <-> Buffer <-> Container    : {}", timerBufferBufferContainer.getTotalTime());
  AutoPasLog(TRACE, "Timer Buffer <-> Container <-> Container : {}", timerBufferContainerContainer.getTotalTime());
}
 
template <class Particle_T>
size_t LogicHandler<Particle_T>::collectBufferParticles(
    std::vector<Particle_T *> &bufferParticles, std::vector<FullParticleCell<Particle_T>> &particleBuffers,
    std::vector<FullParticleCell<Particle_T>> &haloParticleBuffers) {
  // Reserve the needed amount
  auto cellToVec = [](auto &cell) -> std::vector<Particle_T> & { return cell._particles; };
 
  const size_t numOwnedBufferParticles =
      std::transform_reduce(particleBuffers.begin(), particleBuffers.end(), 0, std::plus<>(),
                            [&](auto &vec) { return cellToVec(vec).size(); });
 
  const size_t numHaloBufferParticles =
      std::transform_reduce(haloParticleBuffers.begin(), haloParticleBuffers.end(), 0, std::plus<>(),
                            [&](auto &vec) { return cellToVec(vec).size(); });
 
  bufferParticles.reserve(numOwnedBufferParticles + numHaloBufferParticles);
 
  // Collect owned buffer particles
  for (auto &buffer : particleBuffers) {
    for (auto &particle : buffer._particles) {
      bufferParticles.push_back(&particle);
    }
  }
 
  // Collect halo buffer particles
  for (auto &buffer : haloParticleBuffers) {
    for (auto &particle : buffer._particles) {
      bufferParticles.push_back(&particle);
    }
  }
 
  return numOwnedBufferParticles;
}
 
template <class Particle_T>
template <class TriwiseFunctor>
void LogicHandler<Particle_T>::remainderHelper3bBufferBufferBufferAoS(const std::vector<Particle_T *> &bufferParticles,
                                                                      const size_t numOwnedBufferParticles,
                                                                      TriwiseFunctor *f) {
  AUTOPAS_OPENMP(parallel for)
  for (auto i = 0; i < numOwnedBufferParticles; ++i) {
    Particle_T &p1 = *bufferParticles[i];
 
    for (auto j = 0; j < bufferParticles.size(); ++j) {
      if (i == j) continue;
      Particle_T &p2 = *bufferParticles[j];
 
      for (auto k = j + 1; k < bufferParticles.size(); ++k) {
        if (k == i) continue;
        Particle_T &p3 = *bufferParticles[k];
 
        f->AoSFunctor(p1, p2, p3, false);
      }
    }
  }
}
 
template <class Particle_T>
template <class ContainerType, class TriwiseFunctor>
void LogicHandler<Particle_T>::remainderHelper3bBufferBufferContainerAoS(
    const std::vector<Particle_T *> &bufferParticles, const size_t numOwnedBufferParticles, ContainerType &container,
    TriwiseFunctor *f) {
  using autopas::utils::ArrayUtils::static_cast_copy_array;
  using namespace autopas::utils::ArrayMath::literals;
 
  const auto haloBoxMin = container.getBoxMin() - container.getInteractionLength();
  const auto interactionLengthInv = 1. / container.getInteractionLength();
  const double cutoff = container.getCutoff();
 
  AUTOPAS_OPENMP(parallel for)
  for (auto i = 0; i < bufferParticles.size(); ++i) {
    Particle_T &p1 = *bufferParticles[i];
    const auto pos = p1.getR();
    const auto min = pos - cutoff;
    const auto max = pos + cutoff;
 
    for (auto j = 0; j < bufferParticles.size(); ++j) {
      if (j == i) continue;
      Particle_T &p2 = *bufferParticles[j];
 
      container.forEachInRegion(
          [&](auto &p3) {
            const auto lockCoords = static_cast_copy_array<size_t>((p3.getR() - haloBoxMin) * interactionLengthInv);
            if (i < numOwnedBufferParticles) f->AoSFunctor(p1, p2, p3, false);
            if (!p3.isHalo() && i < j) {
              const std::lock_guard<std::mutex> lock(*_spacialLocks[lockCoords[0]][lockCoords[1]][lockCoords[2]]);
              f->AoSFunctor(p3, p1, p2, false);
            }
          },
          min, max, IteratorBehavior::ownedOrHalo);
    }
  }
}
 
template <class Particle_T>
template <bool newton3, class ContainerType, class TriwiseFunctor>
void LogicHandler<Particle_T>::remainderHelper3bBufferContainerContainerAoS(
    const std::vector<Particle_T *> &bufferParticles, const size_t numOwnedBufferParticles, ContainerType &container,
    TriwiseFunctor *f) {
  // Todo: parallelize without race conditions - https://github.com/AutoPas/AutoPas/issues/904
  using autopas::utils::ArrayUtils::static_cast_copy_array;
  using namespace autopas::utils::ArrayMath::literals;
 
  const double cutoff = container.getCutoff();
 
  for (auto i = 0; i < bufferParticles.size(); ++i) {
    Particle_T &p1 = *bufferParticles[i];
    const auto pos = p1.getR();
    const auto boxmin = pos - cutoff;
    const auto boxmax = pos + cutoff;
 
    auto p2Iter = container.getRegionIterator(
        boxmin, boxmax, IteratorBehavior::ownedOrHalo | IteratorBehavior::forceSequential, nullptr);
    for (; p2Iter.isValid(); ++p2Iter) {
      Particle_T &p2 = *p2Iter;
 
      auto p3Iter = p2Iter;
      ++p3Iter;
 
      for (; p3Iter.isValid(); ++p3Iter) {
        Particle_T &p3 = *p3Iter;
 
        if constexpr (newton3) {
          f->AoSFunctor(p1, p2, p3, true);
        } else {
          if (i < numOwnedBufferParticles) {
            f->AoSFunctor(p1, p2, p3, false);
          }
          if (p2.isOwned()) {
            f->AoSFunctor(p2, p1, p3, false);
          }
          if (p3.isOwned()) {
            f->AoSFunctor(p3, p1, p2, false);
          }
        }
      }
    }
  }
}
 
template <typename Particle_T>
template <class Functor>
std::tuple<Configuration, std::unique_ptr<TraversalInterface>, bool> LogicHandler<Particle_T>::selectConfiguration(
    Functor &functor, const InteractionTypeOption &interactionType) {
  bool stillTuning = false;
  Configuration configuration{};
  std::optional<std::unique_ptr<TraversalInterface>> traversalPtrOpt{};
  auto &autoTuner = *_autoTunerRefs[interactionType];
  // Todo: Make LiveInfo persistent between multiple functor calls in the same timestep (e.g. 2B + 3B)
  // https://github.com/AutoPas/AutoPas/issues/916
  LiveInfo info{};
 
  // if this iteration is not relevant take the same algorithm config as before.
  if (not functor.isRelevantForTuning()) {
    stillTuning = false;
    configuration = autoTuner.getCurrentConfig();
    // The currently selected container might not be compatible with the configuration for this functor. Check and
    // change if necessary. (see https://github.com/AutoPas/AutoPas/issues/871)
    if (_containerSelector.getCurrentContainer().getContainerType() != configuration.container) {
      _containerSelector.selectContainer(
          configuration.container,
          ContainerSelectorInfo(configuration.cellSizeFactor, _containerSelector.getCurrentContainer().getVerletSkin(),
                                _neighborListRebuildFrequency, _verletClusterSize, configuration.loadEstimator));
    }
    const auto &container = _containerSelector.getCurrentContainer();
    traversalPtrOpt = autopas::utils::withStaticCellType<Particle_T>(
        container.getParticleCellTypeEnum(), [&](const auto &particleCellDummy) -> decltype(traversalPtrOpt) {
          // Can't make this unique_ptr const otherwise we can't move it later.
          auto traversalPtr =
              TraversalSelector<std::decay_t<decltype(particleCellDummy)>>::template generateTraversal<Functor>(
                  configuration.traversal, functor, container.getTraversalSelectorInfo(), configuration.dataLayout,
                  configuration.newton3);
 
          // set sortingThreshold of the traversal if it can be casted to a CellTraversal and uses the CellFunctor
          if (auto *cellTraversalPtr =
                  dynamic_cast<autopas::CellTraversal<std::decay_t<decltype(particleCellDummy)>> *>(
                      traversalPtr.get())) {
            cellTraversalPtr->setSortingThreshold(_sortingThreshold);
          }
          if (traversalPtr->isApplicable()) {
            return std::optional{std::move(traversalPtr)};
          } else {
            return std::nullopt;
          }
        });
  } else {
    if (autoTuner.needsLiveInfo()) {
      // Gather Live Info
      utils::Timer timerGatherLiveInfo;
      timerGatherLiveInfo.start();
      auto particleIter = this->begin(IteratorBehavior::ownedOrHalo);
      info.gather(particleIter, _neighborListRebuildFrequency, getNumberOfParticlesOwned(), _logicHandlerInfo.boxMin,
                  _logicHandlerInfo.boxMax, _logicHandlerInfo.cutoff, _logicHandlerInfo.verletSkin);
      timerGatherLiveInfo.stop();
      AutoPasLog(DEBUG, "Gathering of LiveInfo took {} ns.", timerGatherLiveInfo.getTotalTime());
 
      autoTuner.receiveLiveInfo(info);
    }
 
    std::tie(configuration, stillTuning) = autoTuner.getNextConfig();
 
    // loop as long as we don't get a valid configuration
    bool rejectIndefinitely = false;
    while (true) {
      // applicability check also sets the container
      std::tie(traversalPtrOpt, rejectIndefinitely) =
          isConfigurationApplicable(configuration, functor, interactionType);
      if (traversalPtrOpt.has_value()) {
        break;
      }
      // if no config is left after rejecting this one an exception is thrown here.
      std::tie(configuration, stillTuning) = autoTuner.rejectConfig(configuration, rejectIndefinitely);
    }
  }
 
#ifdef AUTOPAS_LOG_LIVEINFO
  // if live info has not been gathered yet, gather it now and log it
  if (info.get().empty()) {
    auto particleIter = this->begin(IteratorBehavior::ownedOrHalo);
    info.gather(particleIter, _neighborListRebuildFrequency, getNumberOfParticlesOwned(), _logicHandlerInfo.boxMin,
                _logicHandlerInfo.boxMax, _logicHandlerInfo.cutoff, _logicHandlerInfo.verletSkin);
  }
  _liveInfoLogger.logLiveInfo(info, _iteration);
#endif
 
  return {configuration, std::move(traversalPtrOpt.value()), stillTuning};
}
 
template <typename Particle_T>
template <class Functor>
bool LogicHandler<Particle_T>::computeInteractionsPipeline(Functor *functor,
                                                           const InteractionTypeOption &interactionType) {
  if (not _interactionTypes.count(interactionType)) {
    autopas::utils::ExceptionHandler::exception(
        "LogicHandler::computeInteractionsPipeline(): AutPas was not initialized for the Functor's interactions type: "
        "{}.",
        interactionType);
  }
  utils::Timer tuningTimer;
  tuningTimer.start();
  const auto [configuration, traversalPtr, stillTuning] = selectConfiguration(*functor, interactionType);
  tuningTimer.stop();
  auto &autoTuner = *_autoTunerRefs[interactionType];
  autoTuner.logTuningResult(stillTuning, tuningTimer.getTotalTime());
 
  // Retrieve rebuild info before calling `computeInteractions()` to get the correct value.
  const auto rebuildIteration = not _neighborListsAreValid.load(std::memory_order_relaxed);
 
  AutoPasLog(DEBUG, "Iterating with configuration: {} tuning: {}", configuration.toString(), stillTuning);
  const IterationMeasurements measurements = computeInteractions(*functor, *traversalPtr);
 
  auto bufferSizeListing = [](const auto &buffers) -> std::string {
    std::stringstream ss;
    size_t sum = 0;
    for (const auto &buffer : buffers) {
      ss << buffer.size() << ", ";
      sum += buffer.size();
    }
    ss << " Total: " << sum;
    return ss.str();
  };
  AutoPasLog(TRACE, "particleBuffer     size : {}", bufferSizeListing(_particleBuffer));
  AutoPasLog(TRACE, "haloParticleBuffer size : {}", bufferSizeListing(_haloParticleBuffer));
  AutoPasLog(DEBUG, "Type of interaction :          {}", interactionType.to_string());
  AutoPasLog(DEBUG, "Container::computeInteractions took {} ns", measurements.timeComputeInteractions);
  AutoPasLog(DEBUG, "RemainderTraversal             took {} ns", measurements.timeRemainderTraversal);
  AutoPasLog(DEBUG, "RebuildNeighborLists           took {} ns", measurements.timeRebuild);
  AutoPasLog(DEBUG, "AutoPas::computeInteractions   took {} ns", measurements.timeTotal);
  if (measurements.energyMeasurementsPossible) {
    AutoPasLog(DEBUG, "Energy Consumption: Watts: {} Joules: {} Seconds: {}", measurements.energyWatts,
               measurements.energyJoules, measurements.energyDeltaT);
  }
  _iterationLogger.logIteration(configuration, _iteration, functor->getName(), stillTuning, tuningTimer.getTotalTime(),
                                measurements);
 
  _flopLogger.logIteration(_iteration, functor->getNumFLOPs(), functor->getHitRate());
 
  // if this was a major iteration add measurements
  if (functor->isRelevantForTuning()) {
    if (stillTuning) {
      // choose the metric of interest
      const auto measurement = [&]() {
        switch (autoTuner.getTuningMetric()) {
          case TuningMetricOption::time:
            return measurements.timeTotal;
          case TuningMetricOption::energy:
            return measurements.energyTotal;
          default:
            autopas::utils::ExceptionHandler::exception(
                "LogicHandler::computeInteractionsPipeline(): Unknown tuning metric.");
            return 0l;
        }
      }();
      autoTuner.addMeasurement(measurement, rebuildIteration);
    }
  } else {
    AutoPasLog(TRACE, "Skipping adding of sample because functor is not marked relevant.");
  }
  ++_functorCalls;
  return stillTuning;
}
 
template <typename Particle_T>
template <class Functor>
std::tuple<std::optional<std::unique_ptr<TraversalInterface>>, bool>
LogicHandler<Particle_T>::isConfigurationApplicable(const Configuration &conf, Functor &functor,
                                                    const InteractionTypeOption &interactionType) {
  // Check if the container supports the traversal
  const auto allContainerTraversals =
      compatibleTraversals::allCompatibleTraversals(conf.container, conf.interactionType);
  if (allContainerTraversals.find(conf.traversal) == allContainerTraversals.end()) {
    AutoPasLog(WARN, "Configuration rejected: Container {} does not support the traversal {}.", conf.container,
               conf.traversal);
    return {std::nullopt, true};
  }
 
  // Check if the required Newton 3 mode is supported by the functor
  if ((conf.newton3 == Newton3Option::enabled and not functor.allowsNewton3()) or
      (conf.newton3 == Newton3Option::disabled and not functor.allowsNonNewton3())) {
    AutoPasLog(DEBUG, "Configuration rejected: The functor doesn't support Newton 3 {}!", conf.newton3);
    return {std::nullopt, true};
  }
 
  // Check if the traversal is applicable to the current state of the container
  _containerSelector.selectContainer(
      conf.container,
      ContainerSelectorInfo(conf.cellSizeFactor, _containerSelector.getCurrentContainer().getVerletSkin(),
                            _neighborListRebuildFrequency, _verletClusterSize, conf.loadEstimator));
  const auto &container = _containerSelector.getCurrentContainer();
  const auto traversalInfo = container.getTraversalSelectorInfo();
 
  auto traversalPtrOpt = autopas::utils::withStaticCellType<Particle_T>(
      container.getParticleCellTypeEnum(),
      [&](const auto &particleCellDummy) -> std::optional<std::unique_ptr<TraversalInterface>> {
        // Can't make this unique_ptr const otherwise we can't move it later.
        auto traversalPtr =
            TraversalSelector<std::decay_t<decltype(particleCellDummy)>>::template generateTraversal<Functor>(
                conf.traversal, functor, traversalInfo, conf.dataLayout, conf.newton3);
 
        // set sortingThreshold of the traversal if it can be cast to a CellTraversal and uses the CellFunctor
        if (auto *cellTraversalPtr =
                dynamic_cast<autopas::CellTraversal<std::decay_t<decltype(particleCellDummy)>> *>(traversalPtr.get())) {
          cellTraversalPtr->setSortingThreshold(_sortingThreshold);
        }
        if (traversalPtr->isApplicable()) {
          return std::optional{std::move(traversalPtr)};
        } else {
          return std::nullopt;
        }
      });
  return {std::move(traversalPtrOpt), false};
}
 
}  // namespace autopas