VerletLists.h

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#pragma once
 
#include "VerletListHelpers.h"
#include "autopas/containers/CellBasedParticleContainer.h"
#include "autopas/containers/linkedCells/LinkedCells.h"
#include "autopas/containers/linkedCells/traversals/LCC08Traversal.h"
#include "autopas/containers/verletListsCellBased/VerletListsLinkedBase.h"
#include "autopas/containers/verletListsCellBased/verletLists/traversals/VLListIterationTraversal.h"
#include "autopas/containers/verletListsCellBased/verletLists/traversals/VLTraversalInterface.h"
#include "autopas/options/DataLayoutOption.h"
#include "autopas/utils/ArrayMath.h"
#include "autopas/utils/StaticBoolSelector.h"
 
namespace autopas {
 
template <class Particle_T>
class VerletLists : public VerletListsLinkedBase<Particle_T> {
  using LinkedParticleCell = FullParticleCell<Particle_T>;
 
 public:
  enum BuildVerletListType {
    VerletAoS,
    VerletSoA,
  };
 
  VerletLists(const std::array<double, 3> &boxMin, const std::array<double, 3> &boxMax, const double cutoff,
              const double skin, const unsigned int rebuildFrequency,
              const BuildVerletListType buildVerletListType = BuildVerletListType::VerletSoA,
              const double cellSizeFactor = 1.0)
      : VerletListsLinkedBase<Particle_T>(boxMin, boxMax, cutoff, skin, rebuildFrequency,
                                          compatibleTraversals::allVLCompatibleTraversals(), cellSizeFactor),
        _buildVerletListType(buildVerletListType) {}
 
  [[nodiscard]] ContainerOption getContainerType() const override { return ContainerOption::verletLists; }
 
  void computeInteractions(TraversalInterface *traversal) override {
    // Check if traversal is allowed for this container and give it the data it needs.
    auto *verletTraversalInterface = dynamic_cast<VLTraversalInterface<LinkedParticleCell> *>(traversal);
    if (verletTraversalInterface) {
      verletTraversalInterface->setCellsAndNeighborLists(this->_linkedCells.getCells(), _aosNeighborLists,
                                                         _soaNeighborLists);
    } else {
      autopas::utils::ExceptionHandler::exception(
          "trying to use a traversal of wrong type in VerletLists::computeInteractions");
    }
 
    traversal->initTraversal();
    traversal->traverseParticles();
    traversal->endTraversal();
  }
 
  typename VerletListHelpers<Particle_T>::NeighborListAoSType &getVerletListsAoS() { return _aosNeighborLists; }
 
  void rebuildNeighborLists(TraversalInterface *traversal) override {
    this->_verletBuiltNewton3 = traversal->getUseNewton3();
    this->updateVerletListsAoS(traversal->getUseNewton3());
    // the neighbor list is now valid
    this->_neighborListIsValid.store(true, std::memory_order_relaxed);
 
    if (not _soaListIsValid and traversal->getDataLayout() == DataLayoutOption::soa) {
      // only do this if we need it, i.e., if we are using soa!
      generateSoAListFromAoSVerletLists();
    }
  }
 
 protected:
  virtual void updateVerletListsAoS(bool useNewton3) {
    generateAoSNeighborLists();
    typename VerletListHelpers<Particle_T>::VerletListGeneratorFunctor f(_aosNeighborLists,
                                                                         this->getCutoff() + this->getVerletSkin());
 
    DataLayoutOption dataLayout;
    if (_buildVerletListType == BuildVerletListType::VerletAoS) {
      dataLayout = DataLayoutOption::aos;
    } else if (_buildVerletListType == BuildVerletListType::VerletSoA) {
      dataLayout = DataLayoutOption::soa;
    } else {
      utils::ExceptionHandler::exception("VerletLists::updateVerletListsAoS(): unsupported BuildVerletListType: {}",
                                         _buildVerletListType);
    }
    auto traversal =
        LCC08Traversal<LinkedParticleCell, typename VerletListHelpers<Particle_T>::VerletListGeneratorFunctor>(
            this->_linkedCells.getCellBlock().getCellsPerDimensionWithHalo(), &f, this->getInteractionLength(),
            this->_linkedCells.getCellBlock().getCellLength(), dataLayout, useNewton3);
    this->_linkedCells.computeInteractions(&traversal);
 
    _soaListIsValid = false;
  }
 
  size_t generateAoSNeighborLists() {
    size_t numParticles = 0;
    _aosNeighborLists.clear();
    // DON'T simply parallelize this loop!!! this needs modifications if you want to parallelize it!
    // We have to iterate also over dummy particles here to ensure a correct size of the arrays.
    for (auto iter = this->begin(IteratorBehavior::ownedOrHaloOrDummy); iter.isValid(); ++iter, ++numParticles) {
      // create the verlet list entries for all particles
      _aosNeighborLists[&(*iter)];
    }
 
    return numParticles;
  }
 
  void generateSoAListFromAoSVerletLists() {
    // resize the list to the size of the aos neighborlist
    _soaNeighborLists.resize(_aosNeighborLists.size());
    // clear the aos 2 soa map
    _particlePtr2indexMap.clear();
 
    _particlePtr2indexMap.reserve(_aosNeighborLists.size());
    size_t index = 0;
 
    // Here we have to iterate over all particles, as particles might be later on marked for deletion, and we cannot
    // differentiate them from particles already marked for deletion.
    for (auto iter = this->begin(IteratorBehavior::ownedOrHaloOrDummy); iter.isValid(); ++iter, ++index) {
      // set the map
      _particlePtr2indexMap[&(*iter)] = index;
    }
    size_t accumulatedListSize = 0;
    for (const auto &[particlePtr, neighborPtrVector] : _aosNeighborLists) {
      accumulatedListSize += neighborPtrVector.size();
      size_t i_id = _particlePtr2indexMap[particlePtr];
      // each soa neighbor list should be of the same size as for aos
      _soaNeighborLists[i_id].resize(neighborPtrVector.size());
      size_t j = 0;
      for (auto &neighborPtr : neighborPtrVector) {
        _soaNeighborLists[i_id][j] = _particlePtr2indexMap[neighborPtr];
        j++;
      }
    }
 
    AutoPasLog(DEBUG,
               "VerletLists::generateSoAListFromAoSVerletLists: average verlet list "
               "size is {}",
               static_cast<double>(accumulatedListSize) / _aosNeighborLists.size());
    _soaListIsValid = true;
  }
 
 private:
  typename VerletListHelpers<Particle_T>::NeighborListAoSType _aosNeighborLists;
 
  std::unordered_map<const Particle_T *, size_t> _particlePtr2indexMap;
 
  std::vector<std::vector<size_t, autopas::AlignedAllocator<size_t>>> _soaNeighborLists;
 
  bool _soaListIsValid{false};
 
  BuildVerletListType _buildVerletListType;
};
 
}  // namespace autopas