BlockSnapshotManager.hpp

/*
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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#ifndef BRAINS_BLOCKSNAPSHOTMANAGER_HPP
#define BRAINS_BLOCKSNAPSHOTMANAGER_HPP
 
#include <vector>
 
#include "brains/SnapshotManager.hpp"
 
namespace OpenMD {
 
  class SimInfo;
  class DumpReader;
 
  using SnapshotBlock = std::pair<int, int>;
 
  /**
   * @class BlockSnapshotManager
   * @todo document
   */
  class BlockSnapshotManager : public SnapshotManager {
  public:
    BlockSnapshotManager(SimInfo* info, const std::string& filename,
                         int atomStorageLayout, int rigidBodyStorageLayout,
                         int cutoffGroupStorageLayout, long long int memSize,
                         int blockCapacity = 2);
    ~BlockSnapshotManager();
 
    virtual Snapshot* getSnapshot(int id);
 
    /** Returns number of snapshot blocks in this BlockSnapshotManager*/
    size_t getNBlocks() { return blocks_.size(); }
 
    SnapshotBlock getSnapshotBlock(int block) { return blocks_.at(block); }
 
    int getNActiveBlocks();
 
    void needCOMprops(bool ncp);
 
    bool isBlockActive(int block) {
      return findActiveBlock(block) != activeBlocks_.end() ? true : false;
    }
 
    bool loadBlock(int block);
 
    bool unloadBlock(int block);
 
    std::vector<int> getActiveBlocks();
 
    int getBlockCapacity() { return blockCapacity_; }
 
    int getNFrames();
 
  private:
    std::vector<int>::iterator findActiveBlock(int block) {
      return std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
    }
 
    bool hasZeroRefBlock();
 
    int getFirstZeroRefBlock();
 
    void internalLoad(int block);
    void internalUnload(int block);
    Snapshot* loadFrame(int frame);
 
    int blockCapacity_;
    long long int memSize_;
 
    std::vector<Snapshot*> snapshots_;
    std::vector<SnapshotBlock> blocks_;
    std::vector<int> activeBlocks_;
    std::vector<int> activeRefCount_;
 
    int nAtoms_;
    int nRigidBodies_;
    int nCutoffGroups_;
    bool usePBC_;
 
    DumpReader* reader_;
    int nframes_;
    int nSnapshotPerBlock_;
  };
}  // namespace OpenMD
 
#endif