CutoffGroup.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 PRIMITIVES_CUTOFFGROUP_HPP
 
#define PRIMITIVES_CUTOFFGROUP_HPP
 
#include "math/Vector3.hpp"
#include "primitives/Atom.hpp"
 
namespace OpenMD {
  class CutoffGroup {
  public:
    CutoffGroup() : globalIndex(-1), localIndex_(-1), snapshotMan_(NULL) {
      storage_      = &Snapshot::cgData;
      haveTotalMass = false;
      totalMass     = 0.0;
    }
 
    /**
     * Sets the Snapshot Manager of this cutoffGroup
     */
    void setSnapshotManager(SnapshotManager* sman) { snapshotMan_ = sman; }
 
    void addAtom(Atom* atom) { cutoffAtomList.push_back(atom); }
 
    Atom* beginAtom(std::vector<Atom*>::iterator& i) {
      i = cutoffAtomList.begin();
      return i != cutoffAtomList.end() ? *i : NULL;
    }
 
    Atom* nextAtom(std::vector<Atom*>::iterator& i) {
      i++;
      return i != cutoffAtomList.end() ? *i : NULL;
    }
 
    std::vector<Atom*> getAtoms() { return cutoffAtomList; }
    RealType getMass() {
      if (!haveTotalMass) {
        totalMass = 0.0;
 
        std::vector<Atom*>::iterator i;
        for (Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
          RealType mass = atom->getMass();
          totalMass += mass;
        }
 
        haveTotalMass = true;
      }
 
      return totalMass;
    }
 
    void updateCOM() {
      DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
      bool needsVel     = false;
      if (data.getStorageLayout() & DataStorage::dslVelocity) needsVel = true;
 
      if (cutoffAtomList.size() == 1) {
        data.position[localIndex_] = cutoffAtomList[0]->getPos();
        if (needsVel) data.velocity[localIndex_] = cutoffAtomList[0]->getVel();
      } else {
        std::vector<Atom*>::iterator i;
        Atom* atom;
        RealType totalMass         = getMass();
        data.position[localIndex_] = V3Zero;
        if (needsVel) data.velocity[localIndex_] = V3Zero;
 
        for (atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
          data.position[localIndex_] += atom->getMass() * atom->getPos();
          if (needsVel)
            data.velocity[localIndex_] += atom->getMass() * atom->getVel();
        }
        data.position[localIndex_] /= totalMass;
        if (needsVel) data.velocity[localIndex_] /= totalMass;
      }
    }
 
    Vector3d getPos() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_)
          .position[localIndex_];
    }
    Vector3d getVel() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_)
          .velocity[localIndex_];
    }
 
    size_t getNumAtom() { return cutoffAtomList.size(); }
 
    int getGlobalIndex() { return globalIndex; }
 
    void setGlobalIndex(int id) { this->globalIndex = id; }
 
    /**
     * Returns the local index of this cutoffGroup
     * @return the local index of this cutoffGroup
     */
    int getLocalIndex() { return localIndex_; }
 
    /**
     * Sets the local index of this cutoffGroup
     * @param index new index to be set
     */
    void setLocalIndex(int index) { localIndex_ = index; }
 
  private:
    std::vector<Atom*> cutoffAtomList;
    bool haveTotalMass;
    RealType totalMass;
    int globalIndex;
 
    int localIndex_;
    DataStoragePointer storage_;
    SnapshotManager* snapshotMan_;
  };
}  // namespace OpenMD
 
#endif  // PRIMITIVES_CUTOFFGROUP_HPP