IndexFinder.cpp

/*
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 * modification, are permitted provided that the following conditions are met:
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 *    this software without specific prior written permission.
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 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * 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).
 */
 
#include "selection/IndexFinder.hpp"
 
#ifdef IS_MPI
#include <mpi.h>
#endif
 
#include "primitives/Molecule.hpp"
 
namespace OpenMD {
 
  IndexFinder::IndexFinder(SimInfo* info) : info_(info) {
    nObjects_.push_back(info_->getNGlobalAtoms() +
                        info_->getNGlobalRigidBodies());
    nObjects_.push_back(info_->getNGlobalBonds());
    nObjects_.push_back(info_->getNGlobalBends());
    nObjects_.push_back(info_->getNGlobalTorsions());
    nObjects_.push_back(info_->getNGlobalInversions());
    nObjects_.push_back(info_->getNGlobalMolecules());
 
    selectionSets_.resize(info_->getNGlobalMolecules());
    init();
  }
 
  void IndexFinder::init() {
    SimInfo::MoleculeIterator mi;
    Molecule::AtomIterator ai;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;
    Molecule::BendIterator bendIter;
    Molecule::TorsionIterator torsionIter;
    Molecule::InversionIterator inversionIter;
 
    Molecule* mol;
    Atom* atom;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;
 
    for (mol = info_->beginMolecule(mi); mol != NULL;
         mol = info_->nextMolecule(mi)) {
      SelectionSet ss(nObjects_);
 
      ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
 
      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
      }
      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
           rb = mol->nextRigidBody(rbIter)) {
        ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
      }
      for (bond = mol->beginBond(bondIter); bond != NULL;
           bond = mol->nextBond(bondIter)) {
        ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
      }
      for (bend = mol->beginBend(bendIter); bend != NULL;
           bend = mol->nextBend(bendIter)) {
        ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
      }
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
           torsion = mol->nextTorsion(torsionIter)) {
        ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
      }
      for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
           inversion = mol->nextInversion(inversionIter)) {
        ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
      }
 
      selectionSets_[mol->getGlobalIndex()] = ss;
    }
  }
 
  SelectionSet IndexFinder::find(int molIndex) {
#ifdef IS_MPI
    int proc;
    int worldRank;
    MPI_Comm_rank(MPI_COMM_WORLD, &worldRank);
    proc = info_->getMolToProc(molIndex);
 
    if (proc == worldRank) {
#endif
      return selectionSets_[molIndex];
#ifdef IS_MPI
    } else {
      return SelectionSet(nObjects_);
    }
#endif
  }
 
  SelectionSet IndexFinder::find(int begMolIndex, int endMolIndex) {
    SelectionSet ss(nObjects_);
 
#ifdef IS_MPI
    int proc;
    int worldRank;
    MPI_Comm_rank(MPI_COMM_WORLD, &worldRank);
#endif
 
    for (int i = begMolIndex; i < endMolIndex; ++i) {
#ifdef IS_MPI
      proc = info_->getMolToProc(i);
 
      if (proc == worldRank) {
#endif
        ss |= selectionSets_[i];
#ifdef IS_MPI
      }
#endif
    }
    return ss;
  }
}  // namespace OpenMD