MultipoleSum.cpp

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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).
 */
 
#include "applications/staticProps/MultipoleSum.hpp"
 
#include <fstream>
 
#include "io/DumpReader.hpp"
#include "primitives/Atom.hpp"
#include "primitives/Molecule.hpp"
#include "types/MultipoleAdapter.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  MultipoleSum::MultipoleSum(SimInfo* info, const std::string& filename,
                             const std::string& sele1, RealType rmax,
                             int nrbins) :
      StaticAnalyser(info, filename, nrbins),
      nRBins_(nrbins), rMax_(rmax), selectionScript1_(sele1), seleMan1_(info),
      evaluator1_(info) {
    setOutputName(getPrefix(filename) + ".multipoleSum");
 
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
 
    aveDlength_.clear();
    aveDlength_.resize(nRBins_, 0.0);
    aveQlength_.clear();
    aveQlength_.resize(nRBins_, 0.0);
    aveDcount_.clear();
    aveDcount_.resize(nRBins_, 0.0);
    aveQcount_.clear();
    aveQcount_.resize(nRBins_, 0.0);
    aveDproj_.clear();
    aveDproj_.resize(nRBins_, 0.0);
    deltaR_ = rMax_ / nRBins_;
  }
 
  void MultipoleSum::process() {
    Molecule* mol;
    SimInfo::MoleculeIterator miter;
    vector<Atom*>::iterator aiter;
    Atom* atom;
    StuntDouble* sd1;
    int i1;
    Vector3d pos1;
    Vector3d ri;
    std::vector<RealType> dipoleHist(nRBins_, 0.0);
    std::vector<RealType> qpoleHist(nRBins_, 0.0);
    std::vector<int> lengthCount(nRBins_, 0);
    std::vector<Vector3d> totalDipole;
    std::vector<Mat3x3d> totalQpole;
    std::vector<int> dipoleCount;
    std::vector<int> qpoleCount;
    std::vector<RealType> dipoleProjection;
    Vector3d dipole;
    Mat3x3d qpole;
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
 
    for (int i = 0; i < nFrames; i += step_) {
      reader.readFrame(i);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
 
      if (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
 
      for (sd1 = seleMan1_.beginSelected(i1); sd1 != NULL;
           sd1 = seleMan1_.nextSelected(i1)) {
        pos1 = sd1->getPos();
 
        totalDipole.clear();
        totalDipole.resize(nRBins_, V3Zero);
        dipoleCount.clear();
        dipoleCount.resize(nRBins_, 0);
        totalQpole.clear();
        totalQpole.resize(nRBins_, M3Zero);
        qpoleCount.clear();
        qpoleCount.resize(nRBins_, 0);
        dipoleProjection.clear();
        dipoleProjection.resize(nRBins_, 0.0);
 
        for (mol = info_->beginMolecule(miter); mol != NULL;
             mol = info_->nextMolecule(miter)) {
          for (atom = mol->beginAtom(aiter); atom != NULL;
               atom = mol->nextAtom(aiter)) {
            // ri is vector difference between central site and this atom:
            ri = atom->getPos() - pos1;
 
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(ri);
 
            dipole               = V3Zero;
            qpole                = M3Zero;
            AtomType* atype2     = atom->getAtomType();
            MultipoleAdapter ma2 = MultipoleAdapter(atype2);
 
            if (ma2.isDipole()) dipole = atom->getDipole();
            if (ma2.isQuadrupole()) qpole = atom->getQuadrupole();
 
            RealType distance = ri.length();
            std::size_t bin   = int(distance / deltaR_);
            // this multipole is contained within the cutoff spheres that are
            // larger than the bin:
            if (bin < nRBins_) {
              for (std::size_t j = bin; j < nRBins_; j++) {
                totalDipole[j] += dipole;
                dipoleCount[j]++;
                totalQpole[j] += qpole;
                qpoleCount[j]++;
              }
            }
          }
        }
        Vector3d myDipole = sd1->getDipole();
 
        for (std::size_t j = 0; j < nRBins_; j++) {
          RealType myProjection =
              dot(myDipole, totalDipole[j]) / myDipole.length();
 
          RealType dipoleLength = totalDipole[j].length();
          RealType Qtrace       = totalQpole[j].trace();
          RealType Qddot        = doubleDot(totalQpole[j], totalQpole[j]);
          RealType qpoleLength  = 2.0 * (3.0 * Qddot - Qtrace * Qtrace);
          dipoleHist[j] += dipoleLength;
          qpoleHist[j] += qpoleLength;
          aveDcount_[j] += dipoleCount[j];
          aveQcount_[j] += qpoleCount[j];
          lengthCount[j] += 1;
          dipoleProjection[j] += myProjection;
        }
      }
    }
 
    int nSelected = seleMan1_.getSelectionCount();
    for (std::size_t j = 0; j < nRBins_; j++) {
      if (lengthCount[j] > 0) {
        aveDlength_[j] = dipoleHist[j] / RealType(lengthCount[j]);
        aveQlength_[j] = qpoleHist[j] / RealType(lengthCount[j]);
        aveDcount_[j] /= RealType(nSelected);
        aveQcount_[j] /= RealType(nSelected);
        aveDproj_[j] = dipoleProjection[j] / RealType(lengthCount[j]);
      } else {
        aveDlength_[j] = 0.0;
        aveQlength_[j] = 0.0;
        aveDcount_[j]  = 0.0;
        aveQcount_[j]  = 0.0;
        aveDproj_[j]   = 0.0;
      }
    }
    writeOut();
  }
 
  void MultipoleSum::writeOut() {
    ofstream os(getOutputFileName().c_str());
    os << "#multipole sum\n";
    os << "#selection1: (" << selectionScript1_ << ")\t";
    os << "#r\taveDlength\taveDdensity\taveDproj\taveQlength\taveQdensity\n";
 
    for (std::size_t i = 0; i < nRBins_; ++i) {
      RealType r = deltaR_ * i;
      os << r << "\t" << aveDlength_[i] << "\t"
         << aveDlength_[i] / aveDcount_[i] << "\t" << aveDproj_[i] << "\t"
         << aveQlength_[i] << "\t" << aveQlength_[i] / aveQcount_[i] << "\n";
    }
    os.close();
  }
}  // namespace OpenMD