TetrahedralityHBMatrix.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/TetrahedralityHBMatrix.hpp"
 
#include <vector>
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/Constants.hpp"
#include "utils/Revision.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  TetrahedralityHBMatrix::TetrahedralityHBMatrix(
      SimInfo* info, const std::string& filename, const std::string& sele,
      double rCut, double OOcut, double thetaCut, double OHcut, int nbins) :
      StaticAnalyser(info, filename, nbins),
      selectionScript_(sele), seleMan_(info), evaluator_(info), rCut_(rCut),
      OOCut_(OOcut), thetaCut_(thetaCut), OHCut_(OHcut) {
    setAnalysisType("Tetrahedrality HBond Matrix");
    setOutputName(getPrefix(filename) + ".hbq");
 
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    Q_histogram_.resize(nBins_);
 
    for (unsigned int i = 0; i < nBins_; i++) {
      Q_histogram_[i].resize(nBins_);
    }
 
    // Q can take values from 0 to 1
 
    MinQ_   = 0.0;
    MaxQ_   = 1.1;
    deltaQ_ = (MaxQ_ - MinQ_) / nBins_;
 
    std::stringstream params;
    params << " rCut = " << rCut_ << ", OOcut = " << OOCut_
           << ", thetacut = " << thetaCut_ << ", OHcut = " << OHCut_
           << ", nbins = " << nBins_ << ", deltaQ = " << deltaQ_;
    const std::string paramString = params.str();
    setParameterString(paramString);
  }
 
  void TetrahedralityHBMatrix::initializeHistogram() {
    for (unsigned int i = 0; i < nBins_; i++) {
      std::fill(Q_histogram_[i].begin(), Q_histogram_[i].end(), 0);
    }
  }
 
  void TetrahedralityHBMatrix::process() {
    Molecule* mol1;
    Molecule* mol2;
    Molecule* moli;
    Molecule* molj;
    SimInfo::MoleculeIterator mi;
    Vector3d vec;
    Vector3d ri, rj, rk, rik, rkj, dposition, tposition;
    RealType r, cospsi;
    std::vector<Molecule::HBondDonor*>::iterator hbdi;
    Molecule::HBondDonor* hbd;
    std::vector<Atom*>::iterator hbai;
    Atom* hba;
    Vector3d dPos;
    Vector3d aPos;
    Vector3d hPos;
    Vector3d DH;
    Vector3d DA;
    Vector3d HA;
    Vector3d uDA;
    RealType DAdist, DHdist, HAdist, theta, ctheta, Qk, q1, q2;
    std::vector<std::pair<RealType, Molecule*>> myNeighbors;
    int myIndex, ii, jj, index1, index2;
 
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
 
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
 
      Q_.clear();
      Q_.resize(info_->getNGlobalMolecules(), 0.0);
 
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
 
      // outer loop is over the selected Molecules:
 
      for (mol1 = seleMan_.beginSelectedMolecule(ii); mol1 != NULL;
           mol1 = seleMan_.nextSelectedMolecule(ii)) {
        myIndex = mol1->getGlobalIndex();
 
        Qk = 1.0;
 
        myNeighbors.clear();
 
        // inner loop is over all Molecules in the system:
 
        for (mol2 = info_->beginMolecule(mi); mol2 != NULL;
             mol2 = info_->nextMolecule(mi)) {
          if (mol2->getGlobalIndex() != myIndex) {
            vec = mol1->getCom() - mol2->getCom();
 
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(vec);
 
            r = vec.length();
 
            // Check to see if neighbor is in bond cutoff
 
            if (r < rCut_) { myNeighbors.push_back(std::make_pair(r, mol2)); }
          }
        }
 
        // Sort the vector using predicate and std::sort
        std::sort(myNeighbors.begin(), myNeighbors.end());
 
        // Use only the 4 closest neighbors to do the rest of the work:
        // int nbors =  myNeighbors.size()> 4 ? 4 : myNeighbors.size();
        int nbors = myNeighbors.size();
        int nang  = int(0.5 * (nbors * (nbors - 1)));
 
        rk = mol1->getCom();
 
        for (int i = 0; i < nbors - 1; i++) {
          moli = myNeighbors[i].second;
          ri   = moli->getCom();
          rik  = rk - ri;
          if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rik);
 
          rik.normalize();
 
          for (int j = i + 1; j < nbors; j++) {
            molj = myNeighbors[j].second;
            rj   = molj->getCom();
            rkj  = rk - rj;
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(rkj);
            rkj.normalize();
 
            cospsi = dot(rik, rkj);
 
            // Calculates scaled Qk for each molecule using calculated
            // angles from the actual number of nearest neighbors.
            Qk = Qk - (pow(cospsi + 1.0 / 3.0, 2) * 9.0 / (4.0 * nang));
          }
        }
 
        if (nang > 0) { Q_[myIndex] = Qk; }
      }
      // Now to scan for histogram:
 
      for (mol1 = seleMan_.beginSelectedMolecule(ii); mol1 != NULL;
           mol1 = seleMan_.nextSelectedMolecule(ii)) {
        for (mol2 = seleMan_.beginSelectedMolecule(jj); mol2 != NULL;
             mol2 = seleMan_.nextSelectedMolecule(jj)) {
          // loop over the possible donors in molecule 1:
          for (hbd = mol1->beginHBondDonor(hbdi); hbd != NULL;
               hbd = mol1->nextHBondDonor(hbdi)) {
            dPos = hbd->donorAtom->getPos();
            hPos = hbd->donatedHydrogen->getPos();
            DH   = hPos - dPos;
            currentSnapshot_->wrapVector(DH);
            DHdist = DH.length();
 
            // loop over the possible acceptors in molecule 2:
            for (hba = mol2->beginHBondAcceptor(hbai); hba != NULL;
                 hba = mol2->nextHBondAcceptor(hbai)) {
              aPos = hba->getPos();
              DA   = aPos - dPos;
              currentSnapshot_->wrapVector(DA);
              DAdist = DA.length();
 
              // Distance criteria: are the donor and acceptor atoms
              // close enough?
              if (DAdist < OOCut_) {
                HA = aPos - hPos;
                currentSnapshot_->wrapVector(HA);
                HAdist = HA.length();
 
                ctheta = dot(DH, DA) / (DHdist * DAdist);
                theta  = acos(ctheta) * 180.0 / Constants::PI;
 
                // Angle criteria: are the D-H and D-A and vectors close?
                if (theta < thetaCut_ && HAdist < OHCut_) {
                  // We have a hydrogen bond!
                  index1 = mol1->getGlobalIndex();
                  index2 = mol2->getGlobalIndex();
                  q1     = Q_[index1];
                  q2     = Q_[index2];
                  collectHistogram(q1, q2);
                }
              }
            }
          }
          // now loop over the possible acceptors in molecule 1:
          for (hba = mol1->beginHBondAcceptor(hbai); hba != NULL;
               hba = mol1->nextHBondAcceptor(hbai)) {
            aPos = hba->getPos();
 
            // loop over the possible donors in molecule 2:
            for (hbd = mol2->beginHBondDonor(hbdi); hbd != NULL;
                 hbd = mol2->nextHBondDonor(hbdi)) {
              dPos = hbd->donorAtom->getPos();
 
              DA = aPos - dPos;
              currentSnapshot_->wrapVector(DA);
              DAdist = DA.length();
 
              // Distance criteria: are the donor and acceptor atoms
              // close enough?
              if (DAdist < OOCut_) {
                hPos = hbd->donatedHydrogen->getPos();
                HA   = aPos - hPos;
                currentSnapshot_->wrapVector(HA);
                HAdist = HA.length();
 
                DH = hPos - dPos;
                currentSnapshot_->wrapVector(DH);
                DHdist = DH.length();
                ctheta = dot(DH, DA) / (DHdist * DAdist);
                theta  = acos(ctheta) * 180.0 / Constants::PI;
                // Angle criteria: are the D-H and D-A and vectors close?
                if (theta < thetaCut_ && HAdist < OHCut_) {
                  // We have a hydrogen bond!
                  // keep these indexed by donor then acceptor:
                  index1 = mol2->getGlobalIndex();
                  index2 = mol1->getGlobalIndex();
                  q1     = Q_[index1];
                  q2     = Q_[index2];
                  collectHistogram(q1, q2);
                }
              }
            }
          }
        }
      }
    }
    writeOutput();
  }
 
  void TetrahedralityHBMatrix::collectHistogram(RealType q1, RealType q2) {
    if (q1 > MinQ_ && q1 < MaxQ_) {
      int bin1 = int((q1 - MinQ_) / deltaQ_);
      if (q2 > MinQ_ && q2 < MaxQ_) {
        int bin2 = int((q2 - MinQ_) / deltaQ_);
        Q_histogram_[bin1][bin2] += 1;
        count_++;
      } else {
        // cerr << "q2 = " << q2 << "\n";
      }
    } else {
      // cerr << "q1 = " << q1 << "\n";
    }
  }
 
  void TetrahedralityHBMatrix::writeOutput() {
    std::ofstream ofs(outputFilename_.c_str());
    if (ofs.is_open()) {
      Revision r;
      ofs << "# " << getAnalysisType() << "\n";
      ofs << "# OpenMD " << r.getFullRevision() << "\n";
      ofs << "# " << r.getBuildDate() << "\n";
      ofs << "# selection script: \"" << selectionScript_ << "\"\n";
 
      if (!paramString_.empty())
        ofs << "# parameters: " << paramString_ << "\n";
 
      ofs << "# Hydrogen Bond count: " << count_ << "\n";
 
      for (unsigned int i = 0; i < Q_histogram_.size(); ++i) {
        for (unsigned int j = 0; j < Q_histogram_[i].size(); ++j) {
          ofs << RealType(Q_histogram_[i][j]) / RealType(count_) << "\t";
        }
        ofs << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "TetrahedralityHBMatrix: unable to open %s\n",
               outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    ofs.close();
  }
}  // namespace OpenMD