HBondPersistence.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/dynamicProps/HBondPersistence.hpp"
 
#include <algorithm>
 
#include "utils/Constants.hpp"
 
namespace OpenMD {
  HBondPersistence::HBondPersistence(SimInfo* info, const std::string& filename,
                                     const std::string& sele1,
                                     const std::string& sele2, double OOcut,
                                     double thetaCut, double OHcut) :
      TimeCorrFunc<RealType>(info, filename, sele1, sele2),
      OOCut_(OOcut), thetaCut_(thetaCut), OHCut_(OHcut) {
    setCorrFuncType("HBondPersistence");
    setOutputName(getPrefix(dumpFilename_) + ".HBpersistence");
 
    std::stringstream params;
    params << " OOcut = " << OOCut_ << ", thetacut = " << thetaCut_
           << ", OHcut = " << OHCut_;
    const std::string paramString = params.str();
    setParameterString(paramString);
 
    // nFrames_ is initialized in MultipassCorrFunc:
    GIDtoDonor_.resize(nFrames_);
    DonorToGID_.resize(nFrames_);
    acceptor_.resize(nFrames_);
  }
 
  void HBondPersistence::computeFrame(int istep) {
    Molecule* mol1;
    Molecule* mol2;
    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;
    int ii, jj;
    int hInd, aInd, index;
 
    // Map of atomic global IDs to donor atoms:
    GIDtoDonor_[istep].resize(info_->getNGlobalAtoms(), -1);
 
    if (!uniqueSelections_) { seleMan2_ = seleMan1_; }
 
    if (evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
 
    if (uniqueSelections_ && evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }
 
    for (mol1 = seleMan1_.beginSelectedMolecule(ii); mol1 != NULL;
         mol1 = seleMan1_.nextSelectedMolecule(ii)) {
      for (mol2 = seleMan2_.beginSelectedMolecule(jj); mol2 != NULL;
           mol2 = seleMan2_.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();
 
          hInd = hbd->donatedHydrogen->getGlobalIndex();
          aInd = -1;
 
          // 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_) {
                // molecule 2 is a Hbond acceptor:
                aInd = hba->getGlobalIndex();
 
                index                    = acceptor_[istep].size();
                GIDtoDonor_[istep][hInd] = index;
 
                acceptor_[istep].push_back(aInd);
                DonorToGID_[istep].push_back(hInd);
              }
            }
          }
        }
 
        // loop over the possible donors in molecule 2:
        for (hbd = mol2->beginHBondDonor(hbdi); hbd != NULL;
             hbd = mol2->nextHBondDonor(hbdi)) {
          dPos = hbd->donorAtom->getPos();
          hPos = hbd->donatedHydrogen->getPos();
          DH   = hPos - dPos;
          currentSnapshot_->wrapVector(DH);
          DHdist = DH.length();
 
          hInd = hbd->donatedHydrogen->getGlobalIndex();
          aInd = -1;
 
          // loop over the possible acceptors in molecule 1:
          for (hba = mol1->beginHBondAcceptor(hbai); hba != NULL;
               hba = mol1->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_) {
                // molecule 1 is a Hbond acceptor:
                aInd                     = hba->getGlobalIndex();
                index                    = acceptor_[istep].size();
                GIDtoDonor_[istep][hInd] = index;
 
                acceptor_[istep].push_back(aInd);
                DonorToGID_[istep].push_back(hInd);
              }
            }
          }
        }
      }
    }
  }
 
  void HBondPersistence::correlation() {
    std::vector<int> s1;
    std::vector<int>::iterator i1;
 
    RealType corrVal;
    int index1, index2, count, gid;
 
    for (int i = 0; i < nFrames_; ++i) {
      RealType time1 = times_[i];
      s1             = DonorToGID_[i];
 
      for (int j = i; j < nFrames_; ++j) {
        // Perform a sanity check on the actual configuration times to
        // make sure the configurations are spaced the same amount the
        // sample time said they were spaced:
 
        RealType time2 = times_[j];
 
        if (fabs((time2 - time1) - (j - i) * deltaTime_) > 1.0e-4) {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                   "HBondPersistence::correlation Error: sampleTime (%f)\n"
                   "\tin %s does not match actual time-spacing between\n"
                   "\tconfigurations %d (t = %f) and %d (t = %f).\n",
                   deltaTime_, dumpFilename_.c_str(), i, time1, j, time2);
          painCave.isFatal = 1;
          simError();
        }
 
        int timeBin = int((time2 - time1) / deltaTime_ + 0.5);
 
        corrVal = 0.0;
        count   = s1.size();
 
        // loop over the H-bond donors found in frame i:
 
        for (i1 = s1.begin(); i1 != s1.end(); ++i1) {
          // gid is the global ID of H-bond donor index1 in frame i:
          gid = *i1;
 
          index1 = GIDtoDonor_[i][gid];
 
          // find matching donor in frame j:
          index2 = GIDtoDonor_[j][gid];
 
          // sometimes the donor doesn't have a Hydrogen bond in a
          // given frame, so the index will default to -1:
 
          if (index2 < 0) {
            corrVal += 0;
          } else {
            if (acceptor_[i][index1] == acceptor_[j][index2])
              corrVal += 1;
            else
              corrVal += 0;
          }
        }
        histogram_[timeBin] += corrVal;
        count_[timeBin] += count;
      }
    }
  }
 
  void HBondPersistence::postCorrelate() {
    for (unsigned int i = 0; i < nTimeBins_; ++i) {
      if (count_[i] > 0) {
        histogram_[i] /= count_[i];
      } else {
        histogram_[i] = 0;
      }
    }
  }
 
}  // namespace OpenMD