HBondZ.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 "HBondZ.hpp"
 
#include <fstream>
#include <string>
#include <vector>
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/Constants.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  HBondZ::HBondZ(SimInfo* info, const std::string& filename,
                 const std::string& sele1, const std::string& sele2,
                 double rCut, double thetaCut, int nzbins, int axis) :
      StaticAnalyser(info, filename, nzbins),
      selectionScript1_(sele1), seleMan1_(info), evaluator1_(info),
      selectionScript2_(sele2), seleMan2_(info), evaluator2_(info),
      axis_(axis) {
    ff_ = info_->getForceField();
 
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
    evaluator2_.loadScriptString(sele2);
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }
 
    // Set up cutoff values:
    nBins_    = nzbins;
    rCut_     = rCut;
    thetaCut_ = thetaCut;
 
    // fixed number of bins
 
    nHBonds_.resize(nBins_);
    nDonor_.resize(nBins_);
    nAcceptor_.resize(nBins_);
    sliceQ_.resize(nBins_);
    sliceCount_.resize(nBins_);
    std::fill(sliceQ_.begin(), sliceQ_.end(), 0.0);
    std::fill(sliceCount_.begin(), sliceCount_.end(), 0);
 
    switch (axis_) {
    case 0:
      axisLabel_ = "x";
      break;
    case 1:
      axisLabel_ = "y";
      break;
    case 2:
    default:
      axisLabel_ = "z";
      break;
    }
 
    setOutputName(getPrefix(filename) + ".hbondz");
  }
 
  void HBondZ::process() {
    Molecule* mol1;
    Molecule* mol2;
    Molecule::HBondDonor* hbd1;
    Molecule::HBondDonor* hbd2;
    std::vector<Molecule::HBondDonor*>::iterator hbdi;
    std::vector<Molecule::HBondDonor*>::iterator hbdj;
    std::vector<Atom*>::iterator hbai;
    std::vector<Atom*>::iterator hbaj;
    Atom* hba1;
    Atom* hba2;
    Vector3d dPos;
    Vector3d aPos;
    Vector3d hPos;
    Vector3d DH;
    Vector3d DA;
    RealType DAdist, DHdist, theta, ctheta;
    int ii, jj;
    int nHB, nA, nD;
 
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames   = reader.getNFrames();
    frameCounter_ = 0;
 
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
 
      Mat3x3d hmat = currentSnapshot_->getHmat();
      zBox_.push_back(hmat(axis_, axis_));
 
      RealType halfBoxZ_ = hmat(axis_, axis_) / 2.0;
 
      if (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
 
      if (evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
      }
 
      for (mol1 = seleMan1_.beginSelectedMolecule(ii); mol1 != NULL;
           mol1 = seleMan1_.nextSelectedMolecule(ii)) {
        // We're collecting statistics on the molecules in selection 1:
        nHB           = 0;
        nA            = 0;
        nD            = 0;
        Vector3d mPos = mol1->getCom();
 
        for (mol2 = seleMan2_.beginSelectedMolecule(jj); mol2 != NULL;
             mol2 = seleMan2_.nextSelectedMolecule(jj)) {
          // loop over the possible donors in molecule 1:
          for (hbd1 = mol1->beginHBondDonor(hbdi); hbd1 != NULL;
               hbd1 = mol1->nextHBondDonor(hbdi)) {
            dPos = hbd1->donorAtom->getPos();
            hPos = hbd1->donatedHydrogen->getPos();
            DH   = hPos - dPos;
            currentSnapshot_->wrapVector(DH);
            DHdist = DH.length();
 
            // loop over the possible acceptors in molecule 2:
            for (hba2 = mol2->beginHBondAcceptor(hbaj); hba2 != NULL;
                 hba2 = mol2->nextHBondAcceptor(hbaj)) {
              aPos = hba2->getPos();
              DA   = aPos - dPos;
              currentSnapshot_->wrapVector(DA);
              DAdist = DA.length();
 
              // Distance criteria: are the donor and acceptor atoms
              // close enough?
              if (DAdist < rCut_) {
                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_) {
                  // molecule 1 is a Hbond donor:
                  nHB++;
                  nD++;
                }
              }
            }
          }
 
          // now loop over the possible acceptors in molecule 1:
          for (hba1 = mol1->beginHBondAcceptor(hbai); hba1 != NULL;
               hba1 = mol1->nextHBondAcceptor(hbai)) {
            aPos = hba1->getPos();
 
            // loop over the possible donors in molecule 2:
            for (hbd2 = mol2->beginHBondDonor(hbdj); hbd2 != NULL;
                 hbd2 = mol2->nextHBondDonor(hbdj)) {
              dPos = hbd2->donorAtom->getPos();
 
              DA = aPos - dPos;
              currentSnapshot_->wrapVector(DA);
              DAdist = DA.length();
 
              // Distance criteria: are the donor and acceptor atoms
              // close enough?
              if (DAdist < rCut_) {
                hPos = hbd2->donatedHydrogen->getPos();
                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_) {
                  // molecule 1 is a Hbond acceptor:
                  nHB++;
                  nA++;
                }
              }
            }
          }
        }
        if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(mPos);
        int binNo =
            int(nBins_ * (halfBoxZ_ + mPos[axis_]) / hmat(axis_, axis_));
        sliceQ_[binNo] += nHB;
        sliceCount_[binNo] += 1;
      }
    }
    writeDensity();
  }
 
  void HBondZ::writeDensity() {
    // compute average box length:
 
    RealType zSum = 0.0;
    for (std::vector<RealType>::iterator j = zBox_.begin(); j != zBox_.end();
         ++j) {
      zSum += *j;
    }
    RealType zAve = zSum / zBox_.size();
 
    std::ofstream qZstream(outputFilename_.c_str());
    if (qZstream.is_open()) {
      qZstream << "#Hydrogen Bonds (" << axisLabel_ << ")\n";
 
      qZstream << "#nFrames:\t" << zBox_.size() << "\n";
      qZstream << "#selection 1: (" << selectionScript1_ << ")\n";
      qZstream << "#selection 2: (" << selectionScript2_ << ")\n";
      qZstream << "#" << axisLabel_ << "\tHydrogen Bonds\n";
      for (unsigned int i = 0; i < sliceQ_.size(); ++i) {
        RealType z = zAve * (i + 0.5) / sliceQ_.size();
        if (sliceCount_[i] != 0) {
          qZstream << z << "\t" << sliceQ_[i] / sliceCount_[i] << "\n";
        } else
          qZstream << z << "\t" << 0 << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "HBondZ: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
    qZstream.close();
  }
}  // namespace OpenMD