BondAngleDistribution.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/BondAngleDistribution.hpp"
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/Constants.hpp"
#include "utils/Revision.hpp"
#include "utils/simError.h"
 
using namespace std;
namespace OpenMD {
 
  BondAngleDistribution::BondAngleDistribution(SimInfo* info,
                                               const string& filename,
                                               const string& sele, double rCut,
                                               int nbins) :
      StaticAnalyser(info, filename, nbins),
      selectionScript_(sele), seleMan_(info), evaluator_(info) {
    setAnalysisType("Bond Angle Distribution");
    setOutputName(getPrefix(filename) + ".bad");
 
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    // Set up cutoff radius:
 
    rCut_ = rCut;
 
    std::stringstream params;
    params << " rcut = " << rCut_ << ", nbins = " << nBins_;
    const std::string paramString = params.str();
    setParameterString(paramString);
 
    // Theta can take values from 0 to 180
 
    deltaTheta_ = (180.0) / nBins_;
    histogram_.resize(nBins_);
  }
 
  void BondAngleDistribution::initializeHistogram() {
    for (int bin = 0; bin < nBins_; bin++) {
      histogram_[bin] = 0;
    }
  }
 
  void BondAngleDistribution::process() {
    Molecule* mol;
    Atom* atom;
    int myIndex;
    SimInfo::MoleculeIterator mi;
    Molecule::AtomIterator ai;
    StuntDouble* sd;
    Vector3d vec;
    std::vector<Vector3d> bondvec;
    RealType r;
    int nBonds;
    int i;
 
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames   = reader.getNFrames();
    frameCounter_ = 0;
 
    nTotBonds_ = 0;
 
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      frameCounter_++;
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
 
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
 
      // outer loop is over the selected StuntDoubles:
 
      for (sd = seleMan_.beginSelected(i); sd != NULL;
           sd = seleMan_.nextSelected(i)) {
        myIndex = sd->getGlobalIndex();
        nBonds  = 0;
        bondvec.clear();
 
        // inner loop is over all other atoms in the system:
 
        for (mol = info_->beginMolecule(mi); mol != NULL;
             mol = info_->nextMolecule(mi)) {
          for (atom = mol->beginAtom(ai); atom != NULL;
               atom = mol->nextAtom(ai)) {
            if (atom->getGlobalIndex() != myIndex) {
              vec = sd->getPos() - atom->getPos();
 
              if (usePeriodicBoundaryConditions_)
                currentSnapshot_->wrapVector(vec);
 
              // Calculate "bonds" and make a pair list
 
              r = vec.length();
 
              // Check to see if neighbor is in bond cutoff
 
              if (r < rCut_) {
                // Add neighbor to bond list's
                bondvec.push_back(vec);
                nBonds++;
                nTotBonds_++;
              }
            }
          }
 
          for (int i = 0; i < nBonds - 1; i++) {
            Vector3d vec1 = bondvec[i];
            vec1.normalize();
            for (int j = i + 1; j < nBonds; j++) {
              Vector3d vec2 = bondvec[j];
 
              vec2.normalize();
 
              RealType theta = acos(dot(vec1, vec2)) * 180.0 / Constants::PI;
 
              if (theta > 180.0) { theta = 360.0 - theta; }
              int whichBin = int(theta / deltaTheta_);
 
              histogram_[whichBin] += 2;
            }
          }
        }
      }
    }
 
    writeBondAngleDistribution();
  }
 
  void BondAngleDistribution::writeBondAngleDistribution() {
    RealType norm = (RealType)nTotBonds_ * ((RealType)nTotBonds_ - 1.0) / 2.0;
 
    std::ofstream ofs(getOutputFileName().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";
 
      // Normalize by number of frames and write it out:
      for (int i = 0; i < nBins_; ++i) {
        RealType Thetaval = i * deltaTheta_;
        ofs << Thetaval;
        ofs << "\t" << (RealType)histogram_[i] / norm / frameCounter_;
        ofs << "\n";
      }
 
      ofs.close();
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "BondAngleDistribution: unable to open %s\n",
               (getOutputFileName() + "q").c_str());
      painCave.isFatal = 1;
      simError();
    }
  }
}  // namespace OpenMD