RhoAngleR.cpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
/* Calculates Angle(R) for DirectionalAtoms*/
#include <algorithm>
#include <cmath>
#include <fstream>
 
#include "applications/staticProps/AngleR.hpp"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  AngleR::AngleR(SimInfo* info, const std::string& filename,
                 const std::string& sele, RealType len, int nrbins) :
      StaticAnalyser(info, filename),
      selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len),
      nRBins_(nrbins) {
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    deltaR_ = len_ / nRBins_;
 
    histogram_.resize(nRBins_);
    count_.resize(nRBins_);
    avgAngleR_.resize(nRBins_);
    setOutputName(getPrefix(filename) + ".AngleR");
  }
 
  void AngleR::process() {
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames / step_;
 
    std::fill(avgAngleR_.begin(), avgAngleR_.end(), 0.0);
    std::fill(histogram_.begin(), histogram_.end(), 0.0);
    std::fill(count_.begin(), count_.end(), 0);
 
    for (int istep = 0; istep < nFrames; istep += step_) {
      int i;
      StuntDouble* sd;
      reader.readFrame(istep);
      currentSnapshot_      = info_->getSnapshotManager()->getCurrentSnapshot();
      Vector3d CenterOfMass = info_->getCom();
 
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
 
      // determine which atom belongs to which slice
      for (sd = seleMan_.beginSelected(i); sd != NULL;
           sd = seleMan_.nextSelected(i)) {
        Vector3d pos = sd->getPos();
        Vector3d r1  = CenterOfMass - pos;
        // only do this if the stunt double actually has a vector associated
        // with it
        if (sd->isDirectional()) {
          Vector3d uz = sd->getA().transpose() * V3Z;
          // std::cerr << "pos = " << pos << " uz = " << uz << "\n";
          RealType distance = r1.length();
 
          uz.normalize();
          r1.normalize();
          RealType cosangle = dot(r1, uz);
 
          if (distance < len_) {
            int whichBin = distance / deltaR_;
            histogram_[whichBin] += cosangle;
            count_[whichBin] += 1;
          }
        }
      }
    }
 
    processHistogram();
    writeAngleR();
  }
 
  void AngleR::processHistogram() {
    for (int i = 0; i < histogram_.size(); ++i) {
      if (count_[i] > 0)
        avgAngleR_[i] += histogram_[i] / count_[i];
      else
        avgAngleR_[i] = 0.0;
 
      std::cerr << " count = " << count_[i] << " avgAngle = " << avgAngleR_[i]
                << "\n";
    }
  }
 
  void AngleR::writeAngleR() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#radial density function Angle(r)\n";
      rdfStream << "#r\tcorrValue\n";
      for (int i = 0; i < avgAngleR_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);
        rdfStream << r << "\t" << avgAngleR_[i] << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "AngleR: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    rdfStream.close();
  }
 
}  // namespace OpenMD