GofZ.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/GofZ.hpp"
 
#include <algorithm>
#include <fstream>
 
#include "utils/simError.h"
 
namespace OpenMD {
 
  GofZ::GofZ(SimInfo* info, const std::string& filename,
             const std::string& sele1, const std::string& sele2, RealType len,
             RealType maxz, int nrbins, int axis) :
      RadialDistrFunc(info, filename, sele1, sele2, nrbins),
      axis_(axis) {
    deltaZ_ = maxz / nBins_;
    rC_     = len;
 
    histogram_.resize(nBins_);
    avgGofz_.resize(nBins_);
 
    setOutputName(getPrefix(filename) + ".gofz");
 
    // Set the axis label for the privileged axis
    switch (axis_) {
    case 0:
      axisLabel_ = "x";
      break;
    case 1:
      axisLabel_ = "y";
      break;
    case 2:
    default:
      axisLabel_ = "z";
      break;
    }
  }
 
  void GofZ::preProcess() { std::fill(avgGofz_.begin(), avgGofz_.end(), 0.0); }
 
  void GofZ::initializeHistogram() {
    std::fill(histogram_.begin(), histogram_.end(), 0);
  }
 
  void GofZ::processHistogram() {
    int nPairs = getNPairs();
    RealType volume =
        info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity  = nPairs / volume * 2.0;
    RealType pairConstant = (2.0 * Constants::PI * pairDensity);
 
    for (unsigned int i = 0; i < histogram_.size(); ++i) {
      RealType zLower   = i * deltaZ_;
      RealType zUpper   = zLower + deltaZ_;
      RealType cylSlice = (zUpper - zLower) * rC_ * rC_;
      RealType nIdeal   = cylSlice * pairConstant;
 
      avgGofz_[i] += histogram_[i] / nIdeal;
    }
  }
 
  void GofZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
    if (sd1 == sd2) { return; }
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12  = pos2 - pos1;
    if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(r12);
 
    RealType distance = r12.length();
    RealType z2       = r12[axis_] * r12[axis_];
    RealType xydist   = sqrt(distance * distance - z2);
 
    if (xydist < rC_) {
      RealType thisZ = abs(r12[axis_]);
      int whichBin   = int(thisZ / deltaZ_);
      if (whichBin < int(nBins_)) histogram_[whichBin] += 2;
    }
  }
 
  void GofZ::writeRdf() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#" << axisLabel_ << "-separation distribution function\n";
      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
      rdfStream << "#r\tcorrValue\n";
      for (unsigned int i = 0; i < avgGofz_.size(); ++i) {
        RealType z = deltaZ_ * (i + 0.5);
        rdfStream << z << "\t" << avgGofz_[i] / nProcessed_ << "\n";
      }
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "GofZ: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
    rdfStream.close();
  }
}  // namespace OpenMD