PositionZ.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).
 */
 
/*
 * Computes the position distribution along preferred axis for the selected atom
 * Created by Hemanta Bhattarai on 02/20/20.
 */
 
#include "applications/staticProps/PositionZ.hpp"
 
#include <algorithm>
#include <fstream>
 
#include "brains/Thermo.hpp"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/FluctuatingChargeAdapter.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  PositionZ::PositionZ(SimInfo* info, const std::string& filename,
                       const std::string& sele, int nzbins, int axis) :
      StaticAnalyser(info, filename, nzbins),
      selectionScript_(sele), evaluator_(info), seleMan_(info), thermo_(info),
      axis_(axis) {
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    // fixed number of bins
 
    sliceSDCount_.resize(nBins_);
    flucSliceSDCount_.resize(nBins_);
    std::fill(sliceSDCount_.begin(), sliceSDCount_.end(), 0);
    std::fill(flucSliceSDCount_.begin(), flucSliceSDCount_.end(), 0);
 
    positionZ_.resize(nBins_);
 
    switch (axis_) {
    case 0:
      axisLabel_ = "x";
      break;
    case 1:
      axisLabel_ = "y";
      break;
    case 2:
    default:
      axisLabel_ = "z";
      break;
    }
 
    setOutputName(getPrefix(filename) + ".CountZ");
  }
 
  void PositionZ::process() {
    StuntDouble* sd;
    int ii;
 
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames / step_;
 
    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 (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
 
      // wrap the stuntdoubles into a cell
      for (sd = seleMan_.beginSelected(ii); sd != NULL;
           sd = seleMan_.nextSelected(ii)) {
        Vector3d pos = sd->getPos();
        if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(pos);
        sd->setPos(pos);
      }
 
      // determine which atom belongs to which slice
      for (sd = seleMan_.beginSelected(ii); sd != NULL;
           sd = seleMan_.nextSelected(ii)) {
        Vector3d pos = sd->getPos();
        // shift molecules by half a box to have bins start at 0
        int binNo = int(nBins_ * (halfBoxZ_ + pos[axis_]) / hmat(axis_, axis_));
        sliceSDCount_[binNo]++;
      }
 
      // loop over the slices to calculate the charge
    }
 
    for (int istep = 0; istep < nFrames; istep += step_) {
      std::map<int, RealType> countInBin;
 
      reader.readFrame(istep);
      currentSnapshot_   = info_->getSnapshotManager()->getCurrentSnapshot();
      Mat3x3d hmat       = currentSnapshot_->getHmat();
      RealType halfBoxZ_ = hmat(axis_, axis_) / 2.0;
 
      // determine which atom belongs to which slice
      for (sd = seleMan_.beginSelected(ii); sd != NULL;
           sd = seleMan_.nextSelected(ii)) {
        Vector3d pos = sd->getPos();
        // shift molecules by half a box to have bins start at 0
        int binNo = int(nBins_ * (halfBoxZ_ + pos[axis_]) / hmat(axis_, axis_));
        countInBin[binNo]++;
      }
 
      // loop over the slices to calculate the charge
 
      for (unsigned int index = 0; index < flucSliceSDCount_.size(); ++index) {
        RealType flucCount =
            (countInBin[index] - (sliceSDCount_[index] / nProcessed_));
        flucSliceSDCount_[index] += flucCount * flucCount;
      }
    }
 
    writePositionZ();
  }
 
  void PositionZ::writePositionZ() {
    // compute average box length:
    std::vector<RealType>::iterator j;
    RealType zSum = 0.0;
    for (j = zBox_.begin(); j != zBox_.end(); ++j) {
      zSum += *j;
    }
    RealType zAve = zSum / zBox_.size();
 
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#position count "
                << "\n";
      rdfStream << "#selection: (" << selectionScript_ << ")\n";
      rdfStream << "#" << axisLabel_
                << "\tAverage Number\tFluctations_in_count\n";
      for (unsigned int i = 0; i < positionZ_.size(); ++i) {
        RealType z = zAve * (i + 0.5) / positionZ_.size();
        rdfStream << z << "\t" << sliceSDCount_[i] / nProcessed_ << "\t"
                  << sqrt(flucSliceSDCount_[i]) / nProcessed_ << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "ChargeZ: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    rdfStream.close();
  }
}  // namespace OpenMD