DensityHistogram.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).
 */
 
/*
 * Calculates average EAM density profile for selected atom.
 * Created by Hemanta Bhattarai on 04/30/19.
 * @author  Hemanta Bhattarai
 */
 
#include "applications/staticProps/DensityHistogram.hpp"
 
#include <algorithm>
#include <fstream>
#include <numeric>
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  DensityHistogram::DensityHistogram(SimInfo* info, const std::string& filename,
                                     const std::string& sele, int nbins) :
      StaticAnalyser(info, filename, nbins),
      selectionScript_(sele), evaluator_(info), seleMan_(info), nBins_(nbins) {
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    setOutputName(getPrefix(filename) + ".EAMDensity");
  }
 
  void DensityHistogram::process() {
    StuntDouble* sd;
    int ii;
 
    if (evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames / step_;
    vector<RealType> density;
 
    nProcessed_ = nFrames / step_;
 
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
 
      for (sd = seleMan_.beginSelected(ii); sd != NULL;
           sd = seleMan_.nextSelected(ii)) {
        if (sd->getDensity()) density.push_back(sd->getDensity());
      }
    }
 
    if (density.empty()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "Density for selected atom not found.\n");
      painCave.isFatal = 1;
      simError();
    }
 
    std::sort(density.begin(), density.end());
 
    RealType min = density.front();
    RealType max = density.back();
 
    RealType delta_density = (max - min) / (nBins_);
    averageDensity_        = 0;
    if (delta_density == 0) {
      bincenter_.push_back(min);
      histList_.push_back(density.size());
      averageDensity_ = min;
    } else {
      // fill the center for histogram
      for (int j = 0; j < nBins_ + 3; ++j) {
        bincenter_.push_back(min + (j - 1) * delta_density);
        histList_.push_back(0);
      }
      // filling up the histogram whith the densities
      int bin_center_pos = 0;
      vector<RealType>::iterator index;
      RealType density_length = static_cast<RealType>(density.size());
 
      bool hist_update;
      for (index = density.begin(); index < density.end(); index++) {
        hist_update = true;
        while (hist_update) {
          if (*index >= bincenter_[bin_center_pos] &&
              *index < bincenter_[bin_center_pos + 1]) {
            histList_[bin_center_pos] += 1.0 / density_length;
            hist_update = false;
          } else {
            averageDensity_ +=
                histList_[bin_center_pos] * bincenter_[bin_center_pos];
            bin_center_pos++;
            hist_update = true;
          }
        }
      }
      averageDensity_ += histList_[bin_center_pos] * bincenter_[bin_center_pos];
    }
    writeDensity();
  }
 
  void DensityHistogram::writeDensity() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#EAMDensity\n";
      rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
      rdfStream << "#selection: (" << selectionScript_ << ")\n";
      rdfStream << "#Average EAM density: " << averageDensity_ << "\n";
      rdfStream << "#"
                << "Bin_center"
                << "\tcount\n";
      for (unsigned int i = 0; i < histList_.size(); ++i) {
        rdfStream << bincenter_[i] << "\t" << histList_[i] << "\n";
      }
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "EAMDensity: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
    rdfStream.close();
  }
}  // namespace OpenMD