NumberR.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/NumberR.hpp"
 
#include <algorithm>
#include <fstream>
 
#include "brains/Thermo.hpp"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  NumberR::NumberR(SimInfo* info, const std::string& filename,
                   const std::string& sele, RealType len, int nrbins) :
      StaticAnalyser(info, filename, nrbins),
      selectionScript_(sele), evaluator_(info), seleMan_(info), thermo_(info),
      len_(len) {
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    deltaR_ = len_ / nBins_;
 
    // fixed number of bins
 
    numberR_.resize(nBins_);
    setOutputName(getPrefix(filename) + ".NumberR");
    std::stringstream params;
    params << " len = " << len_ << ", nrbins = " << nBins_;
    const std::string paramString = params.str();
    setParameterString(paramString);
  }
 
  void NumberR::process() {
    Molecule* mol;
    int ii;
 
    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();
 
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
 
      // determine which molecule belongs to which slice
      for (mol = seleMan_.beginSelectedMolecule(ii); mol != NULL;
           mol = seleMan_.nextSelectedMolecule(ii)) {
        Vector3d pos      = mol->getCom();
        RealType distance = pos.length();
 
        if (distance < len_) {
          int binNo = int(distance / deltaR_);
          numberR_[binNo]++;
        }
      }
    }
    writeNumberR();
  }
 
  void NumberR::writeNumberR() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#NumberR "
                << "\n";
      rdfStream << "#selection: (" << selectionScript_ << ")\n";
      rdfStream << "# r "
                << "\tnumber\n";
      RealType binNumber;
      for (unsigned int i = 0; i < numberR_.size(); ++i) {
        RealType rLower = i * deltaR_;
        RealType rUpper = rLower + deltaR_;
        RealType volShell =
            (4.0 * Constants::PI) * (pow(rUpper, 3) - pow(rLower, 3)) / 3.0;
 
        RealType r = deltaR_ * (i + 0.5);
 
        binNumber = numberR_[i] / (volShell * nProcessed_);
 
        rdfStream << r << "\t" << binNumber << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "NumberR: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    rdfStream.close();
  }
}  // namespace OpenMD