CoordinationNumber.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/CoordinationNumber.hpp"
 
#include <algorithm>
#include <fstream>
#include <sstream>
 
#include "io/DumpReader.hpp"
#include "utils/Revision.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  CoordinationNumber::CoordinationNumber(SimInfo* info,
                                         const std::string& filename,
                                         const std::string& sele1,
                                         const std::string& sele2,
                                         RealType rCut, int bins) :
      StaticAnalyser(info, filename, bins),
      rCut_(rCut), bins_(bins), sele1_(sele1), seleMan1_(info),
      evaluator1_(info), sele2_(sele2), seleMan2_(info), evaluator2_(info) {
    setAnalysisType("Coordination Number Distribution");
    setOutputName(getPrefix(filename) + ".cn");
 
    nnMax_           = 12;
    RealType binMax_ = nnMax_ * 1.5;
    delta_           = binMax_ / bins_;
 
    std::stringstream params;
    params << " rcut = " << rCut_ << ", nbins = " << bins_
           << ", nnMax = " << nnMax_;
    const std::string paramString = params.str();
    setParameterString(paramString);
 
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
      selectionCount1_ = seleMan1_.getSelectionCount();
    }
    evaluator2_.loadScriptString(sele2);
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
      selectionCount2_ = seleMan2_.getSelectionCount();
    }
  }
 
  void CoordinationNumber::process() {
    SelectionManager common(info_);
 
    std::vector<std::vector<int>> listNN;
    std::vector<int> globalToLocal;
 
    StuntDouble* sd1;
    StuntDouble* sd2;
 
    Snapshot* currentSnapshot_;
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    int iterator1;
    int iterator2;
    unsigned int mapIndex1(0);
    unsigned int mapIndex2(0);
    unsigned int whichBin(0);
    RealType cn(0.0);
    Vector3d pos1;
    Vector3d pos2;
    Vector3d diff;
    RealType distance;
 
    histogram_.clear();
    histogram_.resize(bins_, 0.0);
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
    count_      = 0;
 
    // First have to calculate lists of nearest neighbors (listNN_):
 
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
 
      if (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
        selectionCount1_ = seleMan1_.getSelectionCount();
      }
      if (evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
        selectionCount2_ = seleMan2_.getSelectionCount();
      }
 
      // We need a common selection set:
      common          = seleMan1_ | seleMan2_;
      int commonCount = common.getSelectionCount();
 
      globalToLocal.clear();
      globalToLocal.resize(
          info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(), -1);
      for (unsigned int i = 0; i < listNN.size(); i++)
        listNN.at(i).clear();
      listNN.clear();
      listNN.resize(commonCount);
 
      mapIndex1 = 0;
      for (sd1 = common.beginSelected(iterator1); sd1 != NULL;
           sd1 = common.nextSelected(iterator1)) {
        globalToLocal.at(sd1->getGlobalIndex()) = mapIndex1;
 
        pos1 = sd1->getPos();
 
        mapIndex2 = 0;
        for (sd2 = common.beginSelected(iterator2); sd2 != NULL;
             sd2 = common.nextSelected(iterator2)) {
          if (mapIndex1 < mapIndex2) {
            pos2 = sd2->getPos();
            diff = pos2 - pos1;
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(diff);
            distance = diff.length();
            if (distance < rCut_) {
              listNN.at(mapIndex1).push_back(mapIndex2);
              listNN.at(mapIndex2).push_back(mapIndex1);
            }
          }
          mapIndex2++;
        }
        mapIndex1++;
      }
 
      // Fill up the histogram with cn values
 
      for (sd1 = seleMan1_.beginSelected(iterator1); sd1 != NULL;
           sd1 = seleMan1_.nextSelected(iterator1)) {
        mapIndex1 = globalToLocal.at(sd1->getGlobalIndex());
 
        cn       = computeCoordination(mapIndex1, listNN);
        whichBin = int(cn / delta_);
 
        if (whichBin < histogram_.size()) {
          histogram_[whichBin] += 1;
        } else {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                   "Coordination Number: Error: "
                   "In frame, %d, object %d has CN %lf outside of range max.\n",
                   istep, sd1->getGlobalIndex(), cn);
          painCave.isFatal = 1;
          simError();
        }
      }
      count_ += selectionCount1_;
    }
 
    for (unsigned int n = 0; n < histogram_.size(); n++) {
      if (count_ > 0)
        histogram_[n] /= RealType(count_);
      else
        histogram_[n] = 0.0;
    }
 
    writeOutput();
  }
 
  RealType CoordinationNumber::computeCoordination(int a,
                                                   vector<vector<int>> nl) {
    return RealType(nl.at(a).size());
  }
 
  void CoordinationNumber::writeOutput() {
    std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
 
    if (ofs.is_open()) {
      Revision r;
      RealType binValue(0.0);
 
      ofs << "# " << getAnalysisType() << "\n";
      ofs << "# OpenMD " << r.getFullRevision() << "\n";
      ofs << "# " << r.getBuildDate() << "\n";
      ofs << "# selection script1: \"" << sele1_;
      ofs << "\"\tselection script2: \"" << sele2_ << "\"\n";
      if (!paramString_.empty())
        ofs << "# parameters: " << paramString_ << "\n";
 
      for (unsigned int n = 0; n < histogram_.size(); n++) {
        binValue = n * delta_;
        ofs << binValue << "\t" << histogram_[n] / delta_ << "\n";
      }
    }
    ofs.close();
  }
 
  SCN::SCN(SimInfo* info, const std::string& filename, const std::string& sele1,
           const std::string& sele2, RealType rCut, int bins) :
      CoordinationNumber(info, filename, sele1, sele2, rCut, bins) {
    setOutputName(getPrefix(filename) + ".scn");
    setAnalysisType("Secondary Coordination Number");
  }
 
  RealType SCN::computeCoordination(int a, vector<vector<int>> nl) {
    RealType scn = 0.0;
    int b;
 
    if (nl.at(a).size() != 0) {
      for (unsigned int i = 0; i < nl.at(a).size(); i++) {
        // b is the index of one of i's nearest neighbors
        b = nl.at(a).at(i);
        scn += nl.at(b).size();
      }
      return scn / RealType(nl.at(a).size());
    } else {
      return 0.0;
    }
  }
 
  GCN::GCN(SimInfo* info, const std::string& filename, const std::string& sele1,
           const std::string& sele2, RealType rCut, int bins) :
      CoordinationNumber(info, filename, sele1, sele2, rCut, bins) {
    setOutputName(getPrefix(filename) + ".gcn");
    setAnalysisType("Generalized Coordination Number");
  }
 
  RealType GCN::computeCoordination(int a, vector<vector<int>> nl) {
    RealType gcn = 0.0;
    int b;
    for (unsigned int i = 0; i < nl.at(a).size(); i++) {
      // b is the index of one of i's nearest neighbors
      b = nl.at(a).at(i);
      gcn += nl.at(b).size();
    }
    return gcn / RealType(nnMax_);
  }
}  // namespace OpenMD