OrderParameterProbZ.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 Cos\theta distribution along preferred axis for the selected
 * atom
 */
 
#include "applications/staticProps/OrderParameterProbZ.hpp"
 
#include <algorithm>
#include <fstream>
 
#include "brains/Thermo.hpp"
#include "io/DumpReader.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "primitives/Molecule.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/FluctuatingChargeAdapter.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  OrderParameterProbZ::OrderParameterProbZ(
      SimInfo* info, const std::string& filename, const std::string& sele,
      const RealType dipoleX, const RealType dipoleY, const RealType dipoleZ,
      int nbins, int axis) :
      StaticAnalyser(info, filename, nbins),
      selectionScript_(sele), evaluator_(info), seleMan_(info), thermo_(info),
      nbins_(nbins), axis_(axis) {
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    // fixed number of bins
    Count_.resize(nbins);
    std::fill(Count_.begin(), Count_.end(), 0);
 
    switch (axis_) {
    case 0:
      axisLabel_ = "x";
      refAxis_   = Vector3d(1, 0, 0);
      break;
    case 1:
      axisLabel_ = "y";
      refAxis_   = Vector3d(0, 1, 0);
      break;
    case 2:
    default:
      axisLabel_ = "z";
      refAxis_   = Vector3d(0, 0, 1);
      break;
    }
 
    dipoleVector_ = Vector3d(dipoleX, dipoleY, dipoleZ);
    dipoleVector_.normalize();
 
    setOutputName(getPrefix(filename) + ".OrderProb");
  }
 
  void OrderParameterProbZ::process() {
    StuntDouble* sd;
    int ii;
    RealType orderMin   = -1.0;
    RealType orderMax   = 1.0;
    RealType deltaOrder = (orderMax - orderMin) / nbins_;
 
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
    totalCount_ = 0;
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
 
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
 
      // wrap the stuntdoubles into a cell and find order parameter
 
      for (sd = seleMan_.beginSelected(ii); sd != NULL;
           sd = seleMan_.nextSelected(ii)) {
        Vector3d pos = sd->getPos();
        if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(pos);
        sd->setPos(pos);
      }
      SquareMatrix3<RealType> rotMat;
      Vector3d rotatedDipoleVector;
      RealType ctheta;
      for (sd = seleMan_.beginSelected(ii); sd != NULL;
           sd = seleMan_.nextSelected(ii)) {
        if (sd->isDirectional() || sd->isRigidBody()) {
          rotMat              = sd->getA();
          rotatedDipoleVector = rotMat * dipoleVector_;
          rotatedDipoleVector.normalize();
          ctheta    = dot(rotatedDipoleVector, refAxis_);
          int index = int((ctheta - orderMin) / deltaOrder);
          Count_[index]++;
          totalCount_++;
        }
      }
    }
 
    writeOrderCount();
  }
 
  void OrderParameterProbZ::writeOrderCount() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#Order count probablity "
                << "\n";
      rdfStream << "#selection: (" << selectionScript_ << ")\n";
      rdfStream << "# Prefered Axis:" << axisLabel_
                << "\n##Order\tProbOrderCount\n";
      for (unsigned int i = 0; i < Count_.size(); ++i) {
        RealType order = i * (2.0 / Count_.size());
        RealType prop;
        if (totalCount_ == 0)
          prop = Count_[i];
        else
          prop = Count_[i] / totalCount_;
        rdfStream << order << "\t" << prop << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "OrderProb: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    rdfStream.close();
  }
}  // namespace OpenMD