Kirkwood.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/Kirkwood.hpp"
 
#include <algorithm>
#include <fstream>
#include <sstream>
 
#include "types/MultipoleAdapter.hpp"
#include "utils/Revision.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  Kirkwood::Kirkwood(SimInfo* info, const std::string& filename,
                     const std::string& sele1, const std::string& sele2,
                     RealType len, int nrbins) :
      RadialDistrFunc(info, filename, sele1, sele2, nrbins),
      len_(len) {
    setAnalysisType("Distance-dependent Kirkwood G-factor");
    setOutputName(getPrefix(filename) + ".kirkwood");
 
    deltaR_ = len_ / nBins_;
 
    histogram_.resize(nBins_);
    avgKirkwood_.resize(nBins_);
    std::stringstream params;
    params << " len = " << len_ << ", nrbins = " << nBins_;
    const std::string paramString = params.str();
    setParameterString(paramString);
  }
 
  void Kirkwood::preProcess() {
    std::fill(avgKirkwood_.begin(), avgKirkwood_.end(), 0.0);
  }
 
  void Kirkwood::initializeHistogram() {
    std::fill(histogram_.begin(), histogram_.end(), 0);
  }
 
  void Kirkwood::processHistogram() {
    int nSelected1 = seleMan1_.getSelectionCount();
    for (unsigned int i = 0; i < histogram_.size(); ++i) {
      avgKirkwood_[i] += histogram_[i] / nSelected1;
    }
  }
 
  void Kirkwood::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
    if (sd1 == sd2) { return; }
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12  = pos2 - pos1;
    if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(r12);
 
    RealType distance = r12.length();
 
    AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
    AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
 
    MultipoleAdapter ma1 = MultipoleAdapter(atype1);
    MultipoleAdapter ma2 = MultipoleAdapter(atype2);
 
    Vector3d d1(0.0);
    Vector3d d2(0.0);
    RealType dotProduct(0.0);
 
    if (ma1.isDipole()) {
      d1 = sd1->getDipole();
      d1.normalize();
      if (ma2.isDipole()) {
        d2 = sd2->getDipole();
        d2.normalize();
        dotProduct = dot(d1, d2);
      }
    }
 
    if (distance < len_) {
      int whichBin = int(distance / deltaR_);
      // each dipole pair contributes to all of the radii that contain it.
      for (unsigned int i = whichBin; i < nBins_; i++) {
        histogram_[i] += dotProduct;
      }
    }
  }
 
  void Kirkwood::writeRdf() {
    std::ofstream ofs(outputFilename_.c_str());
    if (ofs.is_open()) {
      Revision r;
      ofs << "# " << getAnalysisType() << "\n";
      ofs << "# OpenMD " << r.getFullRevision() << "\n";
      ofs << "# " << r.getBuildDate() << "\n";
      ofs << "# selection script1: \"" << selectionScript1_;
      ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
      if (!paramString_.empty())
        ofs << "# parameters: " << paramString_ << "\n";
 
      ofs << "#r\tcorrValue\n";
      for (unsigned int i = 0; i < avgKirkwood_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);
        ofs << r << "\t" << avgKirkwood_[i] / nProcessed_ << "\n";
      }
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "Kirkwood: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
    ofs.close();
  }
 
  KirkwoodQuadrupoles::KirkwoodQuadrupoles(SimInfo* info,
                                           const std::string& filename,
                                           const std::string& sele1,
                                           const std::string& sele2,
                                           RealType len, int nrbins) :
      Kirkwood(info, filename, sele1, sele2, len, nrbins) {
    setAnalysisType("Distance-dependent Kirkwood G-factor for quadrupoles");
    setOutputName(getPrefix(filename) + ".kirkwoodQ");
  }
 
  void KirkwoodQuadrupoles::collectHistogram(StuntDouble* sd1,
                                             StuntDouble* sd2) {
    if (sd1 == sd2) { return; }
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12  = pos2 - pos1;
    if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(r12);
 
    RealType distance = r12.length();
 
    AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
    AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
 
    MultipoleAdapter ma1 = MultipoleAdapter(atype1);
    MultipoleAdapter ma2 = MultipoleAdapter(atype2);
 
    Mat3x3d Q1(0.0);
    Mat3x3d Q2(0.0);
    RealType trQ1(0.0);
    RealType trQ2(0.0);
    RealType Q1dQ1(0.0);
    RealType Q2dQ2(0.0);
 
    RealType quadrupoleProduct(0.0);
 
    // Similar to the dipole case, but the effective quadrupole moment
    // is defined (in our electrostatics work) as:
    //    sqrt (3 Q:Q - Tr(Q)^2 )
    // so normalization is a bit different.  Here : denotes a
    // contraction (double dot product) of the quadrupole tensor.
 
    if (ma1.isQuadrupole()) {
      Q1    = sd1->getQuadrupole();
      trQ1  = Q1.trace();
      Q1dQ1 = doubleDot(Q1, Q1);
      Q1 /= sqrt(3.0 * Q1dQ1 - trQ1 * trQ1);
      // recompute the trace after normalizing:
      trQ1 = Q1.trace();
 
      if (ma2.isQuadrupole()) {
        Q2    = sd2->getQuadrupole();
        trQ2  = Q2.trace();
        Q2dQ2 = doubleDot(Q2, Q2);
        Q2 /= sqrt(3.0 * Q2dQ2 - trQ2 * trQ2);
        // recompute the trace after normalizing:
        trQ2 = Q2.trace();
 
        quadrupoleProduct = 3.0 * doubleDot(Q1, Q2) - trQ1 * trQ2;
      }
    }
 
    if (distance < len_) {
      int whichBin = int(distance / deltaR_);
      // each dipole pair contributes to all of the radii that contain it.
      for (unsigned int i = whichBin; i < nBins_; i++) {
        histogram_[i] += quadrupoleProduct;
      }
    }
  }
}  // namespace OpenMD