MomAngMomCorrFunc.cpp

/*
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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#include "applications/dynamicProps/MomAngMomCorrFunc.hpp"
 
namespace OpenMD {
  MomAngMomCorrFunc::MomAngMomCorrFunc(SimInfo* info,
                                       const std::string& filename,
                                       const std::string& sele1,
                                       const std::string& sele2) :
      ObjectCCF<RealType>(info, filename, sele1, sele2) {
    setCorrFuncType("Momentum - Angular Momentum Correlation Function");
    setOutputName(getPrefix(dumpFilename_) + ".pjcorr");
 
    momenta_.resize(nFrames_);
    js_.resize(nFrames_);
  }
 
  int MomAngMomCorrFunc::computeProperty1(int frame, StuntDouble* sd) {
    momenta_[frame].push_back(sd->getMass() * sd->getVel());
    return momenta_[frame].size() - 1;
  }
 
  int MomAngMomCorrFunc::computeProperty2(int frame, StuntDouble* sd) {
    // The lab frame vector corresponding to the body-fixed
    // z-axis is simply the second column of A.transpose()
    // or, identically, the second row of A itself.
    Vector3d u = sd->getA().getRow(2);
    Vector3d j = sd->getJ();
 
    js_[frame].push_back(cross(j, u));
    return js_[frame].size() - 1;
  }
 
  RealType MomAngMomCorrFunc::calcCorrVal(int frame1, int frame2, int id1,
                                          int id2) {
    RealType pj = dot(momenta_[frame1][id1], js_[frame2][id2]);
    return pj;
  }
 
  void MomAngMomCorrFunc::validateSelection(SelectionManager& seleMan) {
    StuntDouble* sd;
    int i;
 
    for (sd = seleMan.beginSelected(i); sd != NULL;
         sd = seleMan.nextSelected(i)) {
      if (!sd->isDirectional()) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "MomAngMomCorrFunc::validateSelection Error: selection "
                 "%d (%s)\n"
                 "\t is not a Directional object\n",
                 sd->getGlobalIndex(), sd->getType().c_str());
        painCave.isFatal = 1;
        simError();
      }
    }
  }
 
}  // namespace OpenMD