MeanDisplacement.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/MeanDisplacement.hpp"
 
#include <sstream>
 
#include "utils/Revision.hpp"
 
namespace OpenMD {
  MeanDisplacement::MeanDisplacement(SimInfo* info, const std::string& filename,
                                     const std::string& sele1,
                                     const std::string& sele2) :
      ObjectACF<Vector3d>(info, filename, sele1, sele2) {
    setCorrFuncType("Mean Displacement");
    setOutputName(getPrefix(dumpFilename_) + ".meandisp");
 
    positions_.resize(nFrames_);
  }
 
 
  int MeanDisplacement::computeProperty1(int frame, StuntDouble* sd) {
    positions_[frame].push_back(sd->getPos());
    return positions_[frame].size() - 1;
  }
 
  Vector3d MeanDisplacement::calcCorrVal(int frame1, int frame2, int id1,
                                         int id2) {
    Vector3d diff = positions_[frame2][id2] - positions_[frame1][id1];
    return diff;
  }
}