BondCorrFunc.cpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
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 * 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/BondCorrFunc.hpp"
 
namespace OpenMD {
  BondCorrFunc::BondCorrFunc(SimInfo* info, const std::string& filename,
                             const std::string& sele1,
                             const std::string& sele2) :
      AutoCorrFunc<RealType>(info, filename, sele1, sele2) {
    setCorrFuncType("Bond Correlation Function");
    setOutputName(getPrefix(dumpFilename_) + ".bondcorr");
 
    this->autoCorrFunc_          = true;
    this->doSystemProperties_    = false;
    this->doMolecularProperties_ = false;
    this->doObjectProperties_    = false;
    this->doBondProperties_      = true;
 
    delta_.resize(nFrames_);
  }
 
  int BondCorrFunc::computeProperty1(int frame, Bond* bond) {
    RealType re = bond->getBondType()->getEquilibriumBondLength();
    RealType r  = bond->getValue();
 
    delta_[frame].push_back(r - re);
    return delta_[frame].size() - 1;
  }
 
  RealType BondCorrFunc::calcCorrVal(int frame1, int frame2, int id1, int id2) {
    return delta_[frame1][id1] * delta_[frame2][id2];
  }
}  // namespace OpenMD