HBondPersistence.hpp

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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).
 */
 
#ifndef APPLICATIONS_DYNAMICPROPS_HBONDPERSISTENCE_HPP
#define APPLICATIONS_DYNAMICPROPS_HBONDPERSISTENCE_HPP
 
#include "applications/dynamicProps/TimeCorrFunc.hpp"
 
namespace OpenMD {
 
  class HBondPersistence : public TimeCorrFunc<RealType> {
  public:
    HBondPersistence(SimInfo* info, const std::string& filename,
                     const std::string& sele1, const std::string& sele2,
                     double OOCut, double thetaCut, double OHCut);
 
  private:
    virtual void correlation();
    virtual void computeFrame(int istep);
 
    virtual void computeProperty1(int) { return; }
    virtual void computeProperty2(int) { return; }
    virtual int computeProperty1(int, Molecule*) { return -1; }
    virtual int computeProperty1(int, StuntDouble*) { return -1; }
    virtual int computeProperty1(int, Bond*) { return -1; }
    virtual int computeProperty2(int, Molecule*) { return -1; }
    virtual int computeProperty2(int, StuntDouble*) { return -1; }
    virtual int computeProperty2(int, Bond*) { return -1; }
 
    virtual RealType calcCorrVal(int, int, int, int) { return 0.0; }
    virtual RealType calcCorrVal(int, int) { return 0.0; }
 
    virtual void postCorrelate();
 
    std::vector<std::vector<int>> GIDtoDonor_;
    std::vector<std::vector<int>> DonorToGID_;
    std::vector<std::vector<int>> acceptor_;
 
    RealType OOCut_;
    RealType thetaCut_;
    RealType OHCut_;
  };
}  // namespace OpenMD
 
#endif