Displacement.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_DISPLACEMENT_HPP
#define APPLICATIONS_DYNAMICPROPS_DISPLACEMENT_HPP
 
#include "applications/dynamicProps/TimeCorrFunc.hpp"
 
namespace OpenMD {
 
  class Displacement : public ObjectACF<Vector3d> {
  public:
    Displacement(SimInfo* info, const std::string& filename,
                 const std::string& sele1, const std::string& sele2);
 
  private:
    virtual int computeProperty1(int frame, StuntDouble* sd);
    virtual Vector3d calcCorrVal(int frame1, int frame2, int id1, int id2);
    std::vector<std::vector<Vector3d>> positions_;
  };
 
  class DisplacementZ : public ObjectACF<Vector3d> {
  public:
    DisplacementZ(SimInfo* info, const std::string& filename,
                  const std::string& sele1, const std::string& sele2,
                  int nZbins, int axis = 2);
 
  private:
    virtual void computeFrame(int frame);
    virtual int computeProperty1(int frame, StuntDouble* sd);
    virtual void correlateFrames(int frame1, int frame2, int timeBin);
    Vector3d calcCorrValImpl(int frame1, int frame2, int id1, int id2,
                             int timeBin);
    virtual Vector3d calcCorrVal(int, int, int, int) { return Vector3d(0.0); }
 
    virtual void postCorrelate();
    virtual void writeCorrelate();
 
    std::vector<std::vector<Vector3d>> positions_;
    std::vector<std::vector<int>> zBins_;
    std::vector<std::vector<Vector3d>> histograms_;
    std::vector<std::vector<int>> counts_;
    Mat3x3d hmat_;
    RealType halfBoxZ_;
    unsigned int nZBins_;
    int axis_;
    std::string axisLabel_;
  };
}  // namespace OpenMD
 
#endif