HBondGeometric.hpp

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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_STATICPROPS_HBONDGEOMETRIC_HPP
#define APPLICATIONS_STATICPROPS_HBONDGEOMETRIC_HPP
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  /**
   * @class HBondGeometric
   * @brief Hydrogen Bonding statistics using geometric criteria
   *
   * Computes hydrogen bonding statistics using structural information:
   *
   *   "Hydrogen-bond dynamics for the extended simple point-carge
   *   model of water" by F. W. Starr, J. K. Nielsen, and
   *   H. E. Stanley, Phys. Rev. E 62(1), 579-587 (2000).
   *
   */
  class HBondGeometric : public StaticAnalyser {
  public:
    HBondGeometric(SimInfo* info, const std::string& filename,
                   const std::string& sele1, const std::string& sele2,
                   double rCut, double thetaCut, int nbins);
 
    virtual void process();
 
  private:
    virtual void initializeHistogram();
    virtual void collectHistogram(int nHB, int nD, int nA);
    void writeHistogram();
 
    Snapshot* currentSnapshot_;
    std::string selectionScript1_;
    SelectionManager seleMan1_;
    SelectionEvaluator evaluator1_;
    std::string selectionScript2_;
    SelectionManager seleMan2_;
    SelectionEvaluator evaluator2_;
    ForceField* ff_;
 
    RealType rCut_;
    RealType thetaCut_;
    int frameCounter_;
    int nBins_;
 
    std::vector<int> nHBonds_;
    std::vector<int> nDonor_;
    std::vector<int> nAcceptor_;
    int nSelected_;
  };
}  // namespace OpenMD
 
#endif