HBondZvol.hpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#ifndef APPLICATIONS_STATICPROPS_HBONDZVOL_HPP
#define APPLICATIONS_STATICPROPS_HBONDZVOL_HPP
 
#include <string>
#include <vector>
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  /**
   * @class HBondZvol
   * @brief Hydrogen Bonding density binned by z
   *
   * Computes hydrogen bonding density
   *
   */
  class HBondZvol : public StaticAnalyser {
  public:
    HBondZvol(SimInfo* info, const std::string& filename,
              const std::string& sele1, const std::string& sele2, double rCut,
              double thetaCut, int nzbins, int axis = 2);
    int getNZBins() { return nZBins_; }
 
    virtual void process();
 
  private:
    void writeDensity();
 
    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 nZBins_;
    std::vector<RealType> zBox_;
    std::vector<RealType> sliceQ_;
    std::vector<int> sliceCount_;
    std::vector<RealType> vol_;
    int axis_;
    std::string axisLabel_;
 
    std::vector<int> nHBonds_;
    std::vector<int> nDonor_;
    std::vector<int> nAcceptor_;
    int nSelected_;
  };
}  // namespace OpenMD
 
#endif