TetrahedralityHBMatrix.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_TETRAHEDRALITYHBMATRIX_HPP
#define APPLICATIONS_STATICPROPS_TETRAHEDRALITYHBMATRIX_HPP
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "math/Vector3.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  /**
   * @class TetrahedralityHBMatrix
   * @brief Tetrahedrality Hydrogen Bonding Matrix
   *
   * Computes hydrogen-bonding probabilities for molecules that are
   * categorized by the local tetrahedral order parameter Q as
   * introduced in:
   *
   *   "A new order parameter for tetrahedral configurations," by
   *    P.-L. Chau and A.J. Hardwick, Mol. Phys. 93, pp. 511-518
   *    (1998).
   *
   *
   * Note that we use a rescaled version of the tetrahedral order
   * parameter 'Q' such that a perfectly tetrahedral configuration has
   * a Q value of 1 and an ideal gas configuration has a Q value of
   * 0. This rescaled version of the tetrahedrality parameter was
   * first introduced in:
   *
   *   "Relationship between structural order and the anomalies of
   *    liquid water," by J.R. Errington and P.G. Debenedetti, Nature
   *    409, pp. 318-321 (2001).
   */
  class TetrahedralityHBMatrix : public StaticAnalyser {
  public:
    TetrahedralityHBMatrix(SimInfo* info, const std::string& filename,
                           const std::string& sele, double rCut, double OOCut,
                           double thetaCut, double OHCut, int nbins);
 
    virtual void process();
 
  private:
    virtual void initializeHistogram();
    virtual void collectHistogram(RealType q1, RealType q2);
    void writeOutput();
 
    Snapshot* currentSnapshot_;
    std::string selectionScript_;
    SelectionManager seleMan_;
    SelectionEvaluator evaluator_;
 
    RealType rCut_;
    RealType OOCut_;
    RealType thetaCut_;
    RealType OHCut_;
    unsigned int count_;
 
    RealType MinQ_;
    RealType MaxQ_;
    RealType deltaQ_;
 
    std::vector<RealType> Q_;
 
    std::vector<std::vector<unsigned int>> Q_histogram_;
  };
}  // namespace OpenMD
 
#endif