BondOrderParameter.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_BONDORDERPARAMETER_HPP
#define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "math/SphericalHarmonic.hpp"
#include "math/Vector3.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  /**
   * @class BondOrderParameter
   * @brief Bond Order Parameter
   *
   * Computes orientational bond order parameters as outlined in:
   *
   *   "Bond-orientaional order in liquids and glasses," by
   *    P. J. Steinhart, D. R. Nelson, and M. Ronchetti,
   *    Phys. Rev. B, 28, 784 (1983).
   *
   * A somewhat more useful reference which has formulae for these order
   * parameters for individual atoms is:
   *
   *   "Numerical calculation of the rate of crystal nucleation in a
   *    Lennard-Jones system at moderate undercooling," by
   *    Pieter Rein ten Wolde, Maria J. Ruiz-Montero, and Daan Frenkel,
   *    J. Chem. Phys. 104, pp. 9932-9947 (1996).
   *
   * Note that this version uses a single cutoff radius to decide
   * membership in the list of neighbors, and does not have use a
   * distance-dependent weighting as used in the second reference above.
   *
   * The selection script can be utilized to look at specific types of
   * central atoms.  A dynamic selector can also be utilized.  By
   * default, this class computes the \f[ Q_{l} \f] and
   * \f[ \hat{W}_{l} \f] parameters up to \f[ l = 12 \f].  The completed
   * configurational averages of these values as well as the
   * distributions of atomic \f[ q_{l} \f] and \f[ \hat{w}_{l} \f]
   * values are then placed in .boq and .bow files.
   */
  class BondOrderParameter : public StaticAnalyser {
  public:
    BondOrderParameter(SimInfo* info, const std::string& filename,
                       const std::string& sele, double rCut,
                       unsigned int nbins);
 
    virtual void process();
 
  private:
    virtual void initializeHistogram();
    virtual void collectHistogram(std::vector<RealType> q,
                                  std::vector<ComplexType> what);
    void writeOrderParameter(std::vector<RealType> Q,
                             std::vector<ComplexType> What);
 
    Snapshot* currentSnapshot_;
    std::string selectionScript_;
    SelectionManager seleMan_;
    SelectionEvaluator evaluator_;
 
    RealType rCut_;
    static const int lMax_ = 12;
    int frameCounter_;
    int nBins_;
 
    std::map<std::pair<int, int>, int> m2Min;
    std::map<std::pair<int, int>, int> m2Max;
    std::map<std::pair<int, int>, std::vector<RealType>> w3j;
 
    RealType MinQ_;
    RealType MaxQ_;
    RealType deltaQ_;
    std::vector<int> Qcount_;
    std::map<std::pair<int, int>, int> Q_histogram_;
 
    RealType MinW_;
    RealType MaxW_;
    RealType deltaW_;
    std::vector<int> Wcount_;
    std::map<std::pair<int, int>, int> W_histogram_;
  };
}  // namespace OpenMD
 
#endif