TetrahedralityParamXYZ.hpp

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 * [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_TETRAHEDRALITYPARAMXYZ_HPP
#define APPLICATIONS_STATICPROPS_TETRAHEDRALITYPARAMXYZ_HPP
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "math/Vector3.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  /**
   * @class TetrahedralityParamXYZ
   * @brief Tetrahedrality Parameter XYZ
   *
   * Computes 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).
   *
   *
   * Characterization of the spatial correlations of the the local
   * order parameter Q are done according to the procedure outlined
   * in:
   *
   *   "Space-time correlations in the orientational order parameter and the
   *    orientational entropy of water," by P. Kumar, S.V. Buldyrev, and
   *    H.E. Stanley, arXiv:0807.4699v1 [cond-mat.soft] 29 Jul 2008.
   *
   */
  class TetrahedralityParamXYZ : public StaticAnalyser {
  public:
    TetrahedralityParamXYZ(SimInfo* info, const std::string& filename,
                           const std::string& sele1, const std::string& sele2,
                           RealType rCut, RealType voxelSize,
                           RealType gaussWidth);
 
    virtual void process();
 
  private:
    void writeQxyz();
    void writeVTKGrid();
 
    Snapshot* currentSnapshot_;
    std::string selectionScript1_;
    std::string selectionScript2_;
    SelectionManager seleMan1_;
    SelectionManager seleMan2_;
    SelectionEvaluator evaluator1_;
    SelectionEvaluator evaluator2_;
 
    RealType rCut_;
    RealType voxelSize_;
    RealType gaussWidth_;
 
    Vector3i nBins_;
    std::vector<std::vector<std::vector<RealType>>> count_;
    std::vector<std::vector<std::vector<RealType>>> hist_;
  };
}  // namespace OpenMD
 
#endif