TranslationalOrderParamZ.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_TRANSLATIONALORDERPARAMZ_HPP
#define APPLICATIONS_STATICPROPS_TRANSLATIONALORDERPARAMZ_HPP
 
#include "applications/staticProps/RadialDistrFunc.hpp"
 
namespace OpenMD {
 
  /**
   * @class TranslationalOrderParamZ
   * @brief TranslationalOrder ParameterZ
   *
   * Computes local translational order parameter t as introduced in:
   *
   * "Towards a quantification of disorder in materials: Distinguishing
   *  equilibrium and glassy sphere packings," by T. M. Truskett, S. Torquato,
   *  and P. G. Debenedetti, Phys. Rev. E 62(1), pp. 994-1001 (2000).
   *
   * and in:
   *
   * "Molecular structural order and anomalies in liquid silica," by
   *  M. Scott Shell, Pablo G. Debenedetti, and Athanassios
   *  Z. Panagiotopoulos, Phys. Rev. E 66, 011202 (2002).
   */
  class TranslationalOrderParamZ : public RadialDistrFunc {
  public:
    TranslationalOrderParamZ(SimInfo* info, const std::string& filename,
                             const std::string& sele1, const std::string& sele2,
                             double rCut, int nrbins, int nzbins, RealType len,
                             RealType zlen, int axis = 2);
 
    int getNRBins() { return nRBins_; }
    RealType getLength() { return len_; }
    int getNZBins() { return nZBins_; }
 
  private:
    virtual void preProcess();
    virtual void initializeHistogram();
    virtual void processHistogram();
    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
    virtual void postProcess();
    virtual void writeRdf();
 
    RealType len_;
    RealType zLen_;
    int nRBins_;
    RealType deltaR_;
    int nZBins_;
    RealType deltaZ_;
    RealType rCut_;
 
    std::vector<std::vector<int>> histogram_;
    std::vector<std::vector<RealType>> avgGofr_;
    std::vector<RealType> Tz_;
    std::vector<RealType> zBox_;
 
    int axis_;
    std::string axisLabel_;
    int xaxis_;
    int yaxis_;
  };
}  // namespace OpenMD
 
#endif