SCDOrderParameter.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_SCDRDERPARAMETER_HPP
#define APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
 
#include <string>
#include <tuple>
#include <vector>
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
  class SCDElem {
  public:
    SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2,
            const std::string& sele3);
 
    std::string getSelection1() const { return sele1_; }
    std::string getSelection2() const { return sele2_; }
    std::string getSelection3() const { return sele3_; }
    RealType calcSCD(Snapshot* snapshot);
 
  private:
    std::string sele1_;
    std::string sele2_;
    std::string sele3_;
    bool usePeriodicBoundaryConditions_;
 
    using SDTuple3 = std::tuple<StuntDouble*, StuntDouble*, StuntDouble*>;
 
    std::vector<SDTuple3> tuples_;
  };
 
  class SCDOrderParameter : public StaticAnalyser {
  public:
    SCDOrderParameter(SimInfo* info, const std::string& filename,
                      const std::string& sele1, const std::string& sele2,
                      const std::string& sele3);
 
    SCDOrderParameter(SimInfo* info, const std::string& filename,
                      const std::string& molname, int beginIndex, int endIndex);
    virtual void process();
 
  private:
    void writeSCD();
 
    std::vector<SCDElem> scdElems_;
    std::vector<RealType> scdParam_;
 
    Snapshot* currentSnapshot_;
  };
}  // namespace OpenMD
 
#endif