SurfaceDiffusion.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_SURFACEDIFFUSION_HPP
#define APPLICATIONS_STATICPROPS_SURFACEDIFFUSION_HPP
 
#include <fstream>
#include <string>
#include <vector>
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  class SurfaceDiffusion : public StaticAnalyser {
  public:
    SurfaceDiffusion(SimInfo* info, const std::string& filename,
                     const std::string& sele, RealType len);
 
    virtual void process();
 
  private:
    double round(double r);
    void solventAccessible();
    void mobileAtomsFirst();
    void mobileAtomsLast();
    void mobileAtoms();
    void positionCorrelation();
 
    Snapshot* currentSnapshot_;
 
    int nProcessed_;
    std::string selectionScript_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan1_;
 
    string filename_;
    int bins_;
    int selectionCount_;
    double singleMoveDistance_;
    int frames_;
    bool doSolvent_;
 
    // All positions of all frames of selected indices
    // positions_[0][i]
    // First particle at frame i
    std::vector<std::vector<Vector3d>> positions_;
    std::vector<std::vector<Vector3d>> positions2_;
 
    // mobility of particle i at time j
    // moBool[i][j]
    // moBool.resize(selectionCount_);
    // for(){
    //  moBool[i].resize(frames);
    // }
    std::vector<std::vector<bool>> moBool_;
    std::vector<std::vector<bool>> moBool2_;
 
    std::vector<std::vector<StuntDouble*>> gridSD_;
    std::vector<StuntDouble*> gridHighZ_;
    std::vector<StuntDouble*> gridLowZ_;
    std::vector<StuntDouble*> forIndex_;
    std::vector<Vector3d> firstPosition_;
    std::vector<Vector3d> lastPosition_;
 
    std::vector<int> SAIndices_;
    std::vector<int> mobileIndices_;
    std::vector<int> indices_;
    std::vector<int> count_;
 
    std::vector<RealType> xHist_;
    std::vector<RealType> yHist_;
    std::vector<RealType> rHist_;
 
    RealType minDistance_;
    RealType probe_;
  };
}  // namespace OpenMD
 
#endif