SpatialStatistics.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_SPATIALSTATISTICS_HPP
#define APPLICATIONS_STATICPROPS_SPATIALSTATISTICS_HPP
 
#include <string>
#include <vector>
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Snapshot.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "primitives/StuntDouble.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  class SpatialStatistics : public StaticAnalyser {
  public:
    SpatialStatistics(SimInfo* info, const std::string& filename,
                      const std::string& sele, int nbins);
 
    virtual void process();
    virtual void processFrame(int frame);
    virtual int getBin(Vector3d pos)                          = 0;
    virtual void processStuntDouble(StuntDouble* sd, int bin) = 0;
 
  protected:
    Snapshot* currentSnapshot_ {};
    int nProcessed_ {};
    std::string selectionScript_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;
  };
 
  class SlabStatistics : public SpatialStatistics {
  public:
    SlabStatistics(SimInfo* info, const std::string& filename,
                   const std::string& sele, int nbins, int axis);
 
    virtual int getBin(Vector3d pos);
    virtual void processFrame(int frame);
 
  protected:
    Mat3x3d hmat_;
    RealType volume_ {};
    int axis_;
    std::string axisLabel_;
  };
 
  class ShellStatistics : public SpatialStatistics {
  public:
    ShellStatistics(SimInfo* info, const std::string& filename,
                    const std::string& sele, const std::string& comsele,
                    int nbins, RealType binWidth);
 
    virtual void processFrame(int frame);
    virtual int getBin(Vector3d pos);
    void setCoordinateOrigin(Vector3d co) { coordinateOrigin_ = co; }
 
  protected:
    Vector3d coordinateOrigin_;
    RealType binWidth_;
    std::string comSele_;
    SelectionManager comSeleMan_;
    SelectionEvaluator comEvaluator_;
  };
}  // namespace OpenMD
 
#endif