HullFinder.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 SELECTION_HULLFINDER_HPP
#define SELECTION_HULLFINDER_HPP
 
#include "brains/SimInfo.hpp"
#include "math/Hull.hpp"
#include "math/Triangle.hpp"
#include "primitives/StuntDouble.hpp"
#include "selection/SelectionSet.hpp"
 
namespace OpenMD {
 
  class HullFinder {
  public:
    HullFinder(SimInfo* si);
    ~HullFinder();
 
    SelectionSet findHull();
    SelectionSet findHull(int frame);
    RealType getSurfaceArea() { return surfaceArea_; }
    RealType getVolume() { return volume_; }
 
    SimInfo* info_ {nullptr};
    std::vector<StuntDouble*> stuntdoubles_;
    std::vector<Bond*> bonds_;
    std::vector<Bend*> bends_;
    std::vector<Torsion*> torsions_;
    std::vector<Inversion*> inversions_;
    std::vector<Molecule*> molecules_;
    vector<int> nObjects_;
 
    Hull* surfaceMesh_;
    RealType surfaceArea_;
    RealType volume_;
    std::vector<StuntDouble*> localSites_;
 
  private:
    // Unified implementation. computeVolume controls whether volume_
    // is computed (the frameless overload historically did not).
    SelectionSet findHullImpl(bool computeVolume);
  };
 
  class AlphaHullFinder : public HullFinder {
  public:
    AlphaHullFinder(SimInfo* si);
    void setAlpha(RealType alpha);
  };
}  // namespace OpenMD
 
#endif