BeadModel.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 HYDRODYNAMICS_BEADMODEL_HPP
#define HYDRODYNAMICS_BEADMODEL_HPP
 
#include <vector>
 
#include "hydrodynamics/ApproximateModel.hpp"
#include "math/DynamicRectMatrix.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "primitives/Molecule.hpp"
 
namespace OpenMD {
 
  class Shape;
 
  /**
   * References:
   *
   * For overlapping beads and overlapping volume:
   *
   * Beatriz Carrasco and Jose Garcia de la Torre and Peter Zipper;
   * "Calculation of hydrodynamic properties of macromolecular bead
   * models with overlapping spheres", Eur Biophys J (1999) 28:
   * 510-515
   *
   * For overlapping volume between two spherical beads:
   * http://mathworld.wolfram.com/Sphere-SphereIntersection.html
   *
   * For non-overlapping and overlapping translation-translation
   * mobility tensors:
   *
   * Zuk, P. J., E. Wajnryb, K. A. Mizerski, and P. Szymczak;
   * “Rotne–Prager–Yamakawa Approximation for Different-Sized
   * Particles in Application to Macromolecular Bead Models.”, Journal
   * of Fluid Mechanics, 741 (2014)
   *
   * For distinctions between centers of resistance and diffusion:
   * Steven Harvey and Jose Garcia de la Torre; "Coordinate Systems
   * for Modeling the Hydrodynamic Resistance and Diffusion
   * Coefficients of Irregularly Shaped Rigid Macromolecules",
   * Macromolecules 1980 13 (4), 960-964
   **/
  class BeadModel : public ApproximateModel {
  public:
    BeadModel();
 
    virtual std::size_t assignElements() = 0;
    virtual void checkElement(std::size_t i);
    virtual void writeElements(std::ostream& os);
 
    virtual Mat3x3d interactionTensor(const std::size_t i, const std::size_t j,
                                      const RealType viscosity);
    virtual RealType volumeCorrection();
 
  protected:
    RealType volumeOverlap_;
  };
}  // namespace OpenMD
 
#endif