Ellipsoid.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_ELLIPSOID_HPP
#define HYDRODYNAMICS_ELLIPSOID_HPP
 
#include "hydrodynamics/Shape.hpp"
#include "math/SquareMatrix3.hpp"
 
namespace OpenMD {
 
  /** @class Ellipsoid
   *
   * An ellipsoid in OpenMD is restricted to having two equal
   * equatorial semi-axes.  OpenMD treats the "special" axis as the
   * z-coordinate in the body fixed reference frame.  That is:
   *
   *  \f[ z^2 / a^2  +  (x^2 + y^2) / b^2   = 1 \f]
   *
   * If  \f$a >= b\f$, the ellipsoid is a prolate spheroid, and if \f$a < b\f$,
   * the ellipsoid is oblate.  Ellipsoids are specified in the constructor
   * using an axial length (a), and a equatorial length (b).  A Vector3d
   * can be used to position the center of the ellipsoid, and a rotation
   * matrix can also be used to orient the ellipsoid to a preferred lab-fixed
   * coordinate frame.
   */
  class Ellipsoid : public Shape {
  public:
    Ellipsoid(Vector3d origin, RealType rAxial, RealType rEquatorial,
              Mat3x3d rotMat);
    virtual bool isInterior(Vector3d pos);
    virtual std::pair<Vector3d, Vector3d> getBoundingBox();
    virtual bool hasAnalyticalSolution() { return true; }
    virtual bool isComposite() { return false; }
    virtual bool isSpherical() { return false; }
    virtual bool isMesh() { return false; }
 
    virtual HydroProp* getHydroProp(RealType viscosity);
 
    RealType getRAxial() { return rAxial_; }
    RealType getREquatorial() { return rEquatorial_; }
    RealType getRMajor() { return rMajor_; }
    RealType getRMinor() { return rMinor_; }
    virtual Vector3d getOrigin() { return origin_; }
    Mat3x3d getRotMat() { return rotMat_; }
 
  private:
    Vector3d origin_;
    RealType rAxial_;
    RealType rEquatorial_;
    RealType rMajor_;
    RealType rMinor_;
    Mat3x3d rotMat_;
  };
}  // namespace OpenMD
 
#endif