BAOAB.hpp

/*
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 * non-exclusive, royalty free, license to use, modify and
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 *    notice, this list of conditions and the following disclaimer.
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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#ifndef INTEGRATOR_BAOAB_HPP
#define INTEGRATOR_BAOAB_HPP
#include <map>
#include <vector>
#include "integrators/Integrator.hpp"
#include "primitives/Molecule.hpp"
#include "math/SeqRandNumGen.hpp"
#include "hydrodynamics/Shape.hpp"
#include "brains/Velocitizer.hpp"
 
namespace OpenMD {
 
  struct SDShape {
    StuntDouble* sd;
    Shape* shape;
  };
 
  struct MomentData {
    Vector3d rcr;   /**< Distance between CoM and Center of Resistance */
    Mat3x3d Icr;    /**< Moment of Inertia at Center of Resistance */
    Mat3x3d IcrInv; /**< Icr^{-1}  */
  };
 
  /**
   * @brief Declaration of the Langevin Dynamics BAOAB Integrator
   *
   * Langevin Dynamics based on the BAOAB splitting of Matthews and
   * Leimkuhler for details see http://dx.doi.org/10.1063/1.4802990
   * Optionally, one can use the ABOBA splitting.  Rigid body
   * hydrodynamics are from Sun, Lin, and Gezelter. For details see
   * https://doi.org/10.1063/1.2936991
   *
   */
  class BAOAB: public Integrator {
    /**
    * @brief Selects the ordering of the integration steps
    *
    * The integrator implements both the BAOAB (better for configurational
    * averages) and ABOBA splittings.  This enum is used to select one or the
    * other.  BAOAB is the default.
    */
    enum method_t
    {
        LANGEVIN_METHOD_BAOAB,
        LANGEVIN_METHOD_ABOBA
    };
 
    
  public:
    BAOAB(SimInfo* info);
    virtual void step();
 
  private:
    /**
    * @brief Integrates all particle positions by dt
    *
    * @param dt the time interval to integrate over
    */
    void PositionStep(double dt);
    
    /**
    * @brief Integrates all particle velocities by dt
    *
    * @param dt the time interval to integrate over
    */
    virtual void VelocityStep(double dt);
    
    /**
     * @brief Computes the O part (Ornstein-Uhlenbeck solve) of the BAOAB scheme
     *
     * @param dt the time interval to integrate over
     */
    virtual void OStep(RealType dt);
    
    std::map<std::string, HydroProp*> parseFrictionFile(const std::string& filename);
    MomentData* getMomentData(StuntDouble* sd);
    
    void genRandomForceAndTorque(Vector3d& force, Vector3d& torque,
                                 unsigned int index, RealType variance);
 
    std::map<std::string, HydroProp*> hydroPropMap_;
    std::vector<HydroProp*> hydroProps_;
    std::map<std::string, MomentData*> momentsMap_; 
    std::vector<MomentData*> moments_;
    
    SeqRandNumGen randNumGen_;   /**< @brief the Random Number Generator(s) */
    RealType variance_;
    RealType langevinBufferRadius_;
    RealType frozenBufferRadius_;
    bool sphericalBoundaryConditions_;
    Globals* simParams;
    Velocitizer* veloMunge;
  };
 
}
#endif