src/primitives/StuntDouble.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file StuntDouble.hpp
 * @author    tlin
 * @date  10/22/2004
 * @version 1.0
 */ 
   
#ifndef PRIMITIVES_STUNTDOUBLE_HPP
#define PRIMITIVES_STUNTDOUBLE_HPP

#include <vector>

#include "visitors/BaseVisitor.hpp"
#include "math/Quaternion.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "utils/PropertyMap.hpp"
#include "brains/Snapshot.hpp"
#include "brains/SnapshotManager.hpp"
namespace OpenMD{


  /**
   * @class StuntDouble StuntDouble.hpp "Primitives/StuntDouble.hpp"
   * @brief 
   *     "Don't move, or you're dead! Stand up! Captain, we've got them!"
   *
   *     "Spectacular stunt, my friends, but all for naught. Turn around
   *      please. Ha. What a pity. What a pity. So, Princess, you thought
   *      you could outwit the imperious forces of...."
   *
   *     "You idiots! These are not them. You've captured their stunt
   *      doubles! Search the area. Find them! Find them!"
   *
   * StuntDouble is a very strange idea.  A StuntDouble stands in for
   * some object that can be manipulated by the Integrators or
   * Minimizers.  Some of the manipulable objects are Atoms, some are
   * DirectionalAtoms, and some are RigidBodies.  StuntDouble
   * provides an interface for the Integrators and Minimizers to use,
   * and does some preliminary sanity checking so that the program
   * doesn't try to do something stupid like torque an Atom (The
   * quotes above are from Spaceballs...)
   *
   * @note the dynamic data of stuntDouble will be stored outside of the class
   */
  class StuntDouble{
  public:    

    enum ObjectType{
      otAtom,
      otDAtom,
      otRigidBody
    };

    virtual ~StuntDouble();
        
    /**
     * Returns the global index of this stuntDouble.
     * @return  the global index of this stuntDouble 
     */
    int getGlobalIndex() {
      return globalIndex_;
    }

    /**
     * Sets the global index of this stuntDouble.
     * @param index new global index to be set
     */
    void setGlobalIndex(int index) {
      globalIndex_ = index;
    }
    
    /** 
     * Returns the local index of this stuntDouble 
     * @return the local index of this stuntDouble
     */
    int getLocalIndex() {
      return localIndex_;
    }

    /**
     * Sets the local index of this stuntDouble
     * @param index new index to be set
     */        
    void setLocalIndex(int index) {
      localIndex_ = index;
    }
    
    int getGlobalIntegrableObjectIndex(){
      return globalIntegrableObjectIndex_; 
    }
    void setGlobalIntegrableObjectIndex(int index) {
      globalIntegrableObjectIndex_ = index;
    }

    /**
     * Sets the Snapshot Manager of this stuntDouble
     */
    void setSnapshotManager(SnapshotManager* sman) {
      snapshotMan_ = sman;
    }

    /**
     * Tests if this stuntDouble is an atom 
     * @return true is this stuntDouble is an atom(or a directional atom), return false otherwise
     */
    bool isAtom(){
      return objType_ == otAtom || objType_ == otDAtom;
    }

    /** 
     * Tests if this stuntDouble is an directional atom 
     * @return true if this stuntDouble is an directional atom, return false otherwise
     */
    bool isDirectionalAtom(){
      return objType_ == otDAtom;
    }

    /**
     * Tests if this stuntDouble is a rigid body. 
     * @return true if this stuntDouble is a rigid body, otherwise return false
     */
    bool isRigidBody(){
      return objType_ == otRigidBody;
    }

    /**
     * Tests if this stuntDouble is a directional one. 
     * @return true is this stuntDouble is a directional atom or a rigid body, return false otherwise
     */
    bool isDirectional(){
      return isDirectionalAtom() || isRigidBody();
    }

    /**
     * Freezes out all velocity, angular velocity, forces and torques
     * on this StuntDouble.  Also computes the number of frozen degrees
     * of freedom.
     * @return the total number of frozen degrees of freedom
     */   
    int freeze() {
      
      int fdf = 3;

      setVel(V3Zero);
      setFrc(V3Zero);
      if (isDirectional()){
        setJ(V3Zero);
        setTrq(V3Zero);
        if (isLinear()) 
          fdf +=2;
        else 
          fdf +=3;        
      }      
      return fdf;
    }

    /**
     * Returns the previous position of this stuntDouble
     * @return the position of this stuntDouble
     */    
    Vector3d getPrevPos() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).position[localIndex_];
    }
       
    /**
     * Returns the current position of this stuntDouble
     * @return the position of this stuntDouble
     */    
    Vector3d getPos() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
    }

    /**
     * Returns the position of this stuntDouble in specified snapshot 
     * @return the position of this stuntDouble
     * @param snapshotNo
     */    
    Vector3d getPos(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).position[localIndex_];
    }

    /**
     * Sets  the previous position of this stuntDouble
     * @param pos  new position 
     * @see #getPos
     */         
    void setPrevPos(const Vector3d& pos) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).position[localIndex_] = pos;
    }
       
    /**
     * Sets  the current position of this stuntDouble
     * @param pos  new position 
     */         
    void setPos(const Vector3d& pos) {
      DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
      data.position[localIndex_] = pos;
      //((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_] = pos;
    }

    /**
     * Sets  the position of this stuntDouble in specified snapshot
     * @param pos position to be set 
     * @param snapshotNo 
     * @see #getPos
     */         
    void setPos(const Vector3d& pos, int snapshotNo) {

      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).position[localIndex_] = pos;

    }
       
    /**
     * Returns the previous velocity of this stuntDouble
     * @return the velocity of this stuntDouble
     */    
    Vector3d getPrevVel() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).velocity[localIndex_];
    }
       
    /**
     * Returns the current velocity of this stuntDouble
     * @return the velocity of this stuntDouble
     */    
    Vector3d getVel() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
    }

    /**
     * Returns the velocity of this stuntDouble in specified snapshot 
     * @return the velocity of this stuntDouble
     * @param snapshotNo
     */    
    Vector3d getVel(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).velocity[localIndex_];
    }

    /**
     * Sets  the previous velocity of this stuntDouble
     * @param vel  new velocity 
     * @see #getVel
     */         
    void setPrevVel(const Vector3d& vel) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).velocity[localIndex_] = vel;
    }
       
    /**
     * Sets  the current velocity of this stuntDouble
     * @param vel  new velocity 
     */         
    void setVel(const Vector3d& vel) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_] = vel;
    }

    /**
     * Sets  the velocity of this stuntDouble in specified snapshot
     * @param vel velocity to be set 
     * @param snapshotNo 
     * @see #getVel
     */         
    void setVel(const Vector3d& vel, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).velocity[localIndex_] = vel;
    }

    /**
     * Returns the previous rotation matrix of this stuntDouble
     * @return the rotation matrix of this stuntDouble
     */    
    RotMat3x3d getPrevA() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_];
    }
       
    /**
     * Returns the current rotation matrix of this stuntDouble
     * @return the rotation matrix of this stuntDouble
     */    
    RotMat3x3d getA() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_];
    }

    /**
     * Returns the rotation matrix of this stuntDouble in specified snapshot 
     *
     * @return the rotation matrix of this stuntDouble
     * @param snapshotNo
     */    
    RotMat3x3d getA(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_];
    }

    /**
     * Sets  the previous rotation matrix of this stuntDouble
     * @param a  new rotation matrix 
     * @see #getA
     */         
    virtual void setPrevA(const RotMat3x3d& a) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
    }
       
    /**
     * Sets  the current rotation matrix of this stuntDouble
     * @param a  new rotation matrix 
     */         
    virtual void setA(const RotMat3x3d& a) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
    }

    /**
     * Sets  the rotation matrix of this stuntDouble in specified snapshot
     * @param a rotation matrix to be set 
     * @param snapshotNo 
     * @see #getA
     */         
    virtual void setA(const RotMat3x3d& a, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
    }       

    /**
     * Returns the previous angular momentum of this stuntDouble (body-fixed).
     * @return the angular momentum of this stuntDouble
     */    
    Vector3d getPrevJ() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).angularMomentum[localIndex_];
    }
       
    /**
     * Returns the current angular momentum of this stuntDouble (body -fixed).
     * @return the angular momentum of this stuntDouble
     */    
    Vector3d getJ() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).angularMomentum[localIndex_];
    }

    /**
     * Returns the angular momentum of this stuntDouble in specified snapshot (body-fixed).
     * @return the angular momentum of this stuntDouble
     * @param snapshotNo
     */    
    Vector3d getJ(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).angularMomentum[localIndex_];
    }

    /**
     * Sets  the previous angular momentum of this stuntDouble (body-fixed).
     * @param angMom  new angular momentum 
     * @see #getJ
     */         
    void setPrevJ(const Vector3d& angMom) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).angularMomentum[localIndex_] = angMom;
    }
       
    /**
     * Sets  the current angular momentum of this stuntDouble (body-fixed).
     * @param angMom  new angular momentum 
     */         
    void setJ(const Vector3d& angMom) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).angularMomentum[localIndex_] = angMom;
    }

    /**
     * Sets the angular momentum of this stuntDouble in specified snapshot(body-fixed).
     * @param angMom angular momentum to be set 
     * @param snapshotNo 
     * @see #getJ
     */         
    void setJ(const Vector3d& angMom, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).angularMomentum[localIndex_] = angMom;
    }
    
    /**
     * Returns system Center of Mass for stuntDouble frame from snapshot
     *
     */ 
    Vector3d getCOM(){
      return (snapshotMan_->getCurrentSnapshot())->getCOM();
    }
    
    /**
      * Returns system Center of Mass velocity for stuntDouble frame from snapshot
     *
     */ 
    
    Vector3d getCOMvel(){
      return (snapshotMan_->getCurrentSnapshot())->getCOMvel();
    }
    
    /**
      * Returns system Center of Mass angular momentum for stuntDouble frame from snapshot
     *
     */ 
    Vector3d getCOMw(){
      return (snapshotMan_->getCurrentSnapshot())->getCOMw();
    }
    
/**
     * Returns system Center of Mass for stuntDouble frame from snapshot
     *
     */ 
    Vector3d getCOM(int snapshotNo){
      return (snapshotMan_->getSnapshot(snapshotNo))->getCOM();
    }
    
    /**
      * Returns system Center of Mass velocity for stuntDouble frame from snapshot
     *
     */ 
    
    Vector3d getCOMvel(int snapshotNo){
      return (snapshotMan_->getSnapshot(snapshotNo))->getCOMvel();
    }
    
    /**
      * Returns system Center of Mass angular momentum for stuntDouble frame from snapshot
     *
     */ 
    Vector3d getCOMw(int snapshotNo){
      return (snapshotMan_->getSnapshot(snapshotNo))->getCOMw();
    }

    /**
     * Returns the previous quaternion of this stuntDouble
     * @return the quaternion of this stuntDouble
     */    
    Quat4d getPrevQ() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_].toQuaternion();
    }
       
    /**
     * Returns the current quaternion of this stuntDouble
     * @return the quaternion of this stuntDouble
     */    
    Quat4d getQ() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_].toQuaternion();
    }

    /**
     * Returns the quaternion of this stuntDouble in specified snapshot 
     * @return the quaternion of this stuntDouble
     * @param snapshotNo
     */    
    Quat4d getQ(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_].toQuaternion();
    }

    /**
     * Sets  the previous quaternion of this stuntDouble
     * @param q  new quaternion 
     * @note actual storage data is rotation matrix
     */         
    void setPrevQ(const Quat4d& q) {
      setPrevA(q);
    }
       
    /**
     * Sets  the current quaternion of this stuntDouble
     * @param q  new quaternion 
     * @note actual storage data is rotation matrix
     */         
    void setQ(const Quat4d& q) {
      setA(q);
    }

    /**
     * Sets  the quaternion of this stuntDouble in specified snapshot
     *
     * @param q quaternion to be set 
     * @param snapshotNo 
     * @note actual storage data is rotation matrix
     */         
    void setQ(const Quat4d& q, int snapshotNo) {
      setA(q, snapshotNo);
    }

    /**
     * Returns the previous euler angles of this stuntDouble
     * @return the euler angles of this stuntDouble
     */    
    Vector3d getPrevEuler() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_].toEulerAngles();
    }
       
    /**
     * Returns the current euler angles of this stuntDouble
     * @return the euler angles of this stuntDouble
     */    
    Vector3d getEuler() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_].toEulerAngles();
    }

    /**
     * Returns the euler angles of this stuntDouble in specified snapshot.
     * @return the euler angles of this stuntDouble
     * @param snapshotNo
     */    
    Vector3d getEuler(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_].toEulerAngles();
    }

    /**
     * Sets  the previous euler angles of this stuntDouble.
     * @param euler  new euler angles 
     * @see #getEuler
     * @note actual storage data is rotation matrix         
     */         
    void setPrevEuler(const Vector3d& euler) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = euler;
    }
       
    /**
     * Sets  the current euler angles of this stuntDouble
     * @param euler  new euler angles 
     */         
    void setEuler(const Vector3d& euler) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = euler;
    }

    /**
     * Sets  the euler angles  of this stuntDouble in specified snapshot
     *
     * @param euler euler angles to be set 
     * @param snapshotNo 
     * @note actual storage data is rotation matrix                  
     */         
    void setEuler(const Vector3d& euler, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = euler;
    }

    /**
     * Returns the previous dipole vector of this stuntDouble
     * @return the dipole vector of this stuntDouble
     */    
    Vector3d getPrevDipole() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_];
    }
    
    /**
     * Returns the current dipole vector of this stuntDouble
     * @return the dipole vector of this stuntDouble
     */    
    Vector3d getDipole() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_];
    }
    
    /**
     * Returns the dipole vector of this stuntDouble in specified snapshot 
     *
     * @return the dipole vector of this stuntDouble
     * @param snapshotNo
     */    
    Vector3d getDipole(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).dipole[localIndex_];
    }


    /**
     * Returns the previous quadrupole tensor of this stuntDouble
     * @return the quadrupole tensor of this stuntDouble
     */    
    Mat3x3d getPrevQuadrupole() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_];
    }
    
    /**
     * Returns the current quadrupole tensor of this stuntDouble
     * @return the quadrupole tensor of this stuntDouble
     */    
    Mat3x3d getQuadrupole() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).quadrupole[localIndex_];
    }
    
    /**
     * Returns the quadrupole tensor of this stuntDouble in specified snapshot 
     *
     * @return the quadrupole tensor of this stuntDouble
     * @param snapshotNo
     */    
    Mat3x3d getQuadrupole(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).quadrupole[localIndex_];
    }
        
    /**
     * Returns the previous force of this stuntDouble
     * @return the force of this stuntDouble
     */    
    Vector3d getPrevFrc() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).force[localIndex_];
    }
       
    /**
     * Returns the current force of this stuntDouble
     * @return the force of this stuntDouble
     */    
    Vector3d getFrc() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).force[localIndex_];
    }

    /**
     * Returns the force of this stuntDouble in specified snapshot 
     *
     * @return the force of this stuntDouble
     * @param snapshotNo
     */    
    Vector3d getFrc(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).force[localIndex_];
    }

    /**
     * Sets  the previous force of this stuntDouble
     *
     * @param frc  new force 
     * @see #getFrc
     */         
    void setPrevFrc(const Vector3d& frc) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).force[localIndex_] = frc;
    }
       
    /**
     * Sets  the current force of this stuntDouble
     * @param frc  new force 
     */         
    void setFrc(const Vector3d& frc) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).force[localIndex_] = frc;
    }

    /**
     * Sets  the force of this stuntDouble in specified snapshot
     *
     * @param frc force to be set 
     * @param snapshotNo 
     * @see #getFrc
     */         
    void setFrc(const Vector3d& frc, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).force[localIndex_] = frc;
    }

    /**
     * Adds force into the previous force of this stuntDouble
     *
     * @param frc  new force 
     * @see #getFrc
     */         
    void addPrevFrc(const Vector3d& frc) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).force[localIndex_] += frc;
    }
       
    /**
     * Adds force into the current force of this stuntDouble
     * @param frc  new force 
     */         
    void addFrc(const Vector3d& frc) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).force[localIndex_] += frc;
    }

    /**
     * Adds force into the force of this stuntDouble in specified snapshot
     *
     * @param frc force to be set 
     * @param snapshotNo 
     * @see #getFrc
     */         
    void addFrc(const Vector3d& frc, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).force[localIndex_] += frc;
    }

    /**
     * Returns the previous torque of this stuntDouble
     * @return the torque of this stuntDouble
     */    
    Vector3d getPrevTrq() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).torque[localIndex_];
    }
       
    /**
     * Returns the current torque of this stuntDouble
     * @return the torque of this stuntDouble
     */    
    Vector3d getTrq() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).torque[localIndex_];
    }

    /**
     * Returns the torque of this stuntDouble in specified snapshot 
     *
     * @return the torque of this stuntDouble
     * @param snapshotNo
     */    
    Vector3d getTrq(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).torque[localIndex_];
    }

    /**
     * Sets  the previous torque of this stuntDouble
     *
     * @param trq  new torque 
     * @see #getTrq
     */         
    void setPrevTrq(const Vector3d& trq) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).torque[localIndex_] = trq;
    }
       
    /**
     * Sets  the current torque of this stuntDouble
     * @param trq  new torque 
     */         
    void setTrq(const Vector3d& trq) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).torque[localIndex_] = trq;
    }

    /**
     * Sets  the torque of this stuntDouble in specified snapshot
     *
     * @param trq torque to be set 
     * @param snapshotNo 
     * @see #getTrq
     */         
    void setTrq(const Vector3d& trq, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).torque[localIndex_] = trq;
    }

    /**
     * Adds torque into the previous torque of this stuntDouble
     *
     * @param trq  new torque 
     * @see #getTrq
     */         
    void addPrevTrq(const Vector3d& trq) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).torque[localIndex_] += trq;
    }
       
    /**
     * Adds torque into the current torque of this stuntDouble
     * @param trq  new torque 
     */         
    void addTrq(const Vector3d& trq) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).torque[localIndex_] += trq;
    }

    /**
     * Adds torque into the torque of this stuntDouble in specified snapshot
     *
     * @param trq torque to be add 
     * @param snapshotNo 
     * @see #getTrq
     */         
    void addTrq(const Vector3d& trq, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).torque[localIndex_] += trq;
    }       


    /**
     * Returns the previous particlePot of this stuntDouble
     * @return the particlePot of this stuntDouble
     */    
    RealType getPrevParticlePot() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).particlePot[localIndex_];
    }
       
    /**
     * Returns the current particlePot of this stuntDouble
     * @return the particlePot of this stuntDouble
     */    
    RealType getParticlePot() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).particlePot[localIndex_];
    }

    /**
     * Returns the particlePot of this stuntDouble in specified snapshot 
     *
     * @return the particlePot of this stuntDouble
     * @param snapshotNo
     */    
    RealType getParticlePot(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).particlePot[localIndex_];
    }

    /**
     * Sets  the previous particlePot of this stuntDouble
     *
     * @param particlePot  new particlePot 
     * @see #getParticlePot
     */         
    void setPrevParticlePot(const RealType& particlePot) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).particlePot[localIndex_] = particlePot;
    }
       
    /**
     * Sets  the current particlePot of this stuntDouble
     * @param particlePot  new particlePot 
     */         
    void setParticlePot(const RealType& particlePot) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).particlePot[localIndex_] = particlePot;
    }

    /**
     * Sets  the particlePot of this stuntDouble in specified snapshot
     *
     * @param particlePot particlePot to be set 
     * @param snapshotNo 
     * @see #getParticlePot
     */         
    void setParticlePot(const RealType& particlePot, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).particlePot[localIndex_] = particlePot;
    }

    /**
     * Adds particlePot into the previous particlePot of this stuntDouble
     *
     * @param particlePot  new particlePot 
     * @see #getParticlePot
     */         
    void addPrevParticlePot(const RealType& particlePot) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).particlePot[localIndex_] += particlePot;
    }
       
    /**
     * Adds particlePot into the current particlePot of this stuntDouble
     * @param particlePot  new particlePot 
     */         
    void addParticlePot(const RealType& particlePot) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).particlePot[localIndex_] += particlePot;
    }

    /**
     * Adds particlePot into the particlePot of this stuntDouble in specified snapshot
     *
     * @param particlePot particlePot to be add 
     * @param snapshotNo 
     * @see #getParticlePot
     */         
    void addParticlePot(const RealType& particlePot, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).particlePot[localIndex_] += particlePot;
    }       

    /**
     * Returns the previous fluctuating charge of this stuntDouble
     * @return the fluctuating charge of this stuntDouble
     */    
    RealType getPrevFlucQPos() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).flucQPos[localIndex_];
    }
       
    /**
     * Returns the current fluctuating charge of this stuntDouble
     * @return the fluctuating charge of this stuntDouble
     */    
    RealType getFlucQPos() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQPos[localIndex_];
    }

    /**
     * Returns the fluctuating charge of this stuntDouble in specified snapshot
     * @return the fluctuating charge of this stuntDouble
     * @param snapshotNo
     */    
    RealType getFlucQPos(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQPos[localIndex_];
    }

    /**
     * Sets  the previous fluctuating charge of this stuntDouble
     * @param charge  new fluctuating charge 
     * @see #getFlucQPos
     */         
    void setPrevFlucQPos(RealType charge) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQPos[localIndex_] = charge;
    }
       
    /**
     * Sets  the current fluctuating charge of this stuntDouble
     * @param charge  new fluctuating charge 
     */         
    void setFlucQPos(RealType charge) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQPos[localIndex_] = charge;
    }

    /**
     * Sets  the fluctuating charge of this stuntDouble in specified snapshot
     * @param charge fluctuating charge to be set 
     * @param snapshotNo 
     * @see #getFlucQPos
     */         
    void setFlucQPos(RealType charge, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQPos[localIndex_] = charge;
    }

    /**
     * Adds fluctuating charge into the previous fluctuating charge of this stuntDouble
     * @param charge  new fluctuating charge 
     * @see #getFlucQPos
     */         
    void addPrevFlucQPos(RealType charge) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQPos[localIndex_] += charge;
    }
       
    /**
     * Adds fluctuating charge into the current fluctuating charge of this stuntDouble
     * @param charge  new fluctuating charge 
     */         
    void addFlucQPos(RealType charge) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQPos[localIndex_] += charge;
    }

    /**
     * Adds fluctuating charge into the fluctuating charge of this stuntDouble in specified snapshot
     * @param charge fluctuating charge to be add 
     * @param snapshotNo 
     * @see #getFlucQPos
     */         
    void addFlucQPos(RealType charge, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQPos[localIndex_] += charge;
    }       


    /**
     * Returns the previous charge velocity of this stuntDouble
     * @return the charge velocity of this stuntDouble
     */    
    RealType getPrevFlucQVel() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).flucQVel[localIndex_];
    }
       
    /**
     * Returns the current charge velocity of this stuntDouble
     * @return the charge velocity of this stuntDouble
     */    
    RealType getFlucQVel() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQVel[localIndex_];
    }

    /**
     * Returns the charge velocity of this stuntDouble in specified snapshot
     * @return the charge velocity of this stuntDouble
     * @param snapshotNo
     */    
    RealType getFlucQVel(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQVel[localIndex_];
    }

    /**
     * Sets  the previous charge velocity of this stuntDouble
     * @param cvel  new charge velocity 
     * @see #getFlucQVel
     */         
    void setPrevFlucQVel(RealType cvel) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQVel[localIndex_] = cvel;
    }
       
    /**
     * Sets  the current charge velocity of this stuntDouble
     * @param cvel  new charge velocity 
     */         
    void setFlucQVel(RealType cvel) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQVel[localIndex_] = cvel;
    }

    /**
     * Sets  the charge velocity of this stuntDouble in specified snapshot
     * @param cvel charge velocity to be set 
     * @param snapshotNo 
     * @see #getFlucQVel
     */         
    void setFlucQVel(RealType cvel, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQVel[localIndex_] = cvel;
    }

    /**
     * Adds charge velocity into the previous charge velocity of this stuntDouble
     * @param cvel  new charge velocity 
     * @see #getFlucQVel
     */         
    void addPrevFlucQVel(RealType cvel) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQVel[localIndex_] += cvel;
    }
       
    /**
     * Adds charge velocity into the current charge velocity of this stuntDouble
     * @param cvel  new charge velocity 
     */         
    void addFlucQVel(RealType cvel) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQVel[localIndex_] += cvel;
    }

    /**
     * Adds charge velocity into the charge velocity of this stuntDouble in specified snapshot
     * @param cvel charge velocity to be add 
     * @param snapshotNo 
     * @see #getFlucQVel
     */         
    void addFlucQVel(RealType cvel, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQVel[localIndex_] += cvel;
    }       


    /**
     * Returns the previous charge force of this stuntDouble
     * @return the charge force of this stuntDouble
     */    
    RealType getPrevFlucQFrc() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).flucQFrc[localIndex_];
    }
       
    /**
     * Returns the current charge force of this stuntDouble
     * @return the charge force of this stuntDouble
     */    
    RealType getFlucQFrc() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQFrc[localIndex_];
    }

    /**
     * Returns the charge force of this stuntDouble in specified snapshot
     * @return the charge force of this stuntDouble
     * @param snapshotNo
     */    
    RealType getFlucQFrc(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQFrc[localIndex_];
    }

    /**
     * Sets  the previous charge force of this stuntDouble
     * @param cfrc  new charge force 
     * @see #getFlucQFrc
     */         
    void setPrevFlucQFrc(RealType cfrc) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQFrc[localIndex_] = cfrc;
    }
       
    /**
     * Sets  the current charge force of this stuntDouble
     * @param cfrc  new charge force 
     */         
    void setFlucQFrc(RealType cfrc) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQFrc[localIndex_] = cfrc;
    }

    /**
     * Sets  the charge force of this stuntDouble in specified snapshot
     * @param cfrc charge force to be set 
     * @param snapshotNo 
     * @see #getFlucQFrc
     */         
    void setFlucQFrc(RealType cfrc, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQFrc[localIndex_] = cfrc;
    }

    /**
     * Adds charge force into the previous charge force of this stuntDouble
     * @param cfrc   charge force to be added 
     * @see #getFlucQFrc
     */         
    void addPrevFlucQFrc(RealType cfrc) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQFrc[localIndex_] += cfrc;
    }
       
    /**
     * Adds charge force into the current charge force of this stuntDouble
     * @param cfrc   charge force to be added 
     */         
    void addFlucQFrc(RealType cfrc) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQFrc[localIndex_] += cfrc;
    }

    /**
     * Adds charge force into the charge force of this stuntDouble in specified snapshot
     * @param cfrc charge force to be added
     * @param snapshotNo 
     * @see #getFlucQFrc
     */         
    void addFlucQFrc(RealType cfrc, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQFrc[localIndex_] += cfrc;
    }       


    /**
     * Returns the previous electric field of this stuntDouble
     * @return the electric field of this stuntDouble
     */    
    Vector3d getPrevElectricField() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).electricField[localIndex_];
    }
       
    /**
     * Returns the current electric field of this stuntDouble
     * @return the electric field of this stuntDouble
     */    
    Vector3d getElectricField() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).electricField[localIndex_];
    }

    /**
     * Returns the electric field of this stuntDouble in specified snapshot 
     * @return the electric field of this stuntDouble
     * @param snapshotNo
     */    
    Vector3d getElectricField(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electricField[localIndex_];
    }

    /**
     * Sets the previous electric field of this stuntDouble
     * @param eField  new electric field 
     * @see #getElectricField
     */         
    void setPrevElectricField(const Vector3d& eField) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).electricField[localIndex_] = eField;
    }
       
    /**
     * Sets the current electric field of this stuntDouble
     * @param eField  new electric field 
     */         
    void setElectricField(const Vector3d& eField) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).electricField[localIndex_] = eField;
    }

    /**
     * Sets the electric field of this stuntDouble in specified snapshot
     * @param eField electric field to be set 
     * @param snapshotNo 
     * @see #getElectricField
     */         
    void setElectricField(const Vector3d& eField, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electricField[localIndex_] = eField;
    }

    /**
     * Adds electric field into the previous electric field of this
     * stuntDouble
     *
     * @param eField new electric field 
     * @see #getElectricField
     */         
    void addPrevEelectricField(const Vector3d& eField) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).electricField[localIndex_] += eField;
    }
       
    /**
     * Adds electric field into the current electric field of this stuntDouble
     * @param eField  new electric field 
     */         
    void addElectricField(const Vector3d& eField) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).electricField[localIndex_] += eField;
    }

    /**
     * Adds electric field into the electric field of this stuntDouble in specified snapshot
     *
     * @param eField electric field to be added
     * @param snapshotNo 
     * @see #getElectricField
     */         
    void addElectricField(const Vector3d& eField, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electricField[localIndex_] += eField;
    }       

    /**
     * Returns the previous charge force of this stuntDouble
     * @return the charge force of this stuntDouble
     */    
    RealType getPrevSitePotential() {
      return ((snapshotMan_->getPrevSnapshot())->*storage_).sitePotential[localIndex_];
    }
       
    /**
     * Returns the current charge force of this stuntDouble
     * @return the charge force of this stuntDouble
     */    
    RealType getSitePotential() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).sitePotential[localIndex_];
    }

    /**
     * Returns the charge force of this stuntDouble in specified snapshot
     * @return the charge force of this stuntDouble
     * @param snapshotNo
     */    
    RealType getSitePotential(int snapshotNo) {
      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).sitePotential[localIndex_];
    }

    /**
     * Sets  the previous charge force of this stuntDouble
     * @param spot  new charge force 
     * @see #getSitePotential
     */         
    void setPrevSitePotential(RealType spot) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).sitePotential[localIndex_] = spot;
    }
       
    /**
     * Sets  the current charge force of this stuntDouble
     * @param spot  new charge force 
     */         
    void setSitePotential(RealType spot) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).sitePotential[localIndex_] = spot;
    }

    /**
     * Sets  the charge force of this stuntDouble in specified snapshot
     * @param spot charge force to be set 
     * @param snapshotNo 
     * @see #getSitePotential
     */         
    void setSitePotential(RealType spot, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).sitePotential[localIndex_] = spot;
    }

    /**
     * Adds charge force into the previous charge force of this stuntDouble
     * @param spot   charge force to be added 
     * @see #getSitePotential
     */         
    void addPrevSitePotential(RealType spot) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).sitePotential[localIndex_] += spot;
    }
       
    /**
     * Adds charge force into the current charge force of this stuntDouble
     * @param spot   charge force to be added 
     */         
    void addSitePotential(RealType spot) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).sitePotential[localIndex_] += spot;
    }

    /**
     * Adds charge force into the charge force of this stuntDouble in specified snapshot
     * @param spot charge force to be added
     * @param snapshotNo 
     * @see #getSitePotential
     */         
    void addSitePotential(RealType spot, int snapshotNo) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).sitePotential[localIndex_] += spot;
    }       


    /** Set the force of this stuntDouble to zero */
    void zeroForcesAndTorques(); 
    /**
     * Returns the inertia tensor of this stuntDouble
     * @return the inertia tensor of this stuntDouble
     */ 
    virtual Mat3x3d getI() = 0;

    /**
     * Returns the gradient of this stuntDouble
     * @return the gradient of this stuntDouble
     */ 
    virtual std::vector<RealType> getGrad() = 0;

    /**
     * Tests the  if this stuntDouble is a  linear rigidbody
     *
     * @return true if this stuntDouble is a  linear rigidbody, otherwise return false
     * @note atom and directional atom will always return false
     * 
     * @see #linearAxis
     */         
    bool isLinear() {
      return linear_;
    }

    /**
     * Returns the linear axis of the rigidbody, atom and directional atom will always return -1
     *
     * @return the linear axis of the rigidbody
     * 
     * @see #isLinear
     */ 
    int linearAxis() {
      return linearAxis_;
    }

    /** Returns the mass of this stuntDouble */
    RealType getMass() {
      return mass_;
    }

    /**
     * Sets the mass of this stuntdoulbe
     * @param mass the mass to be set
     */         
    void setMass(RealType mass) {
      mass_ = mass;
    }

    /** Returns the name of this stuntDouble */
    virtual std::string getType() = 0;
        
    /** Sets the name of this stuntDouble*/
    virtual void setType(const std::string& name) {}

    /**
     * Converts a lab fixed vector to a body fixed vector.
     * @return body fixed vector
     * @param v lab fixed vector
     */
    Vector3d lab2Body(const Vector3d& v) {
      return getA() * v;
    }

    Vector3d lab2Body(const Vector3d& v, int frame) {
      return getA(frame) * v;
    }

    /**
     * Converts a body fixed vector to a lab fixed vector.
     * @return corresponding lab fixed vector
     * @param v body fixed vector
     */
    Vector3d body2Lab(const Vector3d& v){
      return getA().transpose() * v;
    }

    Vector3d body2Lab(const Vector3d& v, int frame){
      return getA(frame).transpose() * v;
    }

    /**
     * <p>
     * The purpose of the Visitor Pattern is to encapsulate an
     * operation that you want to perform on the elements of a data
     * structure. In this way, you can change the operation being
     * performed on a structure without the need of changing the
     * classes of the elements that you are operating on. Using a
     * Visitor pattern allows you to decouple the classes for the data
     * structure and the algorithms used upon them
     * </p>
     * @param v visitor
     */      
    virtual void accept(BaseVisitor* v) = 0;

    //below functions are just forward functions
    /**
     * Adds property into property map
     * @param genData GenericData to be added into PropertyMap
     */
    void addProperty(GenericData* genData);

    /**
     * Removes property from PropertyMap by name
     * @param propName the name of property to be removed
     */
    void removeProperty(const std::string& propName);

    /**
     * clear all of the properties
     */
    void clearProperties();

    /**
     * Returns all names of properties
     * @return all names of properties
     */
    std::vector<std::string> getPropertyNames();

    /**
     * Returns all of the properties in PropertyMap
     * @return all of the properties in PropertyMap
     */      
    std::vector<GenericData*> getProperties();

    /**
     * Returns property 
     * @param propName name of property
     * @return a pointer point to property with propName. If no property named propName
     * exists, return NULL
     */      
    GenericData* getPropertyByName(const std::string& propName);

  protected:
        
    StuntDouble(ObjectType objType, DataStoragePointer storage); 
        
    StuntDouble(const StuntDouble& sd);
    StuntDouble& operator=(const StuntDouble& sd);

    ObjectType objType_;
    DataStoragePointer storage_;
    SnapshotManager* snapshotMan_;
        
    bool linear_;
    int linearAxis_;        

        
    int globalIndex_;
    int globalIntegrableObjectIndex_;
    int localIndex_;


    RealType mass_;
        
  private:
        
    PropertyMap properties_;
  };

}//end namespace OpenMD
#endif //PRIMITIVES_STUNTDOUBLE_HPP
Revision:	1993
Committed:	Tue Apr 29 17:32:31 2014 UTC (11 years ago) by gezelter
File size:	45840 byte(s)
Log Message:	Added sitePotentials for the Choi et al. potential-frequency maps for nitriles