StretchBend.hpp

/*
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 *    notice, this list of conditions and the following disclaimer in the
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 * warranties, including any implied warranty of merchantability,
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 * using, modifying or distributing the software or its
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 * licensors be liable for any lost revenue, profit or data, or for
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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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
 
#ifndef PRIMITIVES_STRETCHBEND_HPP
#define PRIMITIVES_STRETCHBEND_HPP
 
#include "primitives/ShortRangeInteraction.hpp"
#include "primitives/Atom.hpp"
#include "types/BendType.hpp"
 
namespace OpenMD {
  struct BendData {
    RealType angle;
    RealType potential;
  };
  
  struct BendDataSet {
    RealType deltaV;
    BendData prev;
    BendData curr;
  };
  
  class Bend : public ShortRangeInteraction {
  public:
    using ShortRangeInteraction::getValue;
    using ShortRangeInteraction::getPrevValue;
    Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt)
      : ShortRangeInteraction(), bendType_(bt) {
      atoms_.resize(3);
      atoms_[0] = atom1;
      atoms_[1] = atom2;
      atoms_[2] = atom3;
    }
    
    virtual ~Bend() {}
    virtual void calcForce(RealType& angle, bool doParticlePot);
    
    RealType getValue(int snapshotNo) {
      Vector3d pos1 = atoms_[0]->getPos(snapshotNo);
      Vector3d pos2 = atoms_[1]->getPos(snapshotNo);
      Vector3d pos3 = atoms_[2]->getPos(snapshotNo);
      
      Vector3d r21 = pos1 - pos2;
      snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r21);
      RealType d21 = r21.length();
      
      Vector3d r23 = pos3 - pos2;
      snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r23);
      RealType d23 = r23.length();
      
      RealType cosTheta = dot(r21, r23) / (d21 * d23);
      
      //check roundoff     
      if (cosTheta > 1.0) {
        cosTheta = 1.0;
      } else if (cosTheta < -1.0) {
        cosTheta = -1.0;
      }
      
      return acos(cosTheta);
    }
 
 
    RealType getPotential() {
      return potential_;
    }
    
    Atom* getAtomA() {
      return atoms_[0];
    }
    
    Atom* getAtomB() {
      return atoms_[1];
    }
    
    Atom* getAtomC() {
      return atoms_[2];
    }
    
    BendType * getBendType() {
      return bendType_;
    }
    
    virtual std::string getName() { return name_;}        
    /** Sets the name of this bend for selections */
    virtual void setName(const std::string& name) { name_ = name;}
 
    void accept(BaseVisitor* v) {
      v->visit(this);
    }    
 
  protected:
    
    RealType potential_;
    BendType* bendType_; /**< bend type */
    std::string name_;        
 
  };    
} //end namespace OpenMD
#endif //PRIMITIVES_BEND_HPP