Torsion.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).
 */
 
/**
 * @file Torsion.hpp
 * @author    tlin
 * @date  11/01/2004
 * @version 1.0
 */
 
#ifndef PRIMITIVES_TORSION_HPP
#define PRIMITIVES_TORSION_HPP
 
#include <limits>
 
#include "primitives/Atom.hpp"
#include "primitives/ShortRangeInteraction.hpp"
#include "types/TorsionType.hpp"
 
namespace OpenMD {
  struct TorsionData {
    RealType angle;
    RealType potential;
  };
 
  struct TorsionDataSet {
    RealType deltaV;
    TorsionData prev;
    TorsionData curr;
  };
 
  /**
   * @class Torsion Torsion.hpp "types/Torsion.hpp"
   */
  class Torsion : public ShortRangeInteraction {
  public:
    using ShortRangeInteraction::getPrevValue;
    using ShortRangeInteraction::getValue;
 
    Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4,
            TorsionType* tt);
    virtual ~Torsion() {}
    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 pos4 = atoms_[3]->getPos(snapshotNo);
 
      Vector3d r21 = pos1 - pos2;
      snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r21);
      Vector3d r32 = pos2 - pos3;
      snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r32);
      Vector3d r43 = pos3 - pos4;
      snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r43);
 
      //  Calculate the cross products and distances
      Vector3d A  = cross(r21, r32);
      RealType rA = A.length();
      Vector3d B  = cross(r32, r43);
      RealType rB = B.length();
 
      /*
         If either of the two cross product vectors is tiny, that means
         the three atoms involved are colinear, and the torsion angle is
         going to be undefined.  The easiest check for this problem is
         to use the product of the two lengths.
      */
      if (rA * rB < OpenMD::epsilon) return numeric_limits<double>::quiet_NaN();
 
      A.normalize();
      B.normalize();
 
      //  Calculate the sin and cos
      RealType cos_phi = dot(A, B);
      if (cos_phi > 1.0) cos_phi = 1.0;
      if (cos_phi < -1.0) cos_phi = -1.0;
      return acos(cos_phi);
    }
 
    RealType getPotential() { return potential_; }
 
    Atom* getAtomA() { return atoms_[0]; }
 
    Atom* getAtomB() { return atoms_[1]; }
 
    Atom* getAtomC() { return atoms_[2]; }
 
    Atom* getAtomD() { return atoms_[3]; }
 
    TorsionType* getTorsionType() { return torsionType_; }
 
    virtual std::string getName() { return name_; }
    /** Sets the name of this torsion for selections */
    virtual void setName(const std::string& name) { name_ = name; }
 
    void accept(BaseVisitor* v) { v->visit(this); }
 
  protected:
    TorsionType* torsionType_;
    std::string name_;
 
    RealType potential_;
  };
}  // namespace OpenMD
 
#endif  // PRIMITIVES_TORSION_HPP