Inversion.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 Inversion.hpp
 * @author    tlin
 * @date  11/01/2004
 * @version 1.0
 */
 
#ifndef PRIMITIVES_INVERSION_HPP
#define PRIMITIVES_INVERSION_HPP
 
#include "primitives/Atom.hpp"
#include "primitives/ShortRangeInteraction.hpp"
#include "types/InversionType.hpp"
 
namespace OpenMD {
  struct InversionData {
    RealType angle;
    RealType potential;
  };
 
  struct InversionDataSet {
    RealType deltaV;
    InversionData prev;
    InversionData curr;
  };
 
  /**
   * @class Inversion Inversion.hpp "primitives/Inversion.hpp"
   */
  class Inversion : public ShortRangeInteraction {
  public:
    using ShortRangeInteraction::getPrevValue;
    using ShortRangeInteraction::getValue;
 
    Inversion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4,
              InversionType* it);
    virtual ~Inversion() {}
    virtual void calcForce(RealType& angle, bool doParticlePot);
 
    RealType getValue(int snapshotNo) {
      // In OpenMD's version of an inversion, the central atom
      // comes first.  However, to get the planarity in a typical cosine
      // version of this potential (i.e. Amber-style), the central atom
      // is treated as atom *3* in a standard torsion form:
 
      Vector3d pos1 = atoms_[1]->getPos(snapshotNo);
      Vector3d pos2 = atoms_[2]->getPos(snapshotNo);
      Vector3d pos3 = atoms_[0]->getPos(snapshotNo);
      Vector3d pos4 = atoms_[3]->getPos(snapshotNo);
 
      Vector3d r31 = pos1 - pos3;
      snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r31);
      Vector3d r23 = pos3 - pos2;
      snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r23);
      Vector3d r43 = pos3 - pos4;
      snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r43);
 
      //  Calculate the cross products and distances
      Vector3d A = cross(r31, r43);
      Vector3d B = cross(r43, r23);
 
      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]; }
 
    InversionType* getInversionType() { return inversionType_; }
    virtual std::string getName() { return name_; }
    /** Sets the name of this inversion for selections */
    virtual void setName(const std::string& name) { name_ = name; }
 
    void accept(BaseVisitor* v) { v->visit(this); }
 
  protected:
    InversionType* inversionType_;
    InversionKey inversionKey_;
    std::string name_;
 
    RealType potential_;
  };
}  // namespace OpenMD
 
#endif  // PRIMITIVES_INVERSION_HPP