MolecularRestraint.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).
 */
 
#ifndef RESTRAINTS_MOLECULARRESTRAINT_HPP
#define RESTRAINTS_MOLECULARRESTRAINT_HPP
 
#include <vector>
 
#include "math/Vector3.hpp"
#include "restraints/Restraint.hpp"
 
namespace OpenMD {
  /**
   * @class MolecularRestraint
   *
   * MolecularRestraint is the restraint (both positional and
   * orientational) for the configuration of a flexible Molecule
   * relative to some reference structure for the same Molecule.  The
   * angles that define the deflection away from the reference
   * structure are the Euler angles taken from the rotation matrix
   * that gives the lowest root mean square deviation (RMSD), while
   * the displacement of the molecule is simply the displacement of
   * the center of mass relative to the reference structure.
   */
  class MolecularRestraint : public Restraint {
  public:
    MolecularRestraint() : Restraint() {}
 
    void setReferenceStructure(std::vector<Vector3d> ref, Vector3d refCom) {
      ref_    = ref;
      refCom_ = refCom;
 
      std::vector<Vector3d>::iterator i;
 
      for (i = ref_.begin(); i != ref_.end(); ++i) {
        (*i) = (*i) - refCom_;
      }
 
      forces_.clear();
      forces_.resize(ref_.size());
    }
 
    void calcForce(std::vector<Vector3d> struc, Vector3d molCom);
 
    std::vector<Vector3d> getRestraintForces() { return forces_; }
 
  private:
    std::vector<Vector3d> ref_;
    std::vector<Vector3d> forces_;
    Vector3d refCom_;
  };
}  // namespace OpenMD
 
#endif