OpenMD 3.0
Molecular Dynamics in the Open
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MolecularRestraint.hpp
1/*
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32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#ifndef RESTRAINTS_MOLECULARRESTRAINT_HPP
46#define RESTRAINTS_MOLECULARRESTRAINT_HPP
47
48#include <vector>
49
50#include "math/Vector3.hpp"
52
53namespace OpenMD {
54 /**
55 * @class MolecularRestraint
56 *
57 * MolecularRestraint is the restraint (both positional and
58 * orientational) for the configuration of a flexible Molecule
59 * relative to some reference structure for the same Molecule. The
60 * angles that define the deflection away from the reference
61 * structure are the Euler angles taken from the rotation matrix
62 * that gives the lowest root mean square deviation (RMSD), while
63 * the displacement of the molecule is simply the displacement of
64 * the center of mass relative to the reference structure.
65 */
67 public:
69
70 void setReferenceStructure(std::vector<Vector3d> ref, Vector3d refCom) {
71 ref_ = ref;
72 refCom_ = refCom;
73
74 std::vector<Vector3d>::iterator i;
75
76 for (i = ref_.begin(); i != ref_.end(); ++i) {
77 (*i) = (*i) - refCom_;
78 }
79
80 forces_.clear();
81 forces_.resize(ref_.size());
82 }
83
84 void calcForce(std::vector<Vector3d> struc, Vector3d molCom);
85
86 std::vector<Vector3d> getRestraintForces() { return forces_; }
87
88 private:
89 std::vector<Vector3d> ref_;
90 std::vector<Vector3d> forces_;
91 Vector3d refCom_;
92 };
93} // namespace OpenMD
94
95#endif
MolecularRestraint is the restraint (both positional and orientational) for the configuration of a fl...
void calcForce(std::vector< Vector3d > struc, Vector3d molCom)
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.