src/restraints/MolecularRestraint.hpp

/*
 * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * 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 RESTRAINTS_MOLECULARRESTRAINT_HPP
#define RESTRAINTS_MOLECULARRESTRAINT_HPP

#include <vector>
#include "restraints/Restraint.hpp"
#include "math/Vector3.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_;
  };
}
#endif
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	3676 byte(s)
Log Message:	Fixed a widespread typo in the license
#	Content
1	/*
2	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifndef RESTRAINTS_MOLECULARRESTRAINT_HPP
44	#define RESTRAINTS_MOLECULARRESTRAINT_HPP
45
46	#include <vector>
47	#include "restraints/Restraint.hpp"
48	#include "math/Vector3.hpp"
49
50	namespace OpenMD {
51	/**
52	* @class MolecularRestraint
53	*
54	* MolecularRestraint is the restraint (both positional and
55	* orientational) for the configuration of a flexible Molecule
56	* relative to some reference structure for the same Molecule. The
57	* angles that define the deflection away from the reference
58	* structure are the Euler angles taken from the rotation matrix
59	* that gives the lowest root mean square deviation (RMSD), while
60	* the displacement of the molecule is simply the displacement of
61	* the center of mass relative to the reference structure.
62	*/
63	class MolecularRestraint : public Restraint {
64
65	public:
66
67	MolecularRestraint() : Restraint() { }
68
69	void setReferenceStructure(std::vector<Vector3d> ref, Vector3d refCom) {
70	ref_ = ref;
71	refCom_ = refCom;
72
73	std::vector<Vector3d>::iterator i;
74
75	for (i = ref_.begin(); i != ref_.end(); ++i) {
76	(i) = (i) - refCom_;
77	}
78
79	forces_.clear();
80	forces_.resize(ref_.size());
81	}
82
83	void calcForce(std::vector<Vector3d> struc, Vector3d molCom);
84
85	std::vector<Vector3d> getRestraintForces() { return forces_; }
86
87	private:
88	std::vector<Vector3d> ref_;
89	std::vector<Vector3d> forces_;
90	Vector3d refCom_;
91	};
92	}
93	#endif