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, 24107 (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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	3675 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	cli2	1360	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	cli2	1360	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	cli2	1360	* 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	gezelter	1390	*
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, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	cli2	1360	*/
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	gezelter	1390	namespace OpenMD {
51	cli2	1360	/**
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