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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	3609 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	cli2	1360	*/
41
42			#ifndef RESTRAINTS_MOLECULARRESTRAINT_HPP
43			#define RESTRAINTS_MOLECULARRESTRAINT_HPP
44
45			#include <vector>
46			#include "restraints/Restraint.hpp"
47			#include "math/Vector3.hpp"
48
49	gezelter	1390	namespace OpenMD {
50	cli2	1360	/**
51			* @class MolecularRestraint
52			*
53			* MolecularRestraint is the restraint (both positional and
54			* orientational) for the configuration of a flexible Molecule
55			* relative to some reference structure for the same Molecule. The
56			* angles that define the deflection away from the reference
57			* structure are the Euler angles taken from the rotation matrix
58			* that gives the lowest root mean square deviation (RMSD), while
59			* the displacement of the molecule is simply the displacement of
60			* the center of mass relative to the reference structure.
61			*/
62			class MolecularRestraint : public Restraint {
63
64			public:
65
66			MolecularRestraint() : Restraint() { }
67
68			void setReferenceStructure(std::vector<Vector3d> ref, Vector3d refCom) {
69			ref_ = ref;
70			refCom_ = refCom;
71
72			std::vector<Vector3d>::iterator i;
73
74			for (i = ref_.begin(); i != ref_.end(); ++i) {
75			(i) = (i) - refCom_;
76			}
77
78			forces_.clear();
79			forces_.resize(ref_.size());
80			}
81
82			void calcForce(std::vector<Vector3d> struc, Vector3d molCom);
83
84			std::vector<Vector3d> getRestraintForces() { return forces_; }
85
86			private:
87			std::vector<Vector3d> ref_;
88			std::vector<Vector3d> forces_;
89			Vector3d refCom_;
90			};
91			}
92			#endif