src/primitives/Bond.hpp

/*
 * Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
/**
 * @file Bond.hpp
 * @author    tlin
 * @date  11/01/2004
 * @version 1.0
 */ 


#ifndef PRIMITIVES_BOND_HPP
#define PRIMITIVES_BOND_HPP

#include "primitives/Atom.hpp"
#include "types/BondType.hpp"

namespace oopse {
  
  class Bond {
  public:
    Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1), 
                                                   atom2_(atom2), 
                                                   bondType_(bt) {}
    virtual ~Bond() {}
    void calcForce() {
      RealType len;
      RealType dvdr;
      Vector3d r12;
      Vector3d force;
      
      r12 = atom2_->getPos() - atom1_->getPos();
      len = r12.length();            
      bondType_->calcForce(len,  potential_, dvdr);
      
      force = r12 * (-dvdr / len);

      atom1_->addFrc(-force);
      atom2_->addFrc(force);
    }
    
    RealType getPotential() {
      return potential_;
    }
    
    Atom* getAtomA() {
      return atom1_;
    }
    
    Atom* getAtomB() {
      return atom2_;
    }
    
    BondType* getBondType() {
      return bondType_;
    }
    
  private:
    RealType potential_;
    Atom* atom1_;
    Atom* atom2_;        
    BondType* bondType_; /**< bond type */
    
  };    
} //end namespace oopse
#endif //PRIMITIVES_BOND_HPP
Revision:	1290
Committed:	Wed Sep 10 19:51:45 2008 UTC (16 years, 7 months ago) by cli2
Original Path:	*trunk/src/primitives/Bond.hpp*
File size:	3347 byte(s)
Log Message:	Inversion fixes and amber mostly working
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file Bond.hpp
44			* @author tlin
45			* @date 11/01/2004
46			* @version 1.0
47			*/
48
49
50			#ifndef PRIMITIVES_BOND_HPP
51			#define PRIMITIVES_BOND_HPP
52
53			#include "primitives/Atom.hpp"
54			#include "types/BondType.hpp"
55
56			namespace oopse {
57	gezelter	1211
58	gezelter	507	class Bond {
59			public:
60	gezelter	1211	Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1),
61			atom2_(atom2),
62			bondType_(bt) {}
63	gezelter	507	virtual ~Bond() {}
64			void calcForce() {
65	tim	963	RealType len;
66			RealType dvdr;
67	gezelter	507	Vector3d r12;
68			Vector3d force;
69	gezelter	1211
70	gezelter	507	r12 = atom2_->getPos() - atom1_->getPos();
71			len = r12.length();
72			bondType_->calcForce(len, potential_, dvdr);
73	gezelter	1211
74	gezelter	507	force = r12 * (-dvdr / len);
75	cli2	1290
76	gezelter	507	atom1_->addFrc(-force);
77			atom2_->addFrc(force);
78			}
79	gezelter	1211
80	tim	963	RealType getPotential() {
81	gezelter	507	return potential_;
82			}
83	gezelter	1211
84	gezelter	507	Atom* getAtomA() {
85			return atom1_;
86			}
87	gezelter	1211
88	gezelter	507	Atom* getAtomB() {
89			return atom2_;
90			}
91	gezelter	1211
92	gezelter	507	BondType* getBondType() {
93			return bondType_;
94			}
95	gezelter	1211
96	gezelter	507	private:
97	tim	963	RealType potential_;
98	gezelter	507	Atom* atom1_;
99			Atom* atom2_;
100			BondType* bondType_; /*< bond type /
101	gezelter	1211
102	gezelter	507	};
103	gezelter	246	} //end namespace oopse
104			#endif //PRIMITIVES_BOND_HPP