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) {}

        void calcForce() {
            double len;
            double 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);
       }
        
        double getPotential() {
            return potential_;
        }

        Atom* getAtomA() {
            return atom1_;
        }

        Atom* getAtomB() {
            return atom2_;
        }

        BondType* getBondType() {
            return bondType_;
        }
        
    private:
        double potential_;
        Atom* atom1_;
        Atom* atom2_;        
        BondType* bondType_; /**< bond type */

};    


} //end namespace oopse
#endif //PRIMITIVES_BOND_HPP
Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (20 years, 7 months ago) by tim
File size:	3350 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	1694	*
4	tim	1927	* 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	tim	1694	*/
41	tim	1927
42	tim	1694	/**
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	tim	1782	#include "primitives/Atom.hpp"
54	tim	1695	#include "types/BondType.hpp"
55
56	tim	1694	namespace oopse {
57
58			class Bond {
59			public:
60	tim	1803	Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1), atom2_(atom2), bondType_(bt) {}
61	tim	1694
62			void calcForce() {
63			double len;
64	tim	1747	double dvdr;
65	tim	1694	Vector3d r12;
66			Vector3d force;
67
68	tim	1747	r12 = atom2_->getPos() - atom1_->getPos();
69	tim	1694	len = r12.length();
70	tim	1747	bondType_->calcForce(len, potential_, dvdr);
71	tim	1694
72	tim	1747	force = r12 * (-dvdr / len);
73	tim	1694
74	tim	1857	atom1_->addFrc(-force);
75			atom2_->addFrc(force);
76	tim	1694	}
77
78			double getPotential() {
79	tim	1747	return potential_;
80	tim	1694	}
81
82	tim	1803	Atom* getAtomA() {
83			return atom1_;
84			}
85
86			Atom* getAtomB() {
87			return atom2_;
88			}
89
90			BondType* getBondType() {
91			return bondType_;
92			}
93	tim	1883
94	tim	1694	private:
95	tim	1883	double potential_;
96			Atom* atom1_;
97			Atom* atom2_;
98	tim	1694	BondType* bondType_; /*< bond type /
99	tim	1883
100	tim	1694	};
101
102
103
104			} //end namespace oopse
105			#endif //PRIMITIVES_BOND_HPP