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. 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).
 */
 
/**
 * @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 OpenMD {
  
  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);
     
      atom1_->addParticlePot(potential_);
      atom2_->addParticlePot(potential_);
    }
    
    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 OpenMD
#endif //PRIMITIVES_BOND_HPP
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	3546 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	246	*/
42
43			/**
44			* @file Bond.hpp
45			* @author tlin
46			* @date 11/01/2004
47			* @version 1.0
48			*/
49
50
51			#ifndef PRIMITIVES_BOND_HPP
52			#define PRIMITIVES_BOND_HPP
53
54			#include "primitives/Atom.hpp"
55			#include "types/BondType.hpp"
56
57	gezelter	1390	namespace OpenMD {
58	gezelter	1211
59	gezelter	507	class Bond {
60			public:
61	gezelter	1211	Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1),
62			atom2_(atom2),
63			bondType_(bt) {}
64	gezelter	507	virtual ~Bond() {}
65			void calcForce() {
66	tim	963	RealType len;
67			RealType dvdr;
68	gezelter	507	Vector3d r12;
69			Vector3d force;
70	gezelter	1211
71	gezelter	507	r12 = atom2_->getPos() - atom1_->getPos();
72			len = r12.length();
73			bondType_->calcForce(len, potential_, dvdr);
74	gezelter	1211
75	gezelter	507	force = r12 * (-dvdr / len);
76	cli2	1290
77	gezelter	507	atom1_->addFrc(-force);
78			atom2_->addFrc(force);
79	gezelter	1309
80			atom1_->addParticlePot(potential_);
81			atom2_->addParticlePot(potential_);
82	gezelter	507	}
83	gezelter	1211
84	tim	963	RealType getPotential() {
85	gezelter	507	return potential_;
86			}
87	gezelter	1211
88	gezelter	507	Atom* getAtomA() {
89			return atom1_;
90			}
91	gezelter	1211
92	gezelter	507	Atom* getAtomB() {
93			return atom2_;
94			}
95	gezelter	1211
96	gezelter	507	BondType* getBondType() {
97			return bondType_;
98			}
99	gezelter	1211
100	gezelter	507	private:
101	tim	963	RealType potential_;
102	gezelter	507	Atom* atom1_;
103			Atom* atom2_;
104			BondType* bondType_; /*< bond type /
105	gezelter	1211
106	gezelter	507	};
107	gezelter	1390	} //end namespace OpenMD
108	gezelter	246	#endif //PRIMITIVES_BOND_HPP