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root/OpenMD/branches/development/src/primitives/Bond.hpp

Comparing:
trunk/src/primitives/Bond.hpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/primitives/Bond.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	*
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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 53 | Line 54
54		#include "primitives/Atom.hpp"
55		#include "types/BondType.hpp"
56
57	<	namespace oopse {
57	>	namespace OpenMD {
58	>
59	>	class Bond {
60	>	public:
61	>	Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1),
62	>	atom2_(atom2),
63	>	bondType_(bt) {}
64	>	virtual ~Bond() {}
65	>	void calcForce() {
66	>	RealType len;
67	>	RealType dvdr;
68	>	Vector3d r12;
69	>	Vector3d force;
70	>
71	>	r12 = atom2_->getPos() - atom1_->getPos();
72	>	len = r12.length();
73	>	bondType_->calcForce(len,  potential_, dvdr);
74	>
75	>	force = r12 * (-dvdr / len);
76
77	<	class Bond {
78	<	public:
79	<	Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1), atom2_(atom2), bondType_(bt) {}
80	<
81	<	void calcForce() {
82	<	double len;
83	<	double dvdr;
84	<	Vector3d r12;
85	<	Vector3d force;
86	<
87	<	r12 = atom2_->getPos() - atom1_->getPos();
88	<	len = r12.length();
89	<	bondType_->calcForce(len,  potential_, dvdr);
90	<
91	<	force = r12 * (-dvdr / len);
92	<
93	<	atom1_->addFrc(-force);
94	<	atom2_->addFrc(force);
95	<	}
96	<
97	<	double getPotential() {
98	<	return potential_;
99	<	}
100	<
101	<	Atom* getAtomA() {
102	<	return atom1_;
103	<	}
104	<
105	<	Atom* getAtomB() {
106	<	return atom2_;
107	<	}
89	<
90	<	BondType* getBondType() {
91	<	return bondType_;
92	<	}
93	<
94	<	private:
95	<	double potential_;
96	<	Atom* atom1_;
97	<	Atom* atom2_;
98	<	BondType* bondType_; /**< bond type */
99	<
100	<	};
101	<
102	<
103	<
104	<	} //end namespace oopse
77	>	atom1_->addFrc(-force);
78	>	atom2_->addFrc(force);
79	>
80	>	atom1_->addParticlePot(potential_);
81	>	atom2_->addParticlePot(potential_);
82	>	}
83	>
84	>	RealType getPotential() {
85	>	return potential_;
86	>	}
87	>
88	>	Atom* getAtomA() {
89	>	return atom1_;
90	>	}
91	>
92	>	Atom* getAtomB() {
93	>	return atom2_;
94	>	}
95	>
96	>	BondType* getBondType() {
97	>	return bondType_;
98	>	}
99	>
100	>	private:
101	>	RealType potential_;
102	>	Atom* atom1_;
103	>	Atom* atom2_;
104	>	BondType* bondType_; /**< bond type */
105	>
106	>	};
107	>	} //end namespace OpenMD
108		#endif //PRIMITIVES_BOND_HPP

Comparing:
trunk/src/primitives/Bond.hpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/primitives/Bond.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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