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

Comparing:
trunk/src/primitives/Bond.hpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/primitives/Bond.hpp (file contents), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

#	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 {
58	<
57	>	namespace OpenMD {
58	>
59		class Bond {
60		public:
61	<	Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1), atom2_(atom2), bondType_(bt) {}
61	>	Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1),
62	>	atom2_(atom2),
63	>	bondType_(bt) {}
64		virtual ~Bond() {}
65	<	void calcForce() {
66	<	double len;
67	<	double dvdr;
65	>	void calcForce(bool doParticlePot) {
66	>	RealType len;
67	>	RealType dvdr;
68		Vector3d r12;
69		Vector3d force;
70	<
70	>
71		r12 = atom2_->getPos() - atom1_->getPos();
72		len = r12.length();
73		bondType_->calcForce(len,  potential_, dvdr);
74	<
74	>
75		force = r12 * (-dvdr / len);
76	<
76	>
77		atom1_->addFrc(-force);
78		atom2_->addFrc(force);
79	+	if (doParticlePot) {
80	+	atom1_->addParticlePot(potential_);
81	+	atom2_->addParticlePot(potential_);
82	+	}
83		}
84	<
85	<	double getPotential() {
84	>
85	>	RealType getPotential() {
86		return potential_;
87		}
88	<
88	>
89		Atom* getAtomA() {
90		return atom1_;
91		}
92	<
92	>
93		Atom* getAtomB() {
94		return atom2_;
95		}
96	<
96	>
97		BondType* getBondType() {
98		return bondType_;
99		}
100	<
100	>
101		private:
102	<	double potential_;
102	>	RealType potential_;
103		Atom* atom1_;
104		Atom* atom2_;
105		BondType* bondType_; /**< bond type */
106	<
106	>
107		};
108	<
102	<
103	<
104	<	} //end namespace oopse
108	>	} //end namespace OpenMD
109		#endif //PRIMITIVES_BOND_HPP

Comparing:
trunk/src/primitives/Bond.hpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/primitives/Bond.hpp (property svn:keywords), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

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