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root/OpenMD/trunk/src/primitives/Bond.hpp

Comparing trunk/src/primitives/Bond.hpp (file contents):
Revision 490 by tim, Wed Apr 13 18:41:17 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 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, 234107 (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 50 | Line 51
51		#ifndef PRIMITIVES_BOND_HPP
52		#define PRIMITIVES_BOND_HPP
53
54	+	#include "primitives/ShortRangeInteraction.hpp"
55		#include "primitives/Atom.hpp"
56		#include "types/BondType.hpp"
57
58	<	namespace oopse {
58	>	namespace OpenMD {
59	>
60	>	class Bond : public ShortRangeInteraction {
61	>	public:
62	>	Bond(Atom* atom1, Atom* atom2, BondType* bt) : ShortRangeInteraction(),
63	>	bondType_(bt) {
64	>	atoms_.resize(2);
65	>	atoms_[0] = atom1;
66	>	atoms_[1] = atom2;
67	>	}
68	>	virtual ~Bond() {}
69	>	void calcForce(bool doParticlePot) {
70	>	RealType len;
71	>	RealType dvdr;
72	>	Vector3d r12;
73	>	Vector3d force;
74	>
75	>	r12 = atoms_[1]->getPos() - atoms_[0]->getPos();
76	>	len = r12.length();
77	>	bondType_->calcForce(len,  potential_, dvdr);
78	>
79	>	force = r12 * (-dvdr / len);
80
81	<	class Bond {
82	<	public:
83	<	Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1), atom2_(atom2), bondType_(bt) {}
84	<	virtual ~Bond() {}
85	<	void calcForce() {
86	<	double len;
87	<	double dvdr;
88	<	Vector3d r12;
89	<	Vector3d force;
81	>	atoms_[0]->addFrc(-force);
82	>	atoms_[1]->addFrc(force);
83	>	if (doParticlePot) {
84	>	atoms_[0]->addParticlePot(potential_);
85	>	atoms_[1]->addParticlePot(potential_);
86	>	}
87	>	}
88	>
89	>	RealType getValue(int snap) {
90	>	Vector3d r12 = atoms_[1]->getPos(snap) - atoms_[0]->getPos(snap);
91	>	return r12.length();
92	>	}
93
94	<	r12 = atom2_->getPos() - atom1_->getPos();
95	<	len = r12.length();
96	<	bondType_->calcForce(len,  potential_, dvdr);
94	>	RealType getPotential() {
95	>	return potential_;
96	>	}
97	>
98	>	Atom* getAtomA() {
99	>	return atoms_[0];
100	>	}
101	>
102	>	Atom* getAtomB() {
103	>	return atoms_[1];
104	>	}
105	>
106	>	BondType* getBondType() {
107	>	return bondType_;
108	>	}
109
110	<	force = r12 * (-dvdr / len);
111	<
112	<	atom1_->addFrc(-force);
75	<	atom2_->addFrc(force);
76	<	}
77	<
78	<	double getPotential() {
79	<	return potential_;
80	<	}
110	>	virtual std::string getName() { return name_;}
111	>	/** Sets the name of this bond for selections */
112	>	virtual void setName(const std::string& name) { name_ = name; }
113
114	<	Atom* getAtomA() {
115	<	return atom1_;
116	<	}
114	>	void accept(BaseVisitor* v) {
115	>	v->visit(this);
116	>	}
117	>
118	>	private:
119	>	RealType potential_;
120	>	BondType* bondType_; /**< bond type */
121	>	std::string name_;
122
123	<	Atom* getAtomB() {
124	<	return atom2_;
88	<	}
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
123	>	};
124	>	} //end namespace OpenMD
125		#endif //PRIMITIVES_BOND_HPP

Comparing trunk/src/primitives/Bond.hpp (property svn:keywords):
Revision 490 by tim, Wed Apr 13 18:41:17 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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