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

Comparing trunk/src/primitives/Bend.hpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1955 by gezelter, Thu Dec 5 21:55:42 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 49 | Line 50
50
51		#ifndef PRIMITIVES_BEND_HPP
52		#define PRIMITIVES_BEND_HPP
53	+
54	+	#include "primitives/ShortRangeInteraction.hpp"
55		#include "primitives/Atom.hpp"
56		#include "types/BendType.hpp"
54	–	namespace oopse {
57
58	<	class Bend {
59	<	public:
60	<	Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt)
61	<	: atom1_(atom1), atom2_(atom2), atom3_(atom3), bendType_(bt) {}
58	>	namespace OpenMD {
59	>	struct BendData {
60	>	RealType angle;
61	>	RealType potential;
62	>	};
63	>
64	>	struct BendDataSet {
65	>	RealType deltaV;
66	>	BendData prev;
67	>	BendData curr;
68	>	};
69	>
70	>	class Bend : public ShortRangeInteraction {
71	>	public:
72	>	using ShortRangeInteraction::getValue;
73	>	using ShortRangeInteraction::getPrevValue;
74	>	Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt)
75	>	: ShortRangeInteraction(), bendType_(bt) {
76	>	atoms_.resize(3);
77	>	atoms_[0] = atom1;
78	>	atoms_[1] = atom2;
79	>	atoms_[2] = atom3;
80	>	}
81	>
82	>	virtual ~Bend() {}
83	>	virtual void calcForce(RealType& angle, bool doParticlePot);
84	>
85	>	RealType getValue(int snapshotNo) {
86	>	Vector3d pos1 = atoms_[0]->getPos(snapshotNo);
87	>	Vector3d pos2 = atoms_[1]->getPos(snapshotNo);
88	>	Vector3d pos3 = atoms_[2]->getPos(snapshotNo);
89	>
90	>	Vector3d r21 = pos1 - pos2;
91	>	RealType d21 = r21.length();
92	>
93	>	Vector3d r23 = pos3 - pos2;
94	>	RealType d23 = r23.length();
95	>
96	>	RealType cosTheta = dot(r21, r23) / (d21 * d23);
97	>
98	>	//check roundoff
99	>	if (cosTheta > 1.0) {
100	>	cosTheta = 1.0;
101	>	} else if (cosTheta < -1.0) {
102	>	cosTheta = -1.0;
103	>	}
104	>
105	>	return acos(cosTheta);
106	>	}
107
108
109	<	virtual void calcForce();
110	<
111	<	double getPotential() {
112	<	return potential_;
113	<	}
109	>	RealType getPotential() {
110	>	return potential_;
111	>	}
112	>
113	>	Atom* getAtomA() {
114	>	return atoms_[0];
115	>	}
116	>
117	>	Atom* getAtomB() {
118	>	return atoms_[1];
119	>	}
120	>
121	>	Atom* getAtomC() {
122	>	return atoms_[2];
123	>	}
124	>
125	>	BendType * getBendType() {
126	>	return bendType_;
127	>	}
128	>
129	>	virtual std::string getName() { return name_;}
130	>	/** Sets the name of this bend for selections */
131	>	virtual void setName(const std::string& name) { name_ = name;}
132
133	<	Atom* getAtomA() {
134	<	return atom1_;
135	<	}
133	>	void accept(BaseVisitor* v) {
134	>	v->visit(this);
135	>	}
136
137	<	Atom* getAtomB() {
138	<	return atom2_;
139	<	}
137	>	protected:
138	>
139	>	RealType potential_;
140	>	BendType* bendType_; /**< bend type */
141	>	std::string name_;
142
143	<	Atom* getAtomC() {
144	<	return atom3_;
78	<	}
79	<
80	<	BendType * getBendType() {
81	<	return bendType_;
82	<	}
83	<
84	<	protected:
85	<
86	<	double potential_;
87	<	Atom* atom1_;
88	<	Atom* atom2_;
89	<	Atom* atom3_;
90	<	BendType* bendType_; /**< bend type */
91	<
92	<	};
93	<
94	<
95	<
96	<	} //end namespace oopse
143	>	};
144	>	} //end namespace OpenMD
145		#endif //PRIMITIVES_BEND_HPP
146

Comparing trunk/src/primitives/Bend.hpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1955 by gezelter, Thu Dec 5 21:55:42 2013 UTC

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