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

Comparing trunk/src/primitives/Torsion.hpp (file contents):
Revision 494 by tim, Wed Apr 13 22:43:43 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		#ifndef PRIMITIVES_TORSION_HPP
51		#define PRIMITIVES_TORSION_HPP
52
53	+	#include "primitives/ShortRangeInteraction.hpp"
54		#include "primitives/Atom.hpp"
53	–
55		#include "types/TorsionType.hpp"
56	+	#include <limits>
57
58	<	namespace oopse {
58	>	namespace OpenMD {
59	>	struct TorsionData {
60	>	RealType angle;
61	>	RealType potential;
62	>	};
63
64	<	/**
65	<	* @class Torsion Torsion.hpp "types/Torsion.hpp"
66	<	*/
67	<	class Torsion {
68	<	public:
63	<	Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt);
64	<	virtual ~Torsion() {}
65	<	virtual void calcForce();
66	<
67	<	double getPotential() {
68	<	return potential_;
69	<	}
64	>	struct TorsionDataSet {
65	>	RealType deltaV;
66	>	TorsionData prev;
67	>	TorsionData curr;
68	>	};
69
71	–	Atom* getAtomA() {
72	–	return atom1_;
73	–	}
70
71	<	Atom* getAtomB() {
72	<	return atom2_;
73	<	}
71	>	/**
72	>	* @class Torsion Torsion.hpp "types/Torsion.hpp"
73	>	*/
74	>	class Torsion : public ShortRangeInteraction {
75	>	public:
76	>	using ShortRangeInteraction::getValue;
77	>	using ShortRangeInteraction::getPrevValue;
78
79	<	Atom* getAtomC() {
80	<	return atom3_;
81	<	}
79	>	Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt);
80	>	virtual ~Torsion() {}
81	>	virtual void calcForce(RealType& angle, bool doParticlePot);
82	>
83	>	RealType getValue(int snapshotNo) {
84	>	Vector3d pos1 = atoms_[0]->getPos(snapshotNo);
85	>	Vector3d pos2 = atoms_[1]->getPos(snapshotNo);
86	>	Vector3d pos3 = atoms_[2]->getPos(snapshotNo);
87	>	Vector3d pos4 = atoms_[3]->getPos(snapshotNo);
88	>
89	>	Vector3d r21 = pos1 - pos2;
90	>	Vector3d r32 = pos2 - pos3;
91	>	Vector3d r43 = pos3 - pos4;
92	>
93	>	//  Calculate the cross products and distances
94	>	Vector3d A = cross(r21, r32);
95	>	RealType rA = A.length();
96	>	Vector3d B = cross(r32, r43);
97	>	RealType rB = B.length();
98	>
99	>	/*
100	>	If either of the two cross product vectors is tiny, that means
101	>	the three atoms involved are colinear, and the torsion angle is
102	>	going to be undefined.  The easiest check for this problem is
103	>	to use the product of the two lengths.
104	>	*/
105	>	if (rA * rB < OpenMD::epsilon) return numeric_limits<double>::quiet_NaN();
106	>
107	>	A.normalize();
108	>	B.normalize();
109	>
110	>	//  Calculate the sin and cos
111	>	RealType cos_phi = dot(A, B) ;
112	>	if (cos_phi > 1.0) cos_phi = 1.0;
113	>	if (cos_phi < -1.0) cos_phi = -1.0;
114	>	return acos(cos_phi);
115	>	}
116	>
117
118	<	Atom* getAtomD() {
119	<	return atom4_;
120	<	}
118	>	RealType getPotential() {
119	>	return potential_;
120	>	}
121
122	<	TorsionType * getTorsionType() {
123	<	return torsionType_;
124	<	}
122	>	Atom* getAtomA() {
123	>	return atoms_[0];
124	>	}
125	>
126	>	Atom* getAtomB() {
127	>	return atoms_[1];
128	>	}
129	>
130	>	Atom* getAtomC() {
131	>	return atoms_[2];
132	>	}
133	>
134	>	Atom* getAtomD() {
135	>	return atoms_[3];
136	>	}
137	>
138	>	TorsionType * getTorsionType() {
139	>	return torsionType_;
140	>	}
141
142	<	protected:
142	>	virtual std::string getName() { return name_;}
143	>	/** Sets the name of this torsion for selections */
144	>	virtual void setName(const std::string& name) { name_ = name;}
145
146	<	Atom* atom1_;
147	<	Atom* atom2_;
148	<	Atom* atom3_;
96	<	Atom* atom4_;
146	>	void accept(BaseVisitor* v) {
147	>	v->visit(this);
148	>	}
149
150	<	TorsionType* torsionType_;
150	>	protected:
151
152	<	double potential_;
153	<	};
152	>	TorsionType* torsionType_;
153	>	std::string name_;
154
155	+	RealType potential_;
156	+	};
157	+
158		}
159		#endif //PRIMITIVES_TORSION_HPP

Comparing trunk/src/primitives/Torsion.hpp (property svn:keywords):
Revision 494 by tim, Wed Apr 13 22:43:43 2005 UTC vs.
Revision 1955 by gezelter, Thu Dec 5 21:55:42 2013 UTC

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