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

Comparing trunk/src/primitives/Bend.hpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 35 | Line 35
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]  Vardeman & Gezelter, in progress (2009).
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"
57	+
58		namespace OpenMD {
59		struct BendData {
60		RealType angle;
#	Line 63 | Line 67 | namespace OpenMD {
67		BendData curr;
68		};
69
70	<	class Bend {
70	>	class Bend : public ShortRangeInteraction {
71		public:
72		Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt)
73	<	: atom1_(atom1), atom2_(atom2), atom3_(atom3), bendType_(bt) {}
73	>	: ShortRangeInteraction(), bendType_(bt) {
74	>	atoms_.resize(3);
75	>	atoms_[0] = atom1;
76	>	atoms_[1] = atom2;
77	>	atoms_[2] = atom3;
78	>	}
79
80		virtual ~Bend() {}
81	<	virtual void calcForce(RealType& angle);
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	+
88	+	Vector3d r21 = pos1 - pos2;
89	+	RealType d21 = r21.length();
90	+
91	+	RealType d21inv = 1.0 / d21;
92	+
93	+	Vector3d r23 = pos3 - pos2;
94	+	RealType d23 = r23.length();
95	+
96	+	RealType d23inv = 1.0 / d23;
97	+
98	+	RealType cosTheta = dot(r21, r23) / (d21 * d23);
99	+
100	+	//check roundoff
101	+	if (cosTheta > 1.0) {
102	+	cosTheta = 1.0;
103	+	} else if (cosTheta < -1.0) {
104	+	cosTheta = -1.0;
105	+	}
106	+
107	+	return acos(cosTheta);
108	+	}
109	+
110	+
111		RealType getPotential() {
112		return potential_;
113		}
114
115		Atom* getAtomA() {
116	<	return atom1_;
116	>	return atoms_[0];
117		}
118
119		Atom* getAtomB() {
120	<	return atom2_;
120	>	return atoms_[1];
121		}
122
123		Atom* getAtomC() {
124	<	return atom3_;
124	>	return atoms_[2];
125		}
126
127		BendType * getBendType() {
128		return bendType_;
129		}
130
131	+	virtual std::string getName() { return name_;}
132	+	/** Sets the name of this bend for selections */
133	+	virtual void setName(const std::string& name) { name_ = name;}
134	+
135	+	void accept(BaseVisitor* v) {
136	+	v->visit(this);
137	+	}
138	+
139		protected:
140
141		RealType potential_;
97	–	Atom* atom1_;
98	–	Atom* atom2_;
99	–	Atom* atom3_;
142		BendType* bendType_; /**< bend type */
143	<
143	>	std::string name_;
144	>
145		};
146		} //end namespace OpenMD
147		#endif //PRIMITIVES_BEND_HPP

Comparing trunk/src/primitives/Bend.hpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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