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

Comparing trunk/src/primitives/Inversion.hpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2066 by gezelter, Thu Mar 5 15:22:54 2015 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		#ifndef PRIMITIVES_INVERSION_HPP
51		#define PRIMITIVES_INVERSION_HPP
52
53	+	#include "primitives/ShortRangeInteraction.hpp"
54		#include "primitives/Atom.hpp"
53	–
55		#include "types/InversionType.hpp"
56
57		namespace OpenMD {
#	Line 65 | Line 66 | namespace OpenMD {
66		InversionData curr;
67		};
68
68	–
69		/**
70		* @class Inversion Inversion.hpp "primitives/Inversion.hpp"
71		*/
72	<	class Inversion {
72	>	class Inversion : public ShortRangeInteraction {
73		public:
74	+	using ShortRangeInteraction::getValue;
75	+	using ShortRangeInteraction::getPrevValue;
76	+
77		Inversion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, InversionType* it);
78		virtual ~Inversion() {}
79	<	virtual void calcForce(RealType& angle);
79	>	virtual void calcForce(RealType& angle, bool doParticlePot);
80
81	+	RealType getValue(int snapshotNo) {
82	+	// In OpenMD's version of an inversion, the central atom
83	+	// comes first.  However, to get the planarity in a typical cosine
84	+	// version of this potential (i.e. Amber-style), the central atom
85	+	// is treated as atom *3* in a standard torsion form:
86	+
87	+	Vector3d pos1 = atoms_[1]->getPos(snapshotNo);
88	+	Vector3d pos2 = atoms_[2]->getPos(snapshotNo);
89	+	Vector3d pos3 = atoms_[0]->getPos(snapshotNo);
90	+	Vector3d pos4 = atoms_[3]->getPos(snapshotNo);
91	+
92	+	Vector3d r31 = pos1 - pos3;
93	+	Vector3d r23 = pos3 - pos2;
94	+	Vector3d r43 = pos3 - pos4;
95	+
96	+	//  Calculate the cross products and distances
97	+	Vector3d A = cross(r31, r43);
98	+	Vector3d B = cross(r43, r23);
99	+
100	+	A.normalize();
101	+	B.normalize();
102	+
103	+	//  Calculate the sin and cos
104	+	RealType cos_phi = dot(A, B) ;
105	+	if (cos_phi > 1.0) cos_phi = 1.0;
106	+	if (cos_phi < -1.0) cos_phi = -1.0;
107	+	return acos(cos_phi);
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		Atom* getAtomD() {
128	<	return atom4_;
128	>	return atoms_[3];
129		}
130
131		InversionType * getInversionType() {
132		return inversionType_;
133		}
134	<
135	<	protected:
134	>	virtual std::string getName() { return name_;}
135	>	/** Sets the name of this inversion for selections */
136	>	virtual void setName(const std::string& name) { name_ = name;}
137
138	<	Atom* atom1_;
139	<	Atom* atom2_;
140	<	Atom* atom3_;
107	<	Atom* atom4_;
138	>	void accept(BaseVisitor* v) {
139	>	v->visit(this);
140	>	}
141
142	+	protected:
143		InversionType* inversionType_;
144	+	InversionKey inversionKey_;
145	+	std::string name_;
146
147		RealType potential_;
148		};

Comparing trunk/src/primitives/Inversion.hpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2066 by gezelter, Thu Mar 5 15:22:54 2015 UTC

#	Line 0 | Line 1
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