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

Comparing trunk/src/primitives/Inversion.hpp (file contents):
Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
Revision 1955 by gezelter, Thu Dec 5 21:55:42 2013 UTC

#	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_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 oopse {
57	>	namespace OpenMD {
58		struct InversionData {
59		RealType angle;
60		RealType potential;
#	Line 65 | Line 66 | namespace oopse {
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	+	RealType rA = A.length();
99	+	Vector3d B = cross(r43, r23);
100	+	RealType rB = B.length();
101	+	//Vector3d C = cross(r23, A);
102	+	//RealType rC = C.length();
103	+
104	+	A.normalize();
105	+	B.normalize();
106	+	//C.normalize();
107	+
108	+	//  Calculate the sin and cos
109	+	RealType cos_phi = dot(A, B) ;
110	+	if (cos_phi > 1.0) cos_phi = 1.0;
111	+	if (cos_phi < -1.0) cos_phi = -1.0;
112	+	return acos(cos_phi);
113	+	}
114	+
115	+
116		RealType getPotential() {
117		return potential_;
118		}
119
120		Atom* getAtomA() {
121	<	return atom1_;
121	>	return atoms_[0];
122		}
123
124		Atom* getAtomB() {
125	<	return atom2_;
125	>	return atoms_[1];
126		}
127
128		Atom* getAtomC() {
129	<	return atom3_;
129	>	return atoms_[2];
130		}
131
132		Atom* getAtomD() {
133	<	return atom4_;
133	>	return atoms_[3];
134		}
135
136		InversionType * getInversionType() {
137		return inversionType_;
138		}
139	<
140	<	protected:
139	>	virtual std::string getName() { return name_;}
140	>	/** Sets the name of this inversion for selections */
141	>	virtual void setName(const std::string& name) { name_ = name;}
142
143	<	Atom* atom1_;
144	<	Atom* atom2_;
145	<	Atom* atom3_;
107	<	Atom* atom4_;
143	>	void accept(BaseVisitor* v) {
144	>	v->visit(this);
145	>	}
146
147	+	protected:
148		InversionType* inversionType_;
149	+	InversionKey inversionKey_;
150	+	std::string name_;
151
152		RealType potential_;
153		};

Comparing trunk/src/primitives/Inversion.hpp (property svn:keywords):
Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
Revision 1955 by gezelter, Thu Dec 5 21:55:42 2013 UTC

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