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root/OpenMD/trunk/src/brains/ForceField.hpp

Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 514 by chrisfen, Thu Apr 21 14:12:19 2005 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 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, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 50 | Line 50
50		#ifndef USETHEFORCE_FORCEFIELD_HPP
51		#define USETHEFORCE_FORCEFIELD_HPP
52
53	<	#define MK_STR(s) # s
54	<	#define STR_DEFINE(t, s) t = MK_STR(s)
55	<
53	>	#include "config.h"
54		#include <string>
55		#include <utility>
56	+	#include <vector>
57
58	<	#include "io/basic_ifstrstream.hpp"
58	>	#include "io/ifstrstream.hpp"
59	>	#include "io/ForceFieldOptions.hpp"
60		#include "utils/TypeContainer.hpp"
61	+	#include "utils/Tuple.hpp"
62		#include "types/AtomType.hpp"
63		#include "types/BondType.hpp"
64		#include "types/BendType.hpp"
65		#include "types/TorsionType.hpp"
66	+	#include "types/InversionType.hpp"
67	+	#include "types/NonBondedInteractionType.hpp"
68	+	namespace OpenMD {
69
66	–	namespace oopse {
67	–
70		/**
71		* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
72		* @brief
#	Line 77 | Line 79 | namespace oopse {
79		typedef TypeContainer<BondType, 2> BondTypeContainer;
80		typedef TypeContainer<BendType, 3> BendTypeContainer;
81		typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
82	<
83	<	ForceField();
82	>	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
83	>	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
84	>
85	>	ForceField();
86	>
87	>	virtual ~ForceField() {};
88
83	–	virtual ~ForceField();
84	–
89		std::string getForceFieldFileName() {
90		return forceFieldFileName_;
91		}
#	Line 93 | Line 97 | namespace oopse {
97		virtual void parse(const std::string& filename) = 0;
98
99		AtomType* getAtomType(const std::string &at);
100	+	AtomType* getAtomType(int ident);
101		BondType* getBondType(const std::string &at1, const std::string &at2);
102		BendType* getBendType(const std::string &at1, const std::string &at2,
103		const std::string &at3);
104		TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
105		const std::string &at3, const std::string &at4);
106	<
106	>	InversionType* getInversionType(const std::string &at1,
107	>	const std::string &at2,
108	>	const std::string &at3,
109	>	const std::string &at4);
110	>	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
111	>
112		BondType* getExactBondType(const std::string &at1, const std::string &at2);
113		BendType* getExactBendType(const std::string &at1, const std::string &at2,
114		const std::string &at3);
#	Line 106 | Line 116 | namespace oopse {
116		const std::string &at2,
117		const std::string &at3,
118		const std::string &at4);
119	<
120	<
119	>	InversionType* getExactInversionType(const std::string &at1,
120	>	const std::string &at2,
121	>	const std::string &at3,
122	>	const std::string &at4);
123	>	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
124	>
125	>
126		//avoid make virtual function public
127		//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
128	<	virtual double getRcutFromAtomType(AtomType* at);
129	<
128	>	virtual RealType getRcutFromAtomType(AtomType* at);
129	>
130		std::string getWildCard() {
131		return wildCardAtomTypeName_;
132		}
133	<
133	>
134		void setWildCard(const std::string& wildCard) {
135		wildCardAtomTypeName_ = wildCard;
136		}
137	<
123	<
137	>
138		unsigned int getNAtomType() {
139		return atomTypeCont_.size();
140		}
141	+
142	+	AtomTypeContainer* getAtomTypes() {
143	+	return &atomTypeCont_;
144	+	}
145	+
146	+	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
147	+	return &nonBondedInteractionTypeCont_;
148	+	}
149
150		bool addAtomType(const std::string &at, AtomType* atomType);
151
152	+	bool replaceAtomType(const std::string &at, AtomType* atomType);
153	+
154		bool addBondType(const std::string &at1, const std::string &at2,
155		BondType* bondType);
156
#	Line 134 | Line 158 | namespace oopse {
158		const std::string &at3, BendType* bendType);
159
160		bool addTorsionType(const std::string &at1, const std::string &at2,
161	<	const std::string &at3, const std::string &at4, TorsionType* torsionType);
161	>	const std::string &at3, const std::string &at4,
162	>	TorsionType* torsionType);
163
164	+	bool addInversionType(const std::string &at1, const std::string &at2,
165	+	const std::string &at3, const std::string &at4,
166	+	InversionType* inversionType);
167	+
168	+	bool addNonBondedInteractionType(const std::string &at1,
169	+	const std::string &at2,
170	+	NonBondedInteractionType* nbiType);
171	+
172		ifstrstream* openForceFieldFile(const std::string& filename);
173	+
174	+	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
175
176		protected:
177
#	Line 144 | Line 179 | namespace oopse {
179		BondTypeContainer bondTypeCont_;
180		BendTypeContainer bendTypeCont_;
181		TorsionTypeContainer torsionTypeCont_;
182	<
182	>	InversionTypeContainer inversionTypeCont_;
183	>	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
184	>	ForceFieldOptions forceFieldOptions_;
185	>	std::map<int, std::string> atypeIdentToName;
186	>
187		private:
188	<	std::string ffPath_;
189	<
190	<	std::string wildCardAtomTypeName_;
191	<
153	<	std::string forceFieldFileName_;
188	>	std::string ffPath_;
189	>	std::string wildCardAtomTypeName_;
190	>	std::string forceFieldFileName_;
191	>
192		};
193	<
156	<
157	<	}//end namespace oopse
193	>	}//end namespace OpenMD
194		#endif
195

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 514 by chrisfen, Thu Apr 21 14:12:19 2005 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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