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

Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (file contents), Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 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 53 | Line 53
53		#include "config.h"
54		#include <string>
55		#include <utility>
56	+	#include <vector>
57
58		#include "io/basic_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 "UseTheForce/fForceOptions.h"
67	<	namespace oopse {
66	>	#include "types/InversionType.hpp"
67	>	#include "types/NonBondedInteractionType.hpp"
68	>	namespace OpenMD {
69
70		/**
71		* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
#	Line 76 | Line 79 | namespace oopse {
79		typedef TypeContainer<BondType, 2> BondTypeContainer;
80		typedef TypeContainer<BendType, 3> BendTypeContainer;
81		typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
82	<
82	>	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
83	>	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
84	>
85		ForceField();
86	<
86	>
87		virtual ~ForceField();
88
89		std::string getForceFieldFileName() {
#	Line 97 | Line 102 | namespace oopse {
102		const std::string &at3);
103		TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
104		const std::string &at3, const std::string &at4);
105	<
105	>	InversionType* getInversionType(const std::string &at1,
106	>	const std::string &at2,
107	>	const std::string &at3,
108	>	const std::string &at4);
109	>	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
110	>
111		BondType* getExactBondType(const std::string &at1, const std::string &at2);
112		BendType* getExactBendType(const std::string &at1, const std::string &at2,
113		const std::string &at3);
#	Line 105 | Line 115 | namespace oopse {
115		const std::string &at2,
116		const std::string &at3,
117		const std::string &at4);
118	<
119	<
118	>	InversionType* getExactInversionType(const std::string &at1,
119	>	const std::string &at2,
120	>	const std::string &at3,
121	>	const std::string &at4);
122	>	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
123	>
124	>
125		//avoid make virtual function public
126		//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
127		virtual RealType getRcutFromAtomType(AtomType* at);
128	<
128	>
129		std::string getWildCard() {
130		return wildCardAtomTypeName_;
131		}
132	<
132	>
133		void setWildCard(const std::string& wildCard) {
134		wildCardAtomTypeName_ = wildCard;
135		}
136	<
122	<
136	>
137		unsigned int getNAtomType() {
138		return atomTypeCont_.size();
139		}
140	+
141	+	AtomTypeContainer* getAtomTypes() {
142	+	return &atomTypeCont_;
143	+	}
144	+
145	+	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
146	+	return &nonBondedInteractionTypeCont_;
147	+	}
148
149		bool addAtomType(const std::string &at, AtomType* atomType);
150
151	+	bool replaceAtomType(const std::string &at, AtomType* atomType);
152	+
153		bool addBondType(const std::string &at1, const std::string &at2,
154		BondType* bondType);
155
#	Line 133 | Line 157 | namespace oopse {
157		const std::string &at3, BendType* bendType);
158
159		bool addTorsionType(const std::string &at1, const std::string &at2,
160	<	const std::string &at3, const std::string &at4, TorsionType* torsionType);
160	>	const std::string &at3, const std::string &at4,
161	>	TorsionType* torsionType);
162
163	+	bool addInversionType(const std::string &at1, const std::string &at2,
164	+	const std::string &at3, const std::string &at4,
165	+	InversionType* inversionType);
166	+
167	+	bool addNonBondedInteractionType(const std::string &at1,
168	+	const std::string &at2,
169	+	NonBondedInteractionType* nbiType);
170	+
171		ifstrstream* openForceFieldFile(const std::string& filename);
172	<
172	>
173		ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
174
175		void setFortranForceOptions(void);
176	+
177	+
178		protected:
179
180		AtomTypeContainer atomTypeCont_;
181		BondTypeContainer bondTypeCont_;
182		BendTypeContainer bendTypeCont_;
183		TorsionTypeContainer torsionTypeCont_;
184	+	InversionTypeContainer inversionTypeCont_;
185	+	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
186		ForceFieldOptions forceFieldOptions_;
187
188		private:
189		std::string ffPath_;
190	<
190	>
191		std::string wildCardAtomTypeName_;
192	<
193	<	std::string forceFieldFileName_;
192	>
193	>	std::string forceFieldFileName_;
194	>
195		};
196	<
159	<
160	<	}//end namespace oopse
196	>	}//end namespace OpenMD
197		#endif
198

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

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