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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/brains/ForceField.hpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 53 | Line 54
54		#include "config.h"
55		#include <string>
56		#include <utility>
57	+	#include <vector>
58
59	<	#include "io/basic_ifstrstream.hpp"
59	>	#include "io/ifstrstream.hpp"
60		#include "io/ForceFieldOptions.hpp"
61	+	#include "io/SectionParserManager.hpp"
62		#include "utils/TypeContainer.hpp"
63	+	#include "utils/Tuple.hpp"
64		#include "types/AtomType.hpp"
65		#include "types/BondType.hpp"
66		#include "types/BendType.hpp"
67		#include "types/TorsionType.hpp"
68	<	#include "UseTheForce/fForceOptions.h"
69	<	namespace oopse {
68	>	#include "types/InversionType.hpp"
69	>	#include "types/NonBondedInteractionType.hpp"
70
71	<	/**
72	<	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
69	<	* @brief
70	<	*/
71	>	namespace OpenMD {
72	>
73		class ForceField{
74
75		public:
74	–
76		typedef TypeContainer<AtomType, 1> AtomTypeContainer;
77		typedef TypeContainer<BondType, 2> BondTypeContainer;
78		typedef TypeContainer<BendType, 3> BendTypeContainer;
79		typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
80	<
81	<	ForceField();
80	>	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
81	>	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
82	>
83	>	ForceField(std::string ffName);
84	>
85	>	virtual ~ForceField() {};
86
82	–	virtual ~ForceField();
83	–
87		std::string getForceFieldFileName() {
88		return forceFieldFileName_;
89		}
#	Line 89 | Line 92 | namespace oopse {
92		forceFieldFileName_ = filename;
93		}
94
95	<	virtual void parse(const std::string& filename) = 0;
95	>	virtual void parse(const std::string& filename);
96
97		AtomType* getAtomType(const std::string &at);
98	+	AtomType* getAtomType(int ident);
99		BondType* getBondType(const std::string &at1, const std::string &at2);
100		BendType* getBendType(const std::string &at1, const std::string &at2,
101		const std::string &at3);
102		TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
103		const std::string &at3, const std::string &at4);
104	<
104	>	InversionType* getInversionType(const std::string &at1,
105	>	const std::string &at2,
106	>	const std::string &at3,
107	>	const std::string &at4);
108	>	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
109	>
110		BondType* getExactBondType(const std::string &at1, const std::string &at2);
111		BendType* getExactBendType(const std::string &at1, const std::string &at2,
112		const std::string &at3);
#	Line 105 | Line 114 | namespace oopse {
114		const std::string &at2,
115		const std::string &at3,
116		const std::string &at4);
117	<
118	<
117	>	InversionType* getExactInversionType(const std::string &at1,
118	>	const std::string &at2,
119	>	const std::string &at3,
120	>	const std::string &at4);
121	>	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
122	>
123	>
124		//avoid make virtual function public
125		//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
126		virtual RealType getRcutFromAtomType(AtomType* at);
127	<
127	>
128		std::string getWildCard() {
129		return wildCardAtomTypeName_;
130		}
131	<
131	>
132		void setWildCard(const std::string& wildCard) {
133		wildCardAtomTypeName_ = wildCard;
134		}
135	<
122	<
135	>
136		unsigned int getNAtomType() {
137		return atomTypeCont_.size();
138		}
139	+
140	+	AtomTypeContainer* getAtomTypes() {
141	+	return &atomTypeCont_;
142	+	}
143	+
144	+	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
145	+	return &nonBondedInteractionTypeCont_;
146	+	}
147
148		bool addAtomType(const std::string &at, AtomType* atomType);
149
150	+	bool replaceAtomType(const std::string &at, AtomType* atomType);
151	+
152		bool addBondType(const std::string &at1, const std::string &at2,
153		BondType* bondType);
154
#	Line 133 | Line 156 | namespace oopse {
156		const std::string &at3, BendType* bendType);
157
158		bool addTorsionType(const std::string &at1, const std::string &at2,
159	<	const std::string &at3, const std::string &at4, TorsionType* torsionType);
159	>	const std::string &at3, const std::string &at4,
160	>	TorsionType* torsionType);
161
162	+	bool addInversionType(const std::string &at1, const std::string &at2,
163	+	const std::string &at3, const std::string &at4,
164	+	InversionType* inversionType);
165	+
166	+	bool addNonBondedInteractionType(const std::string &at1,
167	+	const std::string &at2,
168	+	NonBondedInteractionType* nbiType);
169	+
170		ifstrstream* openForceFieldFile(const std::string& filename);
171	<
171	>
172		ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
173
142	–	void setFortranForceOptions(void);
174		protected:
175
176		AtomTypeContainer atomTypeCont_;
177		BondTypeContainer bondTypeCont_;
178		BendTypeContainer bendTypeCont_;
179		TorsionTypeContainer torsionTypeCont_;
180	+	InversionTypeContainer inversionTypeCont_;
181	+	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
182		ForceFieldOptions forceFieldOptions_;
183	+	std::map<int, std::string> atypeIdentToName;
184	+	SectionParserManager spMan_;
185	+
186
187		private:
188	<	std::string ffPath_;
189	<
190	<	std::string wildCardAtomTypeName_;
191	<
156	<	std::string forceFieldFileName_;
188	>	std::string ffPath_;
189	>	std::string wildCardAtomTypeName_;
190	>	std::string forceFieldFileName_;
191	>
192		};
193	<
159	<
160	<	}//end namespace oopse
193	>	}//end namespace OpenMD
194		#endif
195

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/brains/ForceField.hpp (property svn:keywords), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

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