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

Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 821 by chuckv, Wed Dec 28 21:42:43 2005 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 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]  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 "utils/TypeContainer.hpp"
62	+	#include "utils/Tuple.hpp"
63		#include "types/AtomType.hpp"
64		#include "types/BondType.hpp"
65		#include "types/BendType.hpp"
66		#include "types/TorsionType.hpp"
67	<	#include "UseTheForce/fForceOptions.h"
68	<	namespace oopse {
67	>	#include "types/InversionType.hpp"
68	>	#include "types/NonBondedInteractionType.hpp"
69	>	namespace OpenMD {
70
71		/**
72		* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
#	Line 76 | Line 80 | namespace oopse {
80		typedef TypeContainer<BondType, 2> BondTypeContainer;
81		typedef TypeContainer<BendType, 3> BendTypeContainer;
82		typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
83	<
84	<	ForceField();
83	>	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
84	>	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
85	>
86	>	ForceField();
87	>
88	>	virtual ~ForceField() {};
89
82	–	virtual ~ForceField();
83	–
90		std::string getForceFieldFileName() {
91		return forceFieldFileName_;
92		}
#	Line 92 | Line 98 | namespace oopse {
98		virtual void parse(const std::string& filename) = 0;
99
100		AtomType* getAtomType(const std::string &at);
101	+	AtomType* getAtomType(int ident);
102		BondType* getBondType(const std::string &at1, const std::string &at2);
103		BendType* getBendType(const std::string &at1, const std::string &at2,
104		const std::string &at3);
105		TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
106		const std::string &at3, const std::string &at4);
107	<
107	>	InversionType* getInversionType(const std::string &at1,
108	>	const std::string &at2,
109	>	const std::string &at3,
110	>	const std::string &at4);
111	>	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
112	>
113		BondType* getExactBondType(const std::string &at1, const std::string &at2);
114		BendType* getExactBendType(const std::string &at1, const std::string &at2,
115		const std::string &at3);
#	Line 105 | Line 117 | namespace oopse {
117		const std::string &at2,
118		const std::string &at3,
119		const std::string &at4);
120	<
121	<
120	>	InversionType* getExactInversionType(const std::string &at1,
121	>	const std::string &at2,
122	>	const std::string &at3,
123	>	const std::string &at4);
124	>	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
125	>
126	>
127		//avoid make virtual function public
128		//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
129	<	virtual double getRcutFromAtomType(AtomType* at);
130	<
129	>	virtual RealType getRcutFromAtomType(AtomType* at);
130	>
131		std::string getWildCard() {
132		return wildCardAtomTypeName_;
133		}
134	<
134	>
135		void setWildCard(const std::string& wildCard) {
136		wildCardAtomTypeName_ = wildCard;
137		}
138	<
122	<
138	>
139		unsigned int getNAtomType() {
140		return atomTypeCont_.size();
141		}
142	+
143	+	AtomTypeContainer* getAtomTypes() {
144	+	return &atomTypeCont_;
145	+	}
146	+
147	+	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
148	+	return &nonBondedInteractionTypeCont_;
149	+	}
150
151		bool addAtomType(const std::string &at, AtomType* atomType);
152
153	+	bool replaceAtomType(const std::string &at, AtomType* atomType);
154	+
155		bool addBondType(const std::string &at1, const std::string &at2,
156		BondType* bondType);
157
#	Line 133 | Line 159 | namespace oopse {
159		const std::string &at3, BendType* bendType);
160
161		bool addTorsionType(const std::string &at1, const std::string &at2,
162	<	const std::string &at3, const std::string &at4, TorsionType* torsionType);
162	>	const std::string &at3, const std::string &at4,
163	>	TorsionType* torsionType);
164
165	+	bool addInversionType(const std::string &at1, const std::string &at2,
166	+	const std::string &at3, const std::string &at4,
167	+	InversionType* inversionType);
168	+
169	+	bool addNonBondedInteractionType(const std::string &at1,
170	+	const std::string &at2,
171	+	NonBondedInteractionType* nbiType);
172	+
173		ifstrstream* openForceFieldFile(const std::string& filename);
174	<
174	>
175		ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
176
142	–	void setFortranForceOptions(void);
177		protected:
178
179		AtomTypeContainer atomTypeCont_;
180		BondTypeContainer bondTypeCont_;
181		BendTypeContainer bendTypeCont_;
182		TorsionTypeContainer torsionTypeCont_;
183	+	InversionTypeContainer inversionTypeCont_;
184	+	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
185		ForceFieldOptions forceFieldOptions_;
186	+	std::map<int, std::string> atypeIdentToName;
187
188		private:
189	<	std::string ffPath_;
190	<
191	<	std::string wildCardAtomTypeName_;
192	<
156	<	std::string forceFieldFileName_;
189	>	std::string ffPath_;
190	>	std::string wildCardAtomTypeName_;
191	>	std::string forceFieldFileName_;
192	>
193		};
194	<
159	<
160	<	}//end namespace oopse
194	>	}//end namespace OpenMD
195		#endif
196

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 821 by chuckv, Wed Dec 28 21:42:43 2005 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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