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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.
trunk/src/brains/ForceField.hpp (file contents), Revision 1879 by gezelter, Sun Jun 16 15:15:42 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		/**
44		* @file ForceField.hpp
45		* @author tlin
46		* @date 11/04/2004
46	–	* @time 22:51am
47		* @version 1.0
48		*/
49
#	Line 53 | Line 53
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 "io/SectionParserManager.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
70	<	/**
71	<	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
69	<	* @brief
70	<	*/
70	>	namespace OpenMD {
71	>
72		class ForceField{
73
74		public:
74	–
75		typedef TypeContainer<AtomType, 1> AtomTypeContainer;
76		typedef TypeContainer<BondType, 2> BondTypeContainer;
77		typedef TypeContainer<BendType, 3> BendTypeContainer;
78		typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
79	<
80	<	ForceField();
79	>	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
80	>	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
81	>
82	>	ForceField(std::string ffName);
83	>
84	>	virtual ~ForceField() {};
85
82	–	virtual ~ForceField();
83	–
86		std::string getForceFieldFileName() {
87		return forceFieldFileName_;
88		}
#	Line 89 | Line 91 | namespace oopse {
91		forceFieldFileName_ = filename;
92		}
93
94	<	virtual void parse(const std::string& filename) = 0;
94	>	virtual void parse(const std::string& filename);
95
96		AtomType* getAtomType(const std::string &at);
97	+	AtomType* getAtomType(int ident);
98		BondType* getBondType(const std::string &at1, const std::string &at2);
99		BendType* getBendType(const std::string &at1, const std::string &at2,
100		const std::string &at3);
101		TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
102		const std::string &at3, const std::string &at4);
103	<
103	>	InversionType* getInversionType(const std::string &at1,
104	>	const std::string &at2,
105	>	const std::string &at3,
106	>	const std::string &at4);
107	>	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
108	>
109		BondType* getExactBondType(const std::string &at1, const std::string &at2);
110		BendType* getExactBendType(const std::string &at1, const std::string &at2,
111		const std::string &at3);
#	Line 105 | Line 113 | namespace oopse {
113		const std::string &at2,
114		const std::string &at3,
115		const std::string &at4);
116	<
117	<
116	>	InversionType* getExactInversionType(const std::string &at1,
117	>	const std::string &at2,
118	>	const std::string &at3,
119	>	const std::string &at4);
120	>	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
121	>
122	>
123		//avoid make virtual function public
124		//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
125	<	virtual double getRcutFromAtomType(AtomType* at);
126	<
125	>	virtual RealType getRcutFromAtomType(AtomType* at);
126	>
127		std::string getWildCard() {
128		return wildCardAtomTypeName_;
129		}
130	<
130	>
131		void setWildCard(const std::string& wildCard) {
132		wildCardAtomTypeName_ = wildCard;
133		}
134	<
122	<
134	>
135		unsigned int getNAtomType() {
136		return atomTypeCont_.size();
137		}
138	+
139	+	AtomTypeContainer* getAtomTypes() {
140	+	return &atomTypeCont_;
141	+	}
142	+
143	+	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
144	+	return &nonBondedInteractionTypeCont_;
145	+	}
146
147		bool addAtomType(const std::string &at, AtomType* atomType);
148
149	+	bool replaceAtomType(const std::string &at, AtomType* atomType);
150	+
151		bool addBondType(const std::string &at1, const std::string &at2,
152		BondType* bondType);
153
#	Line 133 | Line 155 | namespace oopse {
155		const std::string &at3, BendType* bendType);
156
157		bool addTorsionType(const std::string &at1, const std::string &at2,
158	<	const std::string &at3, const std::string &at4, TorsionType* torsionType);
158	>	const std::string &at3, const std::string &at4,
159	>	TorsionType* torsionType);
160
161	+	bool addInversionType(const std::string &at1, const std::string &at2,
162	+	const std::string &at3, const std::string &at4,
163	+	InversionType* inversionType);
164	+
165	+	bool addNonBondedInteractionType(const std::string &at1,
166	+	const std::string &at2,
167	+	NonBondedInteractionType* nbiType);
168	+
169		ifstrstream* openForceFieldFile(const std::string& filename);
170	<
170	>
171		ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
172
142	–	void setFortranForceOptions(void);
173		protected:
174
175		AtomTypeContainer atomTypeCont_;
176		BondTypeContainer bondTypeCont_;
177		BendTypeContainer bendTypeCont_;
178		TorsionTypeContainer torsionTypeCont_;
179	+	InversionTypeContainer inversionTypeCont_;
180	+	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
181		ForceFieldOptions forceFieldOptions_;
182	+	std::map<int, std::string> atypeIdentToName;
183	+	SectionParserManager spMan_;
184	+
185
186		private:
187	<	std::string ffPath_;
188	<
189	<	std::string wildCardAtomTypeName_;
190	<
156	<	std::string forceFieldFileName_;
187	>	std::string ffPath_;
188	>	std::string wildCardAtomTypeName_;
189	>	std::string forceFieldFileName_;
190	>
191		};
192	<
159	<
160	<	}//end namespace oopse
192	>	}//end namespace OpenMD
193		#endif
194

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 821 by chuckv, Wed Dec 28 21:42:43 2005 UTC vs.
trunk/src/brains/ForceField.hpp (property svn:keywords), Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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