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

Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 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 50 | Line 51
51		#ifndef USETHEFORCE_FORCEFIELD_HPP
52		#define USETHEFORCE_FORCEFIELD_HPP
53
54	<	#define MK_STR(s) # s
54	<	#define STR_DEFINE(t, s) t = MK_STR(s)
55	<
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 "types/InversionType.hpp"
69	+	#include "types/NonBondedInteractionType.hpp"
70
71	<	namespace oopse {
71	>	namespace OpenMD {
72
68	–	/**
69	–	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
70	–	* @brief
71	–	*/
73		class ForceField{
74
75		public:
75	–
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
83	–	virtual ~ForceField();
84	–
87		std::string getForceFieldFileName() {
88		return forceFieldFileName_;
89		}
#	Line 90 | 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);
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	<
103	>	const std::string &at3, const std::string &at4);
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);
113	<	TorsionType* getExactTorsionType(const std::string &at1, const std::string &at2,
114	<	const std::string &at3, const std::string &at4);
115	<
116	<
112	>	const std::string &at3);
113	>	TorsionType* getExactTorsionType(const std::string &at1,
114	>	const std::string &at2,
115	>	const std::string &at3,
116	>	const std::string &at4);
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 double getRcutFromAtomType(AtomType* at);
127	<
126	>	virtual RealType getRcutFromAtomType(AtomType* at);
127	>
128		std::string getWildCard() {
129		return wildCardAtomTypeName_;
130		}
131	<
131	>
132		void setWildCard(const std::string& wildCard) {
133		wildCardAtomTypeName_ = wildCard;
134		}
135	<
121	<
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 addBondType(const std::string &at1, const std::string &at2, BondType* bondType);
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	+
155		bool addBendType(const std::string &at1, const std::string &at2,
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	+
172	+	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
173
174		protected:
175
#	Line 141 | Line 177 | namespace oopse {
177		BondTypeContainer bondTypeCont_;
178		BendTypeContainer bendTypeCont_;
179		TorsionTypeContainer torsionTypeCont_;
180	<
181	<	private:
182	<	std::string ffPath_;
180	>	InversionTypeContainer inversionTypeCont_;
181	>	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
182	>	ForceFieldOptions forceFieldOptions_;
183	>	std::map<int, std::string> atypeIdentToName;
184	>	SectionParserManager spMan_;
185
186	<	std::string wildCardAtomTypeName_;
187	<
188	<	std::string forceFieldFileName_;
186	>
187	>	private:
188	>	std::string ffPath_;
189	>	std::string wildCardAtomTypeName_;
190	>	std::string forceFieldFileName_;
191	>
192		};
193	<
153	<
154	<	}//end namespace oopse
193	>	}//end namespace OpenMD
194		#endif
195

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 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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