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

Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 475 by tim, Tue Apr 12 18:30:37 2005 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (file contents), Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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	<	/**
43	<	* @file ForceField.hpp
44	<	* @author tlin
45	<	* @date 11/04/2004
46	<	* @time 22:51am
47	<	* @version 1.0
48	<	*/
42	>	/**
43	>	* @file ForceField.hpp
44	>	* @author tlin
45	>	* @date 11/04/2004
46	>	* @time 22:51am
47	>	* @version 1.0
48	>	*/
49
50		#ifndef USETHEFORCE_FORCEFIELD_HPP
51		#define USETHEFORCE_FORCEFIELD_HPP
52
53	<	#define MK_STR(s) # s
54	<	#define STR_DEFINE(t, s) t = MK_STR(s)
55	<
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 "types/InversionType.hpp"
67	+	#include "types/NonBondedInteractionType.hpp"
68	+	namespace OpenMD {
69
70	<	namespace oopse {
70	>	/**
71	>	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
72	>	* @brief
73	>	*/
74	>	class ForceField{
75
76	<	/**
69	<	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
70	<	* @brief
71	<	*/
72	<	class ForceField{
76	>	public:
77
78	<	public:
78	>	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
79	>	typedef TypeContainer<BondType, 2> BondTypeContainer;
80	>	typedef TypeContainer<BendType, 3> BendTypeContainer;
81	>	typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
82	>	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
83	>	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
84	>
85	>	ForceField();
86	>
87	>	virtual ~ForceField();
88
89	<	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
90	<	typedef TypeContainer<BondType, 2> BondTypeContainer;
91	<	typedef TypeContainer<BendType, 3> BendTypeContainer;
79	<	typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
80	<
81	<	ForceField();
89	>	std::string getForceFieldFileName() {
90	>	return forceFieldFileName_;
91	>	}
92
93	<	virtual ~ForceField();
94	<
95	<	std::string getForceFieldFileName() {
86	<	return forceFieldFileName_;
87	<	}
88	<
89	<	void setForceFieldFileName(const std::string& filename) {
90	<	forceFieldFileName_ = filename;
91	<	}
93	>	void setForceFieldFileName(const std::string& filename) {
94	>	forceFieldFileName_ = filename;
95	>	}
96
97	<	virtual void parse(const std::string& filename) = 0;
97	>	virtual void parse(const std::string& filename) = 0;
98
99	<	AtomType* getAtomType(const std::string &at);
100	<	BondType* getBondType(const std::string &at1, const std::string &at2);
101	<	BendType* getBendType(const std::string &at1, const std::string &at2,
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);
99	>	AtomType* getAtomType(const std::string &at);
100	>	BondType* getBondType(const std::string &at1, const std::string &at2);
101	>	BendType* getBendType(const std::string &at1, const std::string &at2,
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	>	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);
114	>	TorsionType* getExactTorsionType(const std::string &at1,
115	>	const std::string &at2,
116	>	const std::string &at3,
117	>	const std::string &at4);
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	>
129	>	std::string getWildCard() {
130	>	return wildCardAtomTypeName_;
131	>	}
132	>
133	>	void setWildCard(const std::string& wildCard) {
134	>	wildCardAtomTypeName_ = wildCard;
135	>	}
136	>
137	>	unsigned int getNAtomType() {
138	>	return atomTypeCont_.size();
139	>	}
140
141	<	BondType* getExactBondType(const std::string &at1, const std::string &at2);
142	<	BendType* getExactBendType(const std::string &at1, const std::string &at2,
143	<	const std::string &at3);
144	<	TorsionType* getExactTorsionType(const std::string &at1, const std::string &at2,
145	<	const std::string &at3, const std::string &at4);
146	<
147	<
109	<	//avoid make virtual function public
110	<	//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
111	<	virtual double getRcutFromAtomType(AtomType* at);
112	<
113	<	std::string getWildCard() {
114	<	return wildCardAtomTypeName_;
115	<	}
116	<
117	<	void setWildCard(const std::string& wildCard) {
118	<	wildCardAtomTypeName_ = wildCard;
119	<	}
120	<
121	<
122	<	unsigned int getNAtomType() {
123	<	return atomTypeCont_.size();
124	<	}
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);
149	>	bool addAtomType(const std::string &at, AtomType* atomType);
150
151	<	bool addBondType(const std::string &at1, const std::string &at2, BondType* bondType);
151	>	bool replaceAtomType(const std::string &at, AtomType* atomType);
152
153	<	bool addBendType(const std::string &at1, const std::string &at2,
154	<	const std::string &at3, BendType* bendType);
153	>	bool addBondType(const std::string &at1, const std::string &at2,
154	>	BondType* bondType);
155
156	<	bool addTorsionType(const std::string &at1, const std::string &at2,
157	<	const std::string &at3, const std::string &at4, TorsionType* torsionType);
156	>	bool addBendType(const std::string &at1, const std::string &at2,
157	>	const std::string &at3, BendType* bendType);
158
159	<	ifstrstream* openForceFieldFile(const std::string& filename);
159	>	bool addTorsionType(const std::string &at1, const std::string &at2,
160	>	const std::string &at3, const std::string &at4,
161	>	TorsionType* torsionType);
162
163	<	protected:
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	>
173	>	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
174
175	<	AtomTypeContainer atomTypeCont_;
141	<	BondTypeContainer bondTypeCont_;
142	<	BendTypeContainer bendTypeCont_;
143	<	TorsionTypeContainer torsionTypeCont_;
144	<
145	<	private:
146	<	std::string ffPath_;
175	>	void setFortranForceOptions(void);
176
148	–	std::string wildCardAtomTypeName_;
149	–
150	–	std::string forceFieldFileName_;
151	–	};
152	–
177
178	<	}//end namespace oopse
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	>
191	>	std::string wildCardAtomTypeName_;
192	>
193	>	std::string forceFieldFileName_;
194	>
195	>	};
196	>	}//end namespace OpenMD
197		#endif
198

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 475 by tim, Tue Apr 12 18:30:37 2005 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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