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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 1627 by gezelter, Tue Sep 13 22:05:04 2011 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"
58	>	#include "io/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	>	AtomType* getAtomType(int ident);
101	>	BondType* getBondType(const std::string &at1, const std::string &at2);
102	>	BendType* getBendType(const std::string &at1, const std::string &at2,
103	>	const std::string &at3);
104	>	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
105	>	const std::string &at3, const std::string &at4);
106	>	InversionType* getInversionType(const std::string &at1,
107	>	const std::string &at2,
108	>	const std::string &at3,
109	>	const std::string &at4);
110	>	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
111	>
112	>	BondType* getExactBondType(const std::string &at1, const std::string &at2);
113	>	BendType* getExactBendType(const std::string &at1, const std::string &at2,
114	>	const std::string &at3);
115	>	TorsionType* getExactTorsionType(const std::string &at1,
116	>	const std::string &at2,
117	>	const std::string &at3,
118	>	const std::string &at4);
119	>	InversionType* getExactInversionType(const std::string &at1,
120	>	const std::string &at2,
121	>	const std::string &at3,
122	>	const std::string &at4);
123	>	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
124	>
125	>
126	>	//avoid make virtual function public
127	>	//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
128	>	virtual RealType getRcutFromAtomType(AtomType* at);
129	>
130	>	std::string getWildCard() {
131	>	return wildCardAtomTypeName_;
132	>	}
133	>
134	>	void setWildCard(const std::string& wildCard) {
135	>	wildCardAtomTypeName_ = wildCard;
136	>	}
137	>
138	>	unsigned int getNAtomType() {
139	>	return atomTypeCont_.size();
140	>	}
141
142	<	BondType* getExactBondType(const std::string &at1, const std::string &at2);
143	<	BendType* getExactBendType(const std::string &at1, const std::string &at2,
144	<	const std::string &at3);
145	<	TorsionType* getExactTorsionType(const std::string &at1, const std::string &at2,
146	<	const std::string &at3, const std::string &at4);
147	<
148	<
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	<	}
142	>	AtomTypeContainer* getAtomTypes() {
143	>	return &atomTypeCont_;
144	>	}
145	>
146	>	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
147	>	return &nonBondedInteractionTypeCont_;
148	>	}
149
150	<	bool addAtomType(const std::string &at, AtomType* atomType);
150	>	bool addAtomType(const std::string &at, AtomType* atomType);
151
152	<	bool addBondType(const std::string &at1, const std::string &at2, BondType* bondType);
152	>	bool replaceAtomType(const std::string &at, AtomType* atomType);
153
154	<	bool addBendType(const std::string &at1, const std::string &at2,
155	<	const std::string &at3, BendType* bendType);
154	>	bool addBondType(const std::string &at1, const std::string &at2,
155	>	BondType* bondType);
156
157	<	bool addTorsionType(const std::string &at1, const std::string &at2,
158	<	const std::string &at3, const std::string &at4, TorsionType* torsionType);
157	>	bool addBendType(const std::string &at1, const std::string &at2,
158	>	const std::string &at3, BendType* bendType);
159
160	<	ifstrstream* openForceFieldFile(const std::string& filename);
160	>	bool addTorsionType(const std::string &at1, const std::string &at2,
161	>	const std::string &at3, const std::string &at4,
162	>	TorsionType* torsionType);
163
164	<	protected:
164	>	bool addInversionType(const std::string &at1, const std::string &at2,
165	>	const std::string &at3, const std::string &at4,
166	>	InversionType* inversionType);
167	>
168	>	bool addNonBondedInteractionType(const std::string &at1,
169	>	const std::string &at2,
170	>	NonBondedInteractionType* nbiType);
171	>
172	>	ifstrstream* openForceFieldFile(const std::string& filename);
173	>
174	>	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
175
176	<	AtomTypeContainer atomTypeCont_;
141	<	BondTypeContainer bondTypeCont_;
142	<	BendTypeContainer bendTypeCont_;
143	<	TorsionTypeContainer torsionTypeCont_;
144	<
145	<	private:
146	<	std::string ffPath_;
176	>	protected:
177
178	<	std::string wildCardAtomTypeName_;
179	<
180	<	std::string forceFieldFileName_;
181	<	};
182	<
183	<
184	<	}//end namespace oopse
178	>	AtomTypeContainer atomTypeCont_;
179	>	BondTypeContainer bondTypeCont_;
180	>	BendTypeContainer bendTypeCont_;
181	>	TorsionTypeContainer torsionTypeCont_;
182	>	InversionTypeContainer inversionTypeCont_;
183	>	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
184	>	ForceFieldOptions forceFieldOptions_;
185	>	std::map<int, std::string> atypeIdentToName;
186	>
187	>	private:
188	>	std::string ffPath_;
189	>	std::string wildCardAtomTypeName_;
190	>	std::string forceFieldFileName_;
191	>
192	>	};
193	>	}//end namespace OpenMD
194		#endif
195

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 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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