ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1465 by chuckv, Fri Jul 9 23:08:25 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	+	#include "UseTheForce/fForceOptions.h"
69	+	namespace OpenMD {
70
71	<	namespace oopse {
71	>	/**
72	>	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
73	>	* @brief
74	>	*/
75	>	class ForceField{
76
77	<	/**
69	<	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
70	<	* @brief
71	<	*/
72	<	class ForceField{
77	>	public:
78
79	<	public:
79	>	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
80	>	typedef TypeContainer<BondType, 2> BondTypeContainer;
81	>	typedef TypeContainer<BendType, 3> BendTypeContainer;
82	>	typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
83	>	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
84	>	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
85	>
86	>	ForceField();
87	>
88	>	virtual ~ForceField();
89
90	<	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
91	<	typedef TypeContainer<BondType, 2> BondTypeContainer;
92	<	typedef TypeContainer<BendType, 3> BendTypeContainer;
79	<	typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
80	<
81	<	ForceField();
90	>	std::string getForceFieldFileName() {
91	>	return forceFieldFileName_;
92	>	}
93
94	<	virtual ~ForceField();
95	<
96	<	std::string getForceFieldFileName() {
86	<	return forceFieldFileName_;
87	<	}
88	<
89	<	void setForceFieldFileName(const std::string& filename) {
90	<	forceFieldFileName_ = filename;
91	<	}
94	>	void setForceFieldFileName(const std::string& filename) {
95	>	forceFieldFileName_ = filename;
96	>	}
97
98	<	virtual void parse(const std::string& filename) = 0;
98	>	virtual void parse(const std::string& filename) = 0;
99
100	<	AtomType* getAtomType(const std::string &at);
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	<
107	<	BondType* getExactBondType(const std::string &at1, const std::string &at2);
108	<	BendType* getExactBendType(const std::string &at1, const std::string &at2,
109	<	const std::string &at3);
110	<	TorsionType* getExactTorsionType(const std::string &at1, const std::string &at2,
111	<	const std::string &at3, const std::string &at4);
112	<
113	<
114	<	//avoid make virtual function public
115	<	//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
116	<	virtual double getRcutFromAtomType(AtomType* at);
117	<
118	<	std::string getWildCard() {
119	<	return wildCardAtomTypeName_;
120	<	}
121	<
122	<	void setWildCard(const std::string& wildCard) {
123	<	wildCardAtomTypeName_ = wildCard;
124	<	}
125	<
126	<
127	<	unsigned int getNAtomType() {
128	<	return atomTypeCont_.size();
129	<	}
100	>	AtomType* getAtomType(const std::string &at);
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	<	bool addAtomType(const std::string &at, AtomType* atomType);
142	>	bool addAtomType(const std::string &at, AtomType* atomType);
143
144	<	bool addBondType(const std::string &at1, const std::string &at2, BondType* bondType);
144	>	bool replaceAtomType(const std::string &at, AtomType* atomType);
145
146	<	bool addBendType(const std::string &at1, const std::string &at2,
147	<	const std::string &at3, BendType* bendType);
146	>	bool addBondType(const std::string &at1, const std::string &at2,
147	>	BondType* bondType);
148
149	<	bool addTorsionType(const std::string &at1, const std::string &at2,
150	<	const std::string &at3, const std::string &at4, TorsionType* torsionType);
149	>	bool addBendType(const std::string &at1, const std::string &at2,
150	>	const std::string &at3, BendType* bendType);
151
152	<	ifstrstream* openForceFieldFile(const std::string& filename);
152	>	bool addTorsionType(const std::string &at1, const std::string &at2,
153	>	const std::string &at3, const std::string &at4,
154	>	TorsionType* torsionType);
155
156	<	protected:
156	>	bool addInversionType(const std::string &at1, const std::string &at2,
157	>	const std::string &at3, const std::string &at4,
158	>	InversionType* inversionType);
159	>
160	>	bool addNonBondedInteractionType(const std::string &at1,
161	>	const std::string &at2,
162	>	NonBondedInteractionType* nbiType);
163	>
164	>	ifstrstream* openForceFieldFile(const std::string& filename);
165	>
166	>	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
167
168	<	AtomTypeContainer atomTypeCont_;
141	<	BondTypeContainer bondTypeCont_;
142	<	BendTypeContainer bendTypeCont_;
143	<	TorsionTypeContainer torsionTypeCont_;
144	<
145	<	private:
146	<	std::string ffPath_;
168	>	void setFortranForceOptions(void);
169
148	–	std::string wildCardAtomTypeName_;
149	–
150	–	std::string forceFieldFileName_;
151	–	};
152	–
170
171	<	}//end namespace oopse
171	>	protected:
172	>
173	>	AtomTypeContainer atomTypeCont_;
174	>	BondTypeContainer bondTypeCont_;
175	>	BendTypeContainer bendTypeCont_;
176	>	TorsionTypeContainer torsionTypeCont_;
177	>	InversionTypeContainer inversionTypeCont_;
178	>	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
179	>	ForceFieldOptions forceFieldOptions_;
180	>
181	>	private:
182	>	std::string ffPath_;
183	>
184	>	std::string wildCardAtomTypeName_;
185	>
186	>	std::string forceFieldFileName_;
187	>
188	>	};
189	>	}//end namespace OpenMD
190		#endif
191

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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines