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

Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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1	+	/*
2	+	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	+	*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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	+	*/
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)
53	>	#include "config.h"
54	>	#include <string>
55	>	#include <utility>
56	>	#include <vector>
57
58	<	#include <utilities>
59	<
58	>	#include "io/ifstrstream.hpp"
59	>	#include "io/ForceFieldOptions.hpp"
60	>	#include "utils/TypeContainer.hpp"
61		#include "utils/Tuple.hpp"
62	<	#include "types/ShapeAtomType.hpp"
63	<	#include "io/basic_ifstrstream.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	<	using namespace std;
71	<	using namespace oopse;
70	>	/**
71	>	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
72	>	* @brief
73	>	*/
74	>	class ForceField{
75
76	<	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	<	ForceField(){
90	<	hasVariant=false;
91	<	ffPath = getenv("FORCE_PARAM_PATH");
23	<	if( ffPath.empty() ) {
24	<	STR_DEFINE(ffPath, FRC_PATH );
25	<	}
26	<	}
89	>	std::string getForceFieldFileName() {
90	>	return forceFieldFileName_;
91	>	}
92
93	<	virtual ~ForceFields(){}
93	>	void setForceFieldFileName(const std::string& filename) {
94	>	forceFieldFileName_ = filename;
95	>	}
96	>
97	>	virtual void parse(const std::string& filename) = 0;
98
99	<	void setVariant(const string &variant) { hasVariant = true; theVariant = variant; }
100	<	virtual void readParams( void ) = 0;
101	<
102	<	AtomType* getMatchingAtomType(const string &at);
103	<	BondType* getMatchingBondType(const string &at1, const string &at2);
104	<	BendType* getMatchingBendType(const string &at1, const string &at2,
105	<	const string &at3);
106	<	TorsionType* getMatchingTorsionType(const string &at1, const string &at2,
107	<	const string &at3, const 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	<	double getRcutForAtomType(AtomType* at);
143	<
144	<	protected:
145	<
146	<	string ffPath;
147	<	ifstrstream forceFile;
148	<	bool hasVariant;
149	<	string variant;
150	<	map<string, AtomType*> atomTypeMap;
49	<	map<pair<string,string>, BondType*> bondTypeMap;
50	<	map<tuple3<string,string,string>, BendType*> bendTypeMap;
51	<	map<tuple4<string,string,string,string>, TorsionType*> torsionTypeMap;
52	<	string wildCardAtomTypeName;
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);
151
152	<	};
152	>	bool replaceAtomType(const std::string &at, AtomType* atomType);
153
154	+	bool addBondType(const std::string &at1, const std::string &at2,
155	+	BondType* bondType);
156
157	+	bool addBendType(const std::string &at1, const std::string &at2,
158	+	const std::string &at3, BendType* bendType);
159	+
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	+	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	+	protected:
177	+
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 206 by gezelter, Thu Nov 4 20:51:23 2004 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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