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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/brains/ForceField.hpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

#	Line 1 | Line 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
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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	+	*/
42	+
43	+	/**
44	+	* @file ForceField.hpp
45	+	* @author tlin
46	+	* @date 11/04/2004
47	+	* @time 22:51am
48	+	* @version 1.0
49	+	*/
50	+
51		#ifndef USETHEFORCE_FORCEFIELD_HPP
52		#define USETHEFORCE_FORCEFIELD_HPP
53
54	<	#define MK_STR(s) # s
55	<	#define STR_DEFINE(t, s) t = MK_STR(s)
54	>	#include "config.h"
55	>	#include <string>
56	>	#include <utility>
57	>	#include <vector>
58
59	<	#include <utilities>
60	<
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/ShapeAtomType.hpp"
65	<	#include "io/basic_ifstrstream.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	<	using namespace std;
14	<	using namespace oopse;
71	>	namespace OpenMD {
72
73	<	class ForceField{
73	>	class ForceField{
74
75	<	public:
75	>	public:
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	>	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
81	>	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
82	>
83	>	ForceField(std::string ffName);
84	>
85	>	virtual ~ForceField() {};
86
87	<	ForceField(){
88	<	hasVariant=false;
89	<	ffPath = getenv("FORCE_PARAM_PATH");
23	<	if( ffPath.empty() ) {
24	<	STR_DEFINE(ffPath, FRC_PATH );
25	<	}
26	<	}
87	>	std::string getForceFieldFileName() {
88	>	return forceFieldFileName_;
89	>	}
90
91	<	virtual ~ForceFields(){}
91	>	void setForceFieldFileName(const std::string& filename) {
92	>	forceFieldFileName_ = filename;
93	>	}
94	>
95	>	virtual void parse(const std::string& filename);
96
97	<	void setVariant(const string &variant) { hasVariant = true; theVariant = variant; }
98	<	virtual void readParams( void ) = 0;
99	<
100	<	AtomType* getMatchingAtomType(const string &at);
101	<	BondType* getMatchingBondType(const string &at1, const string &at2);
102	<	BendType* getMatchingBendType(const string &at1, const string &at2,
103	<	const string &at3);
104	<	TorsionType* getMatchingTorsionType(const string &at1, const string &at2,
105	<	const string &at3, const string &at4);
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);
102	>	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
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,
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 RealType getRcutFromAtomType(AtomType* at);
127	>
128	>	std::string getWildCard() {
129	>	return wildCardAtomTypeName_;
130	>	}
131	>
132	>	void setWildCard(const std::string& wildCard) {
133	>	wildCardAtomTypeName_ = wildCard;
134	>	}
135	>
136	>	unsigned int getNAtomType() {
137	>	return atomTypeCont_.size();
138	>	}
139
140	<	double getRcutForAtomType(AtomType* at);
141	<
142	<	protected:
143	<
144	<	string ffPath;
145	<	ifstrstream forceFile;
146	<	bool hasVariant;
147	<	string variant;
148	<	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;
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	<	};
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,
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	+
176	+	AtomTypeContainer atomTypeCont_;
177	+	BondTypeContainer bondTypeCont_;
178	+	BendTypeContainer bendTypeCont_;
179	+	TorsionTypeContainer torsionTypeCont_;
180	+	InversionTypeContainer inversionTypeCont_;
181	+	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
182	+	ForceFieldOptions forceFieldOptions_;
183	+	std::map<int, std::string> atypeIdentToName;
184	+	SectionParserManager spMan_;
185	+
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/brains/ForceField.hpp (property svn:keywords), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

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