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

Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
trunk/src/brains/ForceField.hpp (file contents), Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	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, 234107 (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
46	–	* @time 22:51am
47		* @version 1.0
48		*/
49
#	Line 55 | Line 55
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 "io/SectionParserManager.hpp"
61		#include "utils/TypeContainer.hpp"
62		#include "utils/Tuple.hpp"
63		#include "types/AtomType.hpp"
#	Line 65 | Line 66
66		#include "types/TorsionType.hpp"
67		#include "types/InversionType.hpp"
68		#include "types/NonBondedInteractionType.hpp"
68	–	#include "UseTheForce/fForceOptions.h"
69	–	namespace oopse {
69
70	<	/**
71	<	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
73	<	* @brief
74	<	*/
70	>	namespace OpenMD {
71	>
72		class ForceField{
73
74		public:
78	–
75		typedef TypeContainer<AtomType, 1> AtomTypeContainer;
76		typedef TypeContainer<BondType, 2> BondTypeContainer;
77		typedef TypeContainer<BendType, 3> BendTypeContainer;
#	Line 83 | Line 79 | namespace oopse {
79		typedef TypeContainer<InversionType, 4> InversionTypeContainer;
80		typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
81
82	<	ForceField();
82	>	ForceField(std::string ffName);
83
84	<	virtual ~ForceField();
84	>	virtual ~ForceField() {};
85
86		std::string getForceFieldFileName() {
87		return forceFieldFileName_;
#	Line 95 | Line 91 | namespace oopse {
91		forceFieldFileName_ = filename;
92		}
93
94	<	virtual void parse(const std::string& filename) = 0;
94	>	virtual void parse(const std::string& filename);
95
96		AtomType* getAtomType(const std::string &at);
97	+	AtomType* getAtomType(int ident);
98		BondType* getBondType(const std::string &at1, const std::string &at2);
99		BendType* getBendType(const std::string &at1, const std::string &at2,
100		const std::string &at3);
#	Line 138 | Line 135 | namespace oopse {
135		unsigned int getNAtomType() {
136		return atomTypeCont_.size();
137		}
138	+
139	+	AtomTypeContainer* getAtomTypes() {
140	+	return &atomTypeCont_;
141	+	}
142	+
143	+	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
144	+	return &nonBondedInteractionTypeCont_;
145	+	}
146
147		bool addAtomType(const std::string &at, AtomType* atomType);
148
149	+	bool replaceAtomType(const std::string &at, AtomType* atomType);
150	+
151		bool addBondType(const std::string &at1, const std::string &at2,
152		BondType* bondType);
153
#	Line 163 | Line 170 | namespace oopse {
170
171		ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
172
166	–	void setFortranForceOptions(void);
167	–
168	–
173		protected:
174
175		AtomTypeContainer atomTypeCont_;
#	Line 175 | Line 179 | namespace oopse {
179		InversionTypeContainer inversionTypeCont_;
180		NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
181		ForceFieldOptions forceFieldOptions_;
182	+	std::map<int, std::string> atypeIdentToName;
183	+	SectionParserManager spMan_;
184	+
185
186		private:
187	<	std::string ffPath_;
188	<
182	<	std::string wildCardAtomTypeName_;
183	<
187	>	std::string ffPath_;
188	>	std::string wildCardAtomTypeName_;
189		std::string forceFieldFileName_;
190
191		};
192	<	}//end namespace oopse
192	>	}//end namespace OpenMD
193		#endif
194

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
trunk/src/brains/ForceField.hpp (property svn:keywords), Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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