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root/OpenMD/branches/development/src/visitors/AtomVisitor.hpp

Comparing:
trunk/src/visitors/AtomVisitor.hpp (file contents), Revision 954 by tim, Wed May 10 01:44:48 2006 UTC vs.
branches/development/src/visitors/AtomVisitor.hpp (file contents), Revision 1873 by gezelter, Fri May 10 16:09:34 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		#ifndef VISITORS_BASEATOMVISITOR_HPP
#	Line 47 | Line 48
48		#include "visitors/BaseVisitor.hpp"
49		#include "visitors/AtomData.hpp"
50
51	<	namespace oopse {
51	>	namespace OpenMD {
52
53		/**
54		* @class BaseAtomVisitor
#	Line 60 | Line 61 | namespace oopse {
61		virtual void visit(RigidBody* rb);
62		void setVisited(Atom* atom);
63		bool isVisited(Atom* atom);
64	<
64	>
65		protected:
66	<	BaseAtomVisitor(SimInfo* info) : BaseVisitor() {}
66	>	BaseAtomVisitor(SimInfo* info);
67		SimInfo* info;
68	+	int storageLayout_;
69		};
70
69	–	/**
70	–	* @class SSDAtomVisitor
71	–	* @todo document
72	–	*/
73	–	class SSDAtomVisitor : public BaseAtomVisitor{
74	–	public:
75	–	SSDAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
76	–	visitorName = "SSDAtomVisitor";
77	–	ssdAtomType.insert("SSD");
78	–	ssdAtomType.insert("SSD_E");
79	–	ssdAtomType.insert("SSD_RF");
80	–	ssdAtomType.insert("SSD1");
81	–	ssdAtomType.insert("TAP");
82	–	}
83	–
84	–	virtual void visit(Atom* atom) {}
85	–	virtual void visit(DirectionalAtom* datom);
86	–	virtual void visit(RigidBody* rb) {}
87	–
88	–	virtual const std::string toString();
89	–	private:
90	–	inline bool isSSDAtom(const std::string& atomType);
91	–	std::set<std::string> ssdAtomType;
92	–	};
93	–
94	–	class LinearAtomVisitor : public BaseAtomVisitor{
95	–	public:
96	–	LinearAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
97	–	visitorName = "LinearAtomVisitor";
98	–	linearAtomType.insert("linear");
99	–	}
100	–
101	–	void addGayBerneAtomType(const std::string& atomType);
102	–	virtual void visit(Atom* atom) {}
103	–	virtual void visit(DirectionalAtom* datom);
104	–	virtual void visit(RigidBody* rb) {}
105	–
106	–	virtual const std::string toString();
107	–	private:
108	–	inline bool isLinearAtom(const std::string& atomType);
109	–	std::set<std::string> linearAtomType;
110	–	};
111	–
112	–	class GBLipidAtomVisitor : public BaseAtomVisitor{
113	–	public:
114	–	GBLipidAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
115	–	visitorName = "GBLipidAtomVisitor";
116	–	GBLipidAtomType.insert("GBlipid");
117	–	}
118	–
119	–	virtual void visit(Atom* atom) {}
120	–	virtual void visit(DirectionalAtom* datom);
121	–	virtual void visit(RigidBody* rb) {}
122	–
123	–	virtual const std::string toString();
124	–	private:
125	–	inline bool isGBLipidAtom(const std::string& atomType);
126	–	std::set<std::string> GBLipidAtomType;
127	–	};
128	–
129	–
71		class DefaultAtomVisitor : public BaseAtomVisitor{
72		public:
73		DefaultAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) { visitorName = "DefaultAtomVisitor";}
74	<
75	<	virtual void visit(Atom* atom);
74	>
75	>	virtual void visit(Atom* atom);
76		virtual void visit(DirectionalAtom* datom);
77		virtual void visit(RigidBody* rb) {}
78	<
78	>
79		virtual const std::string toString();
80	<
80	>
81		};
82
83	<	}//namespace oopse
83	>	}//namespace OpenMD
84		#endif

Comparing:
trunk/src/visitors/AtomVisitor.hpp (property svn:keywords), Revision 954 by tim, Wed May 10 01:44:48 2006 UTC vs.
branches/development/src/visitors/AtomVisitor.hpp (property svn:keywords), Revision 1873 by gezelter, Fri May 10 16:09:34 2013 UTC

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