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root/OpenMD/branches/development/src/rnemd/RNEMD.hpp

Comparing:
trunk/src/integrators/RNEMD.hpp (file contents), Revision 1332 by gezelter, Thu Apr 2 17:25:59 2009 UTC vs.
branches/development/src/rnemd/RNEMD.hpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 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, 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 RNEMD.hpp
45		* @author gezelter
46		* @date 03/13/2009
46	–	* @time 15:56pm
47		* @version 1.0
48		*/
49
#	Line 53 | Line 53
53		#include "math/RandNumGen.hpp"
54		#include "selection/SelectionEvaluator.hpp"
55		#include "selection/SelectionManager.hpp"
56	+	#include <iostream>
57
58	<	namespace oopse {
58	>	using namespace std;
59	>	namespace OpenMD {
60
59	–	/**
60	–	* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
61	–	* @todo document
62	–	*/
61		class RNEMD {
62		public:
63		RNEMD(SimInfo* info);
64		virtual ~RNEMD();
65	<
65	>
66	>	void doRNEMD();
67		void doSwap();
68	<	void set_RNEMD_swapTime(RealType swapTime) { swapTime_ = swapTime; }
69	<	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
70	<	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
71	<	void set_RNEMD_exchange_total(RealType et) {exchangeSum_ = et;}
68	>	void doNIVS();
69	>	void doVSS();
70	>	void collectData();
71	>	void getStarted();
72	>	bool inSlabA(Vector3d pos);
73	>	bool inSlabB(Vector3d pos);
74	>	void parseOutputFileFormat(const std::string& format);
75	>	void writeOutputFile();
76	>	void writeReal(int index, unsigned int bin);
77	>	void writeVector(int index, unsigned int bin);
78	>	void writeRealStdDev(int index, unsigned int bin);
79	>	void writeVectorStdDev(int index, unsigned int bin);
80
81		private:
82
83	<	enum RNEMDTypeEnum {
84	<	rnemdKinetic,
85	<	rnemdPx,
86	<	rnemdPy,
87	<	rnemdPz,
81	<	rnemdUnknown
83	>	enum RNEMDMethod {
84	>	rnemdSwap,
85	>	rnemdNIVS,
86	>	rnemdVSS,
87	>	rnemdUnkownMethod
88		};
89	<
89	>	enum RNEMDFluxType {
90	>	rnemdKE,       // translational kinetic energy flux
91	>	rnemdRotKE,    // rotational kinetic energy flux
92	>	rnemdFullKE,   // full kinetic energy flux
93	>	rnemdPx,       // flux of momentum along x axis
94	>	rnemdPy,       // flux of momentum along y axis
95	>	rnemdPz,       // flux of momentum along z axis
96	>	rnemdPvector,  // flux of momentum vector
97	>	rnemdKePx,     // flux of translational KE and x-momentum
98	>	rnemdKePy,     // flux of translational KE and y-momentum
99	>	rnemdKePvector, // full combo platter
100	>	rnemdUnknownFluxType
101	>	};
102	>
103	>	enum OutputFields {
104	>	BEGININDEX = 0,
105	>	Z = BEGININDEX,
106	>	TEMPERATURE,
107	>	VELOCITY,
108	>	DENSITY,
109	>	ENDINDEX
110	>	};
111	>
112	>	struct OutputData {
113	>	string title;
114	>	string units;
115	>	string dataType;
116	>	vector<Accumulator*> accumulator;
117	>	};
118	>
119	>	typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
120	>	typedef map<string, OutputFields> OutputMapType;
121	>
122		SimInfo* info_;
123	<	RandNumGen* randNumGen_;
124	<	int nBins_;
125	<	RealType swapTime_;
126	<	RealType exchangeSum_;
127	<	RNEMDTypeEnum rnemdType_;
128	<	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
91	<	std::string rnemdObjectSelection_;
92	<	SelectionManager seleMan_;
123	>
124	>	map<string, RNEMDMethod> stringToMethod_;
125	>	map<string, RNEMDFluxType> stringToFluxType_;
126	>	RNEMDMethod rnemdMethod_;
127	>	RNEMDFluxType rnemdFluxType_;
128	>	string rnemdObjectSelection_;
129		SelectionEvaluator evaluator_;
130	+	SelectionManager seleMan_;
131		bool usePeriodicBoundaryConditions_;
132	<	};
132	>	int nBins_;
133	>	RealType slabWidth_;
134	>	RealType slabACenter_;
135	>	RealType slabBCenter_;
136
137	+	RealType kineticFlux_;        // target or desired *flux*
138	+	Vector3d momentumFluxVector_; // target or desired *flux*
139	+
140	+	RealType kineticTarget_;     // target or desired one-time exchange energy
141	+	Vector3d momentumTarget_;    // target or desired one-time exchange momentum
142	+
143	+	RealType kineticExchange_;    // actual exchange energy (running total)
144	+	Vector3d momentumExchange_;   // actual exchange momentum (running total)
145	+
146	+	RealType exchangeTime_;
147	+
148	+	RealType targetJzpz2_;
149	+
150	+	unsigned int trialCount_;
151	+	unsigned int failTrialCount_;
152	+	unsigned int failRootCount_;
153	+
154	+	string rnemdFileName_;
155	+	ofstream rnemdFile_;
156	+
157	+	RealType runTime_, statusTime_;
158	+
159	+	vector<OutputData> data_;
160	+	OutputBitSet outputMask_;
161	+	OutputMapType outputMap_;
162	+	Accumulator* areaAccumulator_;
163	+	bool doRNEMD_;
164	+
165	+	};
166		}
167	<	#endif //INTEGRATORS_VELOCITIZER_HPP
167	>	#endif //INTEGRATORS_RNEMD_HPP

Comparing:
trunk/src/integrators/RNEMD.hpp (property svn:keywords), Revision 1332 by gezelter, Thu Apr 2 17:25:59 2009 UTC vs.
branches/development/src/rnemd/RNEMD.hpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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