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

Comparing:
trunk/src/integrators/RNEMD.hpp (file contents), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/rnemd/RNEMD.hpp (file contents), Revision 1776 by gezelter, Thu Aug 9 15:52:59 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		/**
#	Line 51 | Line 52
52		#define INTEGRATORS_RNEMD_HPP
53		#include "brains/SimInfo.hpp"
54		#include "math/RandNumGen.hpp"
55	+	#include "selection/SelectionEvaluator.hpp"
56	+	#include "selection/SelectionManager.hpp"
57	+	#include <iostream>
58
59	<	namespace oopse {
59	>	using namespace std;
60	>	namespace OpenMD {
61
57	–	/**
58	–	* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
59	–	* @todo document
60	–	*/
62		class RNEMD {
63		public:
64		RNEMD(SimInfo* info);
65		virtual ~RNEMD();
66	<
66	>
67	>	void doRNEMD();
68		void doSwap();
69	<	void set_RNEMD_swapTime(RealType swapTime) { swapTime_ = swapTime; }
70	<	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
71	<	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
72	<	void set_RNEMD_exchange_total(RealType et) {exchangeSum_ = et;}
73	<
69	>	void doNIVS();
70	>	void doVSS();
71	>	void collectData();
72	>	void getStarted();
73	>	bool inSlabA(Vector3d pos);
74	>	bool inSlabB(Vector3d pos);
75	>	void parseOutputFileFormat(const std::string& format);
76	>	void writeOutputFile();
77	>	void writeReal(int index, unsigned int bin);
78	>	void writeVector(int index, unsigned int bin);
79	>	void writeRealStdDev(int index, unsigned int bin);
80	>	void writeVectorStdDev(int index, unsigned int bin);
81	>
82		private:
83	<
84	<	enum RNEMDTypeEnum {
85	<	rnemdKinetic,
86	<	rnemdPx,
87	<	rnemdPy,
88	<	rnemdPz,
79	<	rnemdUnknown
83	>
84	>	enum RNEMDMethod {
85	>	rnemdSwap,
86	>	rnemdNIVS,
87	>	rnemdVSS,
88	>	rnemdUnkownMethod
89		};
90	<
90	>	enum RNEMDFluxType {
91	>	rnemdKE,       // translational kinetic energy flux
92	>	rnemdRotKE,    // rotational kinetic energy flux
93	>	rnemdFullKE,   // full kinetic energy flux
94	>	rnemdPx,       // flux of momentum along x axis
95	>	rnemdPy,       // flux of momentum along y axis
96	>	rnemdPz,       // flux of momentum along z axis
97	>	rnemdPvector,  // flux of momentum vector
98	>	rnemdKePx,     // flux of translational KE and x-momentum
99	>	rnemdKePy,     // flux of translational KE and y-momentum
100	>	rnemdKePvector, // full combo platter
101	>	rnemdUnknownFluxType
102	>	};
103	>
104	>	enum OutputFields {
105	>	BEGININDEX = 0,
106	>	Z = BEGININDEX,
107	>	TEMPERATURE,
108	>	VELOCITY,
109	>	DENSITY,
110	>	ENDINDEX
111	>	};
112	>
113	>	struct OutputData {
114	>	string title;
115	>	string units;
116	>	string dataType;
117	>	vector<Accumulator*> accumulator;
118	>	};
119	>
120	>	typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
121	>	typedef map<string, OutputFields> OutputMapType;
122	>
123		SimInfo* info_;
83	–	RandNumGen* randNumGen_;
84	–	int nBins_;
85	–	RealType swapTime_;
86	–	RealType exchangeSum_;
87	–	RNEMDTypeEnum rnemdType_;
88	–	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
124
125	+	map<string, RNEMDMethod> stringToMethod_;
126	+	map<string, RNEMDFluxType> stringToFluxType_;
127	+	RNEMDMethod rnemdMethod_;
128	+	RNEMDFluxType rnemdFluxType_;
129	+	string rnemdObjectSelection_;
130	+	SelectionEvaluator evaluator_;
131	+	SelectionManager seleMan_;
132	+	bool usePeriodicBoundaryConditions_;
133	+	int nBins_;
134	+	RealType slabWidth_;
135	+	RealType slabACenter_;
136	+	RealType slabBCenter_;
137
138	<	};
138	>	RealType kineticFlux_;        // target or desired *flux*
139	>	Vector3d momentumFluxVector_; // target or desired *flux*
140
141	+	RealType kineticTarget_;     // target or desired one-time exchange energy
142	+	Vector3d momentumTarget_;    // target or desired one-time exchange momentum
143	+
144	+	RealType kineticExchange_;    // actual exchange energy (running total)
145	+	Vector3d momentumExchange_;   // actual exchange momentum (running total)
146	+
147	+	RealType exchangeTime_;
148	+
149	+	RealType targetJzpz2_;
150	+
151	+	unsigned int trialCount_;
152	+	unsigned int failTrialCount_;
153	+	unsigned int failRootCount_;
154	+
155	+	string rnemdFileName_;
156	+	ofstream rnemdFile_;
157	+
158	+	RealType runTime_, statusTime_;
159	+
160	+	vector<OutputData> data_;
161	+	OutputBitSet outputMask_;
162	+	OutputMapType outputMap_;
163	+	Accumulator* areaAccumulator_;
164	+	bool doRNEMD_;
165	+
166	+	};
167		}
168	<	#endif //INTEGRATORS_VELOCITIZER_HPP
168	>	#endif //INTEGRATORS_RNEMD_HPP

Comparing:
trunk/src/integrators/RNEMD.hpp (property svn:keywords), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/rnemd/RNEMD.hpp (property svn:keywords), Revision 1776 by gezelter, Thu Aug 9 15:52:59 2012 UTC

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