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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 1773 by gezelter, Tue Aug 7 18:26:40 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	>
80		private:
81	<
82	<	enum RNEMDTypeEnum {
83	<	rnemdKinetic,
84	<	rnemdPx,
85	<	rnemdPy,
86	<	rnemdPz,
79	<	rnemdUnknown
81	>
82	>	enum RNEMDMethod {
83	>	rnemdSwap,
84	>	rnemdNIVS,
85	>	rnemdVSS,
86	>	rnemdUnkownMethod
87		};
88	<
88	>	enum RNEMDFluxType {
89	>	rnemdKE,       // translational kinetic energy flux
90	>	rnemdRotKE,    // rotational kinetic energy flux
91	>	rnemdFullKE,   // full kinetic energy flux
92	>	rnemdPx,       // flux of momentum along x axis
93	>	rnemdPy,       // flux of momentum along y axis
94	>	rnemdPz,       // flux of momentum along z axis
95	>	rnemdPvector,  // flux of momentum vector
96	>	rnemdKePx,     // flux of translational KE and x-momentum
97	>	rnemdKePy,     // flux of translational KE and y-momentum
98	>	rnemdKePvector, // full combo platter
99	>	rnemdUnknownFluxType
100	>	};
101	>
102	>	enum OutputFields {
103	>	BEGININDEX = 0,
104	>	Z = BEGININDEX,
105	>	TEMPERATURE,
106	>	VELOCITY,
107	>	DENSITY,
108	>	ENDINDEX
109	>	};
110	>
111	>	struct OutputData {
112	>	string title;
113	>	string units;
114	>	string dataType;
115	>	vector<Accumulator*> accumulator;
116	>	};
117	>
118	>	typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
119	>	typedef map<string, OutputFields> OutputMapType;
120	>
121		SimInfo* info_;
83	–	RandNumGen* randNumGen_;
84	–	int nBins_;
85	–	RealType swapTime_;
86	–	RealType exchangeSum_;
87	–	RNEMDTypeEnum rnemdType_;
88	–	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
122
123	+	map<string, RNEMDMethod> stringToMethod_;
124	+	map<string, RNEMDFluxType> stringToFluxType_;
125	+	RNEMDMethod rnemdMethod_;
126	+	RNEMDFluxType rnemdFluxType_;
127	+	string rnemdObjectSelection_;
128	+	SelectionEvaluator evaluator_;
129	+	SelectionManager seleMan_;
130	+	bool usePeriodicBoundaryConditions_;
131	+	int nBins_;
132	+	RealType slabWidth_;
133	+	RealType slabACenter_;
134	+	RealType slabBCenter_;
135
136	<	};
136	>	RealType kineticFlux_;        // target or desired *flux*
137	>	Vector3d momentumFluxVector_; // target or desired *flux*
138
139	+	RealType kineticTarget_;     // target or desired one-time exchange energy
140	+	Vector3d momentumTarget_;    // target or desired one-time exchange momentum
141	+
142	+	RealType kineticExchange_;    // actual exchange energy (running total)
143	+	Vector3d momentumExchange_;   // actual exchange momentum (running total)
144	+
145	+	RealType exchangeTime_;
146	+
147	+	RealType targetJzpz2_;
148	+
149	+	unsigned int trialCount_;
150	+	unsigned int failTrialCount_;
151	+	unsigned int failRootCount_;
152	+
153	+	string rnemdFileName_;
154	+	ofstream rnemdFile_;
155	+
156	+	RealType runTime_, statusTime_;
157	+
158	+	vector<OutputData> data_;
159	+	OutputBitSet outputMask_;
160	+	OutputMapType outputMap_;
161	+
162	+	};
163		}
164	<	#endif //INTEGRATORS_VELOCITIZER_HPP
164	>	#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 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC

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