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root/OpenMD/trunk/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.
trunk/src/rnemd/RNEMD.hpp (file contents), Revision 2046 by gezelter, Tue Dec 2 22:11:04 2014 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
42	–	/**
43	–	* @file RNEMD.hpp
44	–	* @author gezelter
45	–	* @date 03/13/2009
46	–	* @time 15:56pm
47	–	* @version 1.0
48	–	*/
49	–
43		#ifndef INTEGRATORS_RNEMD_HPP
44		#define INTEGRATORS_RNEMD_HPP
45		#include "brains/SimInfo.hpp"
46		#include "math/RandNumGen.hpp"
47	+	#include "selection/SelectionEvaluator.hpp"
48	+	#include "selection/SelectionManager.hpp"
49	+	#include <iostream>
50
51	<	namespace oopse {
51	>	using namespace std;
52	>	namespace OpenMD {
53
57	–	/**
58	–	* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
59	–	* @todo document
60	–	*/
54		class RNEMD {
55		public:
56		RNEMD(SimInfo* info);
57	<	virtual ~RNEMD();
58	<
59	<	void doSwap();
60	<	void set_RNEMD_swapTime(RealType swapTime) { swapTime_ = swapTime; }
61	<	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
62	<	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
63	<	void set_RNEMD_exchange_total(RealType et) {exchangeSum_ = et;}
64	<
57	>	~RNEMD();
58	>
59	>	void doRNEMD();
60	>	void doSwap(SelectionManager& smanA, SelectionManager& smanB);
61	>	void doNIVS(SelectionManager& smanA, SelectionManager& smanB);
62	>	void doVSS(SelectionManager& smanA, SelectionManager& smanB);
63	>	RealType getDividingArea();
64	>	void collectData();
65	>	void getStarted();
66	>	void parseOutputFileFormat(const std::string& format);
67	>	void writeOutputFile();
68	>	void writeReal(int index, unsigned int bin);
69	>	void writeVector(int index, unsigned int bin);
70	>	void writeRealErrorBars(int index, unsigned int bin);
71	>	void writeVectorErrorBars(int index, unsigned int bin);
72	>
73		private:
74	<
75	<	enum RNEMDTypeEnum {
76	<	rnemdKinetic,
77	<	rnemdPx,
78	<	rnemdPy,
79	<	rnemdPz,
79	<	rnemdUnknown
74	>
75	>	enum RNEMDMethod {
76	>	rnemdSwap,
77	>	rnemdNIVS,
78	>	rnemdVSS,
79	>	rnemdUnkownMethod
80		};
81	<
81	>	enum RNEMDFluxType {
82	>	rnemdKE,       // translational kinetic energy flux
83	>	rnemdRotKE,    // rotational kinetic energy flux
84	>	rnemdFullKE,   // full kinetic energy flux
85	>	rnemdPx,       // flux of momentum along x axis
86	>	rnemdPy,       // flux of momentum along y axis
87	>	rnemdPz,       // flux of momentum along z axis
88	>	rnemdPvector,  // flux of momentum vector
89	>	rnemdLx,       // flux of angular momentum along x axis
90	>	rnemdLy,       // flux of angular momentum along y axis
91	>	rnemdLz,       // flux of angular momentum along z axis
92	>	rnemdLvector,  // flux of angular momentum vector
93	>	rnemdKePx,     // flux of translational KE and x-momentum
94	>	rnemdKePy,     // flux of translational KE and y-momentum
95	>	rnemdKePvector, // full combo flying platter
96	>	rnemdKeLx,     // flux of translational KE and x-angular momentum
97	>	rnemdKeLy,     // flux of translational KE and y-angular momentum
98	>	rnemdKeLz,     // flux of translational KE and z-angular momentum
99	>	rnemdKeLvector, // full combo spinning platter
100	>	rnemdUnknownFluxType
101	>	};
102	>
103	>	enum OutputFields {
104	>	BEGININDEX = 0,
105	>	Z = BEGININDEX,
106	>	R,
107	>	TEMPERATURE,
108	>	VELOCITY,
109	>	ANGULARVELOCITY,
110	>	DENSITY,
111	>	ENDINDEX
112	>	};
113	>
114	>	struct OutputData {
115	>	string title;
116	>	string units;
117	>	string dataType;
118	>	vector<BaseAccumulator*> accumulator;
119	>	};
120	>
121	>	typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
122	>	typedef map<string, OutputFields> OutputMapType;
123	>
124		SimInfo* info_;
83	–	RandNumGen* randNumGen_;
84	–	int nBins_;
85	–	RealType swapTime_;
86	–	RealType exchangeSum_;
87	–	RNEMDTypeEnum rnemdType_;
88	–	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
125
126	+	map<string, RNEMDMethod> stringToMethod_;
127	+	map<string, RNEMDFluxType> stringToFluxType_;
128	+	RNEMDMethod rnemdMethod_;
129	+	RNEMDFluxType rnemdFluxType_;
130
131	<	};
131	>	// object selection for specifying a particular species:
132	>	string rnemdObjectSelection_;
133	>	SelectionEvaluator evaluator_;
134	>	SelectionManager seleMan_;
135
136	+	// Geometric selections for the two regions for the exchange:
137	+	string selectionA_;
138	+	SelectionEvaluator evaluatorA_;
139	+	SelectionManager seleManA_;
140	+	string selectionB_;
141	+	SelectionEvaluator evaluatorB_;
142	+	SelectionManager seleManB_;
143	+	SelectionManager commonA_;
144	+	SelectionManager commonB_;
145	+	bool hasSelectionA_;
146	+	bool hasSelectionB_;
147	+	bool hasSphereBRadius_;
148	+
149	+	bool usePeriodicBoundaryConditions_;
150	+	bool hasDividingArea_;
151	+	RealType dividingArea_;
152	+
153	+	int nBins_;
154	+	RealType binWidth_;
155	+	RealType slabWidth_;
156	+	RealType slabACenter_;
157	+	RealType slabBCenter_;
158	+	RealType sphereARadius_;
159	+	RealType sphereBRadius_;
160	+	RealType areaA_;
161	+	bool AisHull_;
162	+	RealType areaB_;
163	+	bool BisHull_;
164	+
165	+	Vector3d coordinateOrigin_;
166	+
167	+	RealType kineticFlux_;        // target or desired *flux*
168	+	Vector3d momentumFluxVector_; // target or desired *flux*
169	+	Vector3d angularMomentumFluxVector_; // target or desired *flux*
170	+
171	+	RealType kineticTarget_;     // target or desired one-time exchange energy
172	+	Vector3d momentumTarget_;    // target or desired one-time exchange momentum
173	+	Vector3d angularMomentumTarget_; // target or desired one-time
174	+	// exchange angular momentum
175	+
176	+	RealType kineticExchange_;    // actual exchange energy (running total)
177	+	Vector3d momentumExchange_;   // actual exchange momentum (running total)
178	+	Vector3d angularMomentumExchange_; // actual exchange momentum
179	+	// (running total)
180	+	RealType exchangeTime_;
181	+
182	+	RealType targetJzpz2_;
183	+
184	+	unsigned int trialCount_;
185	+	unsigned int failTrialCount_;
186	+	unsigned int failRootCount_;
187	+
188	+	string rnemdFileName_;
189	+	ofstream rnemdFile_;
190	+
191	+	RealType runTime_, statusTime_;
192	+
193	+	vector<OutputData> data_;
194	+	OutputBitSet outputMask_;
195	+	OutputMapType outputMap_;
196	+	Accumulator* areaAccumulator_;
197	+	bool doRNEMD_;
198	+	bool hasData_;
199	+
200	+	};
201		}
202	<	#endif //INTEGRATORS_VELOCITIZER_HPP
202	>	#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.
trunk/src/rnemd/RNEMD.hpp (property svn:keywords), Revision 2046 by gezelter, Tue Dec 2 22:11:04 2014 UTC

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