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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 1854 by gezelter, Thu Mar 28 20:54:06 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		/**
#	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	<
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;}
72	<
66	>
67	>	void doRNEMD();
68	>	void doSwap(SelectionManager& smanA, SelectionManager& smanB);
69	>	void doNIVS(SelectionManager& smanA, SelectionManager& smanB);
70	>	void doVSS(SelectionManager& smanA, SelectionManager& smanB);
71	>	RealType getDividingArea();
72	>	void collectData();
73	>	void getStarted();
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,
79	<	rnemdUnknown
82	>
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	>	rnemdLx,       // flux of angular momentum along x axis
98	>	rnemdLy,       // flux of angular momentum along y axis
99	>	rnemdLz,       // flux of angular momentum along z axis
100	>	rnemdLvector,  // flux of angular momentum vector
101	>	rnemdKePx,     // flux of translational KE and x-momentum
102	>	rnemdKePy,     // flux of translational KE and y-momentum
103	>	rnemdKePvector, // full combo flying platter
104	>	rnemdKeLx,     // flux of translational KE and x-angular momentum
105	>	rnemdKeLy,     // flux of translational KE and y-angular momentum
106	>	rnemdKeLz,     // flux of translational KE and z-angular momentum
107	>	rnemdKeLvector, // full combo spinning platter
108	>	rnemdUnknownFluxType
109	>	};
110	>
111	>	enum OutputFields {
112	>	BEGININDEX = 0,
113	>	Z = BEGININDEX,
114	>	R,
115	>	TEMPERATURE,
116	>	VELOCITY,
117	>	ANGULARVELOCITY,
118	>	DENSITY,
119	>	ENDINDEX
120	>	};
121	>
122	>	struct OutputData {
123	>	string title;
124	>	string units;
125	>	string dataType;
126	>	vector<BaseAccumulator*> accumulator;
127	>	};
128	>
129	>	typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
130	>	typedef map<string, OutputFields> OutputMapType;
131	>
132		SimInfo* info_;
83	–	RandNumGen* randNumGen_;
84	–	int nBins_;
85	–	RealType swapTime_;
86	–	RealType exchangeSum_;
87	–	RNEMDTypeEnum rnemdType_;
88	–	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
133
134	+	map<string, RNEMDMethod> stringToMethod_;
135	+	map<string, RNEMDFluxType> stringToFluxType_;
136	+	RNEMDMethod rnemdMethod_;
137	+	RNEMDFluxType rnemdFluxType_;
138
139	<	};
139	>	// object selection for specifying a particular species:
140	>	string rnemdObjectSelection_;
141	>	SelectionEvaluator evaluator_;
142	>	SelectionManager seleMan_;
143
144	+	// Geometric selections for the two regions for the exchange:
145	+	string selectionA_;
146	+	SelectionEvaluator evaluatorA_;
147	+	SelectionManager seleManA_;
148	+	string selectionB_;
149	+	SelectionEvaluator evaluatorB_;
150	+	SelectionManager seleManB_;
151	+	SelectionManager commonA_;
152	+	SelectionManager commonB_;
153	+	bool hasSelectionA_;
154	+	bool hasSelectionB_;
155	+	bool hasSphereBRadius_;
156	+
157	+	bool usePeriodicBoundaryConditions_;
158	+	bool hasDividingArea_;
159	+	RealType dividingArea_;
160	+
161	+	int nBins_;
162	+	RealType binWidth_;
163	+	RealType slabWidth_;
164	+	RealType slabACenter_;
165	+	RealType slabBCenter_;
166	+	RealType sphereARadius_;
167	+	RealType sphereBRadius_;
168	+
169	+	Vector3d coordinateOrigin_;
170	+
171	+	RealType kineticFlux_;        // target or desired *flux*
172	+	Vector3d momentumFluxVector_; // target or desired *flux*
173	+	Vector3d angularMomentumFluxVector_; // target or desired *flux*
174	+
175	+	RealType kineticTarget_;     // target or desired one-time exchange energy
176	+	Vector3d momentumTarget_;    // target or desired one-time exchange momentum
177	+	Vector3d angularMomentumTarget_; // target or desired one-time
178	+	// exchange angular momentum
179	+
180	+	RealType kineticExchange_;    // actual exchange energy (running total)
181	+	Vector3d momentumExchange_;   // actual exchange momentum (running total)
182	+	Vector3d angularMomentumExchange_; // actual exchange momentum
183	+	// (running total)
184	+	RealType exchangeTime_;
185	+
186	+	RealType targetJzpz2_;
187	+
188	+	unsigned int trialCount_;
189	+	unsigned int failTrialCount_;
190	+	unsigned int failRootCount_;
191	+
192	+	string rnemdFileName_;
193	+	ofstream rnemdFile_;
194	+
195	+	RealType runTime_, statusTime_;
196	+
197	+	vector<OutputData> data_;
198	+	OutputBitSet outputMask_;
199	+	OutputMapType outputMap_;
200	+	Accumulator* areaAccumulator_;
201	+	bool doRNEMD_;
202	+
203	+	};
204		}
205	<	#endif //INTEGRATORS_VELOCITIZER_HPP
205	>	#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 1854 by gezelter, Thu Mar 28 20:54:06 2013 UTC

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