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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/integrators/RNEMD.hpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	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
61		/**
62		* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
#	Line 64 | Line 66 | namespace oopse {
66		public:
67		RNEMD(SimInfo* info);
68		virtual ~RNEMD();
69	<
69	>
70	>	void doRNEMD();
71		void doSwap();
72	<	void set_RNEMD_swapTime(RealType swapTime) { swapTime_ = swapTime; }
72	>	void doScale();
73	>	void collectData();
74	>	void getStarted();
75	>	void getStatus();
76	>	void set_RNEMD_exchange_time(RealType exchangeTime) {
77	>	exchangeTime_ = exchangeTime;
78	>	}
79		void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
80	+	void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; }
81	+	void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
82	+	void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
83		RealType get_RNEMD_exchange_total() { return exchangeSum_; }
72	–	void set_RNEMD_exchange_total(RealType et) {exchangeSum_ = et;}
84
85		private:
86
87		enum RNEMDTypeEnum {
88	<	rnemdKinetic,
88	>	rnemdKineticSwap,
89	>	rnemdKineticScale,
90	>	rnemdPxScale,
91	>	rnemdPyScale,
92	>	rnemdPzScale,
93		rnemdPx,
94		rnemdPy,
95		rnemdPz,
96		rnemdUnknown
97		};
98	<
98	>
99		SimInfo* info_;
100		RandNumGen* randNumGen_;
101	<	int nBins_;
87	<	RealType swapTime_;
88	<	RealType exchangeSum_;
101	>	map<string, RNEMDTypeEnum> stringToEnumMap_;
102		RNEMDTypeEnum rnemdType_;
103	<	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
91	<	std::string rnemdObjectSelection_;
92	<	SelectionManager seleMan_;
103	>	string rnemdObjectSelection_;
104		SelectionEvaluator evaluator_;
105	+	SelectionManager seleMan_;
106		bool usePeriodicBoundaryConditions_;
107	+	bool output3DTemp_;
108	+	int nBins_; /**< The number of bins to divide the simulation box into.  */
109	+	/*!
110	+	The middle bin for the RNEMD method. midBin_ = nBins_/2;
111	+	Depending on the setting of the flux, this box should contain the minimum energy (temperature)
112	+	within the simulation.
113	+	*/
114	+	int midBin_;
115	+	int rnemdLogWidth_; /**< Number of elements to print out in logs */
116	+	RealType zShift_;
117	+	RealType exchangeTime_;
118	+	RealType targetFlux_;
119	+	RealType exchangeSum_;
120	+	int failTrialCount_;
121	+	int failRootCount_;
122	+	ofstream rnemdLog_;
123	+	// keeps track of what's being averaged
124	+	vector<RealType> valueHist_;
125	+	vector<int> valueCount_, xyzTempCount_;
126	+	// keeps track of the number of degrees of freedom being averaged
127	+	vector<RealType> xTempHist_, yTempHist_, zTempHist_;
128	+	ofstream xTempLog_, yTempLog_, zTempLog_;
129		};
130
131		}
132	<	#endif //INTEGRATORS_VELOCITIZER_HPP
132	>	#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/integrators/RNEMD.hpp (property svn:keywords), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

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