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

Comparing:
trunk/src/integrators/RNEMD.hpp (file contents), Revision 1368 by skuang, Mon Oct 19 13:39:04 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 55 | Line 56
56		#include "selection/SelectionManager.hpp"
57		#include <iostream>
58
59	<	namespace oopse {
59	>	using namespace std;
60	>	namespace OpenMD {
61
60	–	/**
61	–	* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
62	–	* @todo document
63	–	*/
62		class RNEMD {
63		public:
64		RNEMD(SimInfo* info);
#	Line 68 | Line 66 | namespace oopse {
66
67		void doRNEMD();
68		void doSwap();
69	<	void doScale();
69	>	void doNIVS();
70	>	void doVSS();
71		void collectData();
72		void getStarted();
73	<	void getStatus();
74	<	void set_RNEMD_exchange_time(RealType exchangeTime) {
75	<	exchangeTime_ = exchangeTime;
76	<	}
77	<	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
78	<	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
79	<	void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
80	<	void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
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	<	rnemdKineticSwap,
86	<	rnemdKineticScale,
87	<	rnemdPxScale,
88	<	rnemdPyScale,
90	<	rnemdPzScale,
91	<	rnemdPx,
92	<	rnemdPy,
93	<	rnemdPz,
94	<	rnemdUnknown
84	>	enum RNEMDMethod {
85	>	rnemdSwap,
86	>	rnemdNIVS,
87	>	rnemdVSS,
88	>	rnemdUnkownMethod
89		};
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_;
124	<	RandNumGen* randNumGen_;
125	<	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
126	<	RNEMDTypeEnum rnemdType_;
127	<	std::string rnemdObjectSelection_;
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	<	int midBin_;
135	<	int rnemdLogWidth_;
133	>	int nBins_;
134	>	RealType slabWidth_;
135	>	RealType slabACenter_;
136	>	RealType slabBCenter_;
137	>
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_;
109	–	RealType targetFlux_;
110	–	RealType exchangeSum_;
111	–	int failTrialCount_;
112	–	int failRootCount_;
113	–	std::ofstream rnemdLog_;
114	–	// keeps track of what's being averaged
115	–	std::vector<RealType> valueHist_;
116	–	std::vector<int> valueCount_;
117	–	// keeps track of the number of degrees of freedom being averaged
118	–	std::vector<RealType> xTempHist_, yTempHist_, zTempHist_;
119	–	std::ofstream xTempLog_, yTempLog_, zTempLog_;
120	–	};
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_RNEMD_HPP

Comparing:
trunk/src/integrators/RNEMD.hpp (property svn:keywords), Revision 1368 by skuang, Mon Oct 19 13:39:04 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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