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

Comparing:
trunk/src/integrators/RNEMD.hpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/rnemd/RNEMD.hpp (file contents), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC

#	Line 36 | Line 36
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).
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	+	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 OpenMD {
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_; }
80	<	void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
81	<	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
80		private:
81
82	<	enum RNEMDTypeEnum {
83	<	rnemdKineticSwap,
84	<	rnemdKineticScale,
85	<	rnemdPxScale,
86	<	rnemdPyScale,
90	<	rnemdPzScale,
91	<	rnemdPx,
92	<	rnemdPy,
93	<	rnemdPz,
94	<	rnemdUnknown
82	>	enum RNEMDMethod {
83	>	rnemdSwap,
84	>	rnemdNIVS,
85	>	rnemdVSS,
86	>	rnemdUnkownMethod
87		};
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_;
122	<	RandNumGen* randNumGen_;
123	<	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
124	<	RNEMDTypeEnum rnemdType_;
125	<	std::string rnemdObjectSelection_;
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	<	int midBin_;
133	<	int rnemdLogWidth_;
131	>	int nBins_;
132	>	RealType slabWidth_;
133	>	RealType slabACenter_;
134	>	RealType slabBCenter_;
135	>
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_;
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	–	};
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_RNEMD_HPP

Comparing:
trunk/src/integrators/RNEMD.hpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 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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