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root/OpenMD/trunk/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.
trunk/src/rnemd/RNEMD.hpp (file contents), Revision 2046 by gezelter, Tue Dec 2 22:11:04 2014 UTC

#	Line 35 | Line 35
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).
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"
#	Line 55 | Line 48
48		#include "selection/SelectionManager.hpp"
49		#include <iostream>
50
51	+	using namespace std;
52		namespace OpenMD {
53
60	–	/**
61	–	* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
62	–	* @todo document
63	–	*/
54		class RNEMD {
55		public:
56		RNEMD(SimInfo* info);
57	<	virtual ~RNEMD();
57	>	~RNEMD();
58
59		void doRNEMD();
60	<	void doSwap();
61	<	void doScale();
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 getStatus();
67	<	void set_RNEMD_exchange_time(RealType exchangeTime) {
68	<	exchangeTime_ = exchangeTime;
69	<	}
70	<	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
71	<	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;}
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	<	rnemdKineticSwap,
77	<	rnemdKineticScale,
78	<	rnemdPxScale,
79	<	rnemdPyScale,
90	<	rnemdPzScale,
91	<	rnemdPx,
92	<	rnemdPy,
93	<	rnemdPz,
94	<	rnemdUnknown
75	>	enum RNEMDMethod {
76	>	rnemdSwap,
77	>	rnemdNIVS,
78	>	rnemdVSS,
79	>	rnemdUnkownMethod
80		};
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_;
125	<	RandNumGen* randNumGen_;
126	<	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
127	<	RNEMDTypeEnum rnemdType_;
128	<	std::string rnemdObjectSelection_;
125	>
126	>	map<string, RNEMDMethod> stringToMethod_;
127	>	map<string, RNEMDFluxType> stringToFluxType_;
128	>	RNEMDMethod rnemdMethod_;
129	>	RNEMDFluxType rnemdFluxType_;
130	>
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	<	int midBin_;
155	<	int rnemdLogWidth_;
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_;
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	–	};
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_RNEMD_HPP

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