ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1808 by gezelter, Mon Oct 22 20:42:10 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		/**
44		* @file RNEMD.hpp
45		* @author gezelter
46		* @date 03/13/2009
46	–	* @time 15:56pm
47		* @version 1.0
48		*/
49
#	Line 55 | Line 55
55		#include "selection/SelectionManager.hpp"
56		#include <iostream>
57
58	<	namespace oopse {
58	>	using namespace std;
59	>	namespace OpenMD {
60
60	–	/**
61	–	* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
62	–	* @todo document
63	–	*/
61		class RNEMD {
62		public:
63		RNEMD(SimInfo* info);
#	Line 68 | Line 65 | namespace oopse {
65
66		void doRNEMD();
67		void doSwap();
68	<	void doScale();
68	>	void doNIVS();
69	>	void doVSS();
70		void collectData();
71		void getStarted();
72	<	void getStatus();
73	<	void set_RNEMD_exchange_time(RealType exchangeTime) {
74	<	exchangeTime_ = exchangeTime;
75	<	}
76	<	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
77	<	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
78	<	void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
79	<	void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
72	>	bool inSlabA(Vector3d pos);
73	>	bool inSlabB(Vector3d pos);
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	<	rnemdKineticSwap,
85	<	rnemdKineticScale,
86	<	rnemdPxScale,
87	<	rnemdPyScale,
90	<	rnemdPzScale,
91	<	rnemdPx,
92	<	rnemdPy,
93	<	rnemdPz,
94	<	rnemdUnknown
83	>	enum RNEMDMethod {
84	>	rnemdSwap,
85	>	rnemdNIVS,
86	>	rnemdVSS,
87	>	rnemdUnkownMethod
88		};
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	+	rnemdKePx,     // flux of translational KE and x-momentum
98	+	rnemdKePy,     // flux of translational KE and y-momentum
99	+	rnemdKePvector, // full combo platter
100	+	rnemdUnknownFluxType
101	+	};
102	+
103	+	enum OutputFields {
104	+	BEGININDEX = 0,
105	+	Z = BEGININDEX,
106	+	TEMPERATURE,
107	+	VELOCITY,
108	+	DENSITY,
109	+	ENDINDEX
110	+	};
111	+
112	+	struct OutputData {
113	+	string title;
114	+	string units;
115	+	string dataType;
116	+	vector<Accumulator*> accumulator;
117	+	};
118	+
119	+	typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
120	+	typedef map<string, OutputFields> OutputMapType;
121
122		SimInfo* info_;
123	<	RandNumGen* randNumGen_;
124	<	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
125	<	RNEMDTypeEnum rnemdType_;
126	<	std::string rnemdObjectSelection_;
123	>
124	>	map<string, RNEMDMethod> stringToMethod_;
125	>	map<string, RNEMDFluxType> stringToFluxType_;
126	>	RNEMDMethod rnemdMethod_;
127	>	RNEMDFluxType rnemdFluxType_;
128	>	string rnemdObjectSelection_;
129		SelectionEvaluator evaluator_;
130		SelectionManager seleMan_;
131		bool usePeriodicBoundaryConditions_;
132	<	int nBins_;
133	<	int midBin_;
134	<	int rnemdLogWidth_;
132	>	int nBins_;
133	>	RealType slabWidth_;
134	>	RealType slabACenter_;
135	>	RealType slabBCenter_;
136	>
137	>	RealType kineticFlux_;        // target or desired *flux*
138	>	Vector3d momentumFluxVector_; // target or desired *flux*
139	>
140	>	RealType kineticTarget_;     // target or desired one-time exchange energy
141	>	Vector3d momentumTarget_;    // target or desired one-time exchange momentum
142	>
143	>	RealType kineticExchange_;    // actual exchange energy (running total)
144	>	Vector3d momentumExchange_;   // actual exchange momentum (running total)
145	>
146		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	–	};
147
148	+	RealType targetJzpz2_;
149	+
150	+	unsigned int trialCount_;
151	+	unsigned int failTrialCount_;
152	+	unsigned int failRootCount_;
153	+
154	+	string rnemdFileName_;
155	+	ofstream rnemdFile_;
156	+
157	+	RealType runTime_, statusTime_;
158	+
159	+	vector<OutputData> data_;
160	+	OutputBitSet outputMask_;
161	+	OutputMapType outputMap_;
162	+	Accumulator* areaAccumulator_;
163	+	bool doRNEMD_;
164	+
165	+	};
166		}
167		#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 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines