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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/integrators/RNEMD.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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
62		/**
#	Line 76 | Line 78 | namespace OpenMD {
78		exchangeTime_ = exchangeTime;
79		}
80		void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
81	<	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
81	>	void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; }
82		void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
83		void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
84	+	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
85
86		private:
87
#	Line 96 | Line 99 | namespace OpenMD {
99
100		SimInfo* info_;
101		RandNumGen* randNumGen_;
102	<	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
102	>	map<string, RNEMDTypeEnum> stringToEnumMap_;
103		RNEMDTypeEnum rnemdType_;
104	<	std::string rnemdObjectSelection_;
104	>	string rnemdObjectSelection_;
105		SelectionEvaluator evaluator_;
106		SelectionManager seleMan_;
107		bool usePeriodicBoundaryConditions_;
108	<	int nBins_;
108	>	bool output3DTemp_;
109	>	int nBins_; /**< The number of bins to divide the simulation box into.  */
110	>	/*!
111	>	The middle bin for the RNEMD method. midBin_ = nBins_/2;
112	>	Depending on the setting of the flux, this box should contain the minimum energy (temperature)
113	>	within the simulation.
114	>	*/
115		int midBin_;
116	<	int rnemdLogWidth_;
116	>	int rnemdLogWidth_; /**< Number of elements to print out in logs */
117	>	RealType zShift_;
118		RealType exchangeTime_;
119		RealType targetFlux_;
120		RealType exchangeSum_;
121		int failTrialCount_;
122		int failRootCount_;
123	<	std::ofstream rnemdLog_;
123	>	ofstream rnemdLog_;
124		// keeps track of what's being averaged
125	<	std::vector<RealType> valueHist_;
126	<	std::vector<int> valueCount_;
125	>	vector<RealType> valueHist_;
126	>	vector<int> valueCount_, xyzTempCount_;
127		// keeps track of the number of degrees of freedom being averaged
128	<	std::vector<RealType> xTempHist_, yTempHist_, zTempHist_;
129	<	std::ofstream xTempLog_, yTempLog_, zTempLog_;
128	>	vector<RealType> xTempHist_, yTempHist_, zTempHist_;
129	>	ofstream xTempLog_, yTempLog_, zTempLog_;
130		};
131
132		}

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/integrators/RNEMD.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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