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Comparing branches/development/src/integrators/RNEMD.hpp (file contents):
Revision 1721 by gezelter, Tue Nov 22 20:38:56 2011 UTC vs.
Revision 1722 by gezelter, Thu May 24 14:23:40 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 < * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 > * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 71 | Line 70 | namespace OpenMD {
70      void doRNEMD();
71      void doSwap();
72      void doScale();
73 +    void doShiftScale();
74      void collectData();
75      void getStarted();
76      void getStatus();
# Line 81 | Line 81 | namespace OpenMD {
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 +    void set_RNEMD_target_JzKE(RealType targetJzKE) {targetJzKE_ = targetJzKE;}
85 +    void set_RNEMD_target_jzpx(RealType targetJzpx) {targetJzpx_ = targetJzpx;}
86 +    void set_RNEMD_target_jzpy(RealType targetJzpy) {targetJzpy_ = targetJzpy;}
87 +    void set_RNEMD_target_jzpz(RealType targetJzpz) {targetJzpz_ = targetJzpz;}
88      RealType get_RNEMD_exchange_total() { return exchangeSum_; }
89  
90    private:
# Line 88 | Line 92 | namespace OpenMD {
92      enum RNEMDTypeEnum {
93        rnemdKineticSwap,
94        rnemdKineticScale,
95 +      rnemdKineticScaleVAM,
96 +      rnemdKineticScaleAM,
97        rnemdPxScale,
98        rnemdPyScale,
99        rnemdPzScale,
100        rnemdPx,
101        rnemdPy,
102        rnemdPz,
103 +      rnemdShiftScaleV,
104 +      rnemdShiftScaleVAM,
105        rnemdUnknown
106      };
107      
# Line 105 | Line 113 | namespace OpenMD {
113      SelectionEvaluator evaluator_;
114      SelectionManager seleMan_;
115      bool usePeriodicBoundaryConditions_;
116 +    bool outputTemp_;
117 +    bool outputVx_;
118 +    bool outputVy_;
119      bool output3DTemp_;
120 +    bool outputRotTemp_;
121      int nBins_; /**< The number of bins to divide the simulation box into.  */
122      /*!
123        The middle bin for the RNEMD method. midBin_ = nBins_/2;
# Line 117 | Line 129 | namespace OpenMD {
129      RealType zShift_;
130      RealType exchangeTime_;
131      RealType targetFlux_;
132 +    RealType targetJzKE_;
133 +    RealType targetJzpx_;
134 +    RealType targetJzpy_;
135 +    RealType targetJzpz_;
136 +    Vector3d jzp_, njzp_;
137      RealType exchangeSum_;
138      int failTrialCount_;
139      int failRootCount_;
140 <    ofstream rnemdLog_;
140 >    ofstream tempLog_, vxzLog_, vyzLog_;
141 >    ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_;
142      // keeps track of what's being averaged
143 <    vector<RealType> valueHist_;
144 <    vector<int> valueCount_, xyzTempCount_;
143 >    vector<RealType> tempHist_, pxzHist_, pyzHist_, mHist_;
144 >    vector<RealType> xTempHist_, yTempHist_, zTempHist_, rotTempHist_;
145      // keeps track of the number of degrees of freedom being averaged
146 <    vector<RealType> xTempHist_, yTempHist_, zTempHist_;
147 <    ofstream xTempLog_, yTempLog_, zTempLog_;
146 >    //vector<int> pxzCount_, pyzCount_;
147 >    vector<int> tempCount_, xyzTempCount_, rotTempCount_;
148    };
149  
150   }

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