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Comparing branches/development/src/integrators/RNEMD.hpp (file contents):
Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC vs.
Revision 1728 by jmarr, Wed May 30 16:07:03 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 70 | Line 71 | namespace OpenMD {
71      void doRNEMD();
72      void doSwap();
73      void doScale();
74 +    void doShiftScale();
75      void collectData();
76      void getStarted();
77      void getStatus();
# Line 80 | Line 82 | namespace OpenMD {
82      void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; }
83      void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
84      void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
85 +    void set_RNEMD_target_JzKE(RealType targetJzKE) {targetJzKE_ = targetJzKE;}
86 +    void set_RNEMD_target_jzpx(RealType targetJzpx) {targetJzpx_ = targetJzpx;}
87 +    void set_RNEMD_target_jzpy(RealType targetJzpy) {targetJzpy_ = targetJzpy;}
88 +    void set_RNEMD_target_jzpz(RealType targetJzpz) {targetJzpz_ = targetJzpz;}
89 +    void set_RNEMD_target_jzpz2(RealType targetJzpz2) {targetJzpz2_ = targetJzpz2;}
90      RealType get_RNEMD_exchange_total() { return exchangeSum_; }
91  
92    private:
# Line 87 | Line 94 | namespace OpenMD {
94      enum RNEMDTypeEnum {
95        rnemdKineticSwap,
96        rnemdKineticScale,
97 +      rnemdKineticScaleVAM,
98 +      rnemdKineticScaleAM,
99        rnemdPxScale,
100        rnemdPyScale,
101        rnemdPzScale,
102        rnemdPx,
103        rnemdPy,
104        rnemdPz,
105 +      rnemdShiftScaleV,
106 +      rnemdShiftScaleVAM,
107        rnemdUnknown
108      };
109      
# Line 104 | Line 115 | namespace OpenMD {
115      SelectionEvaluator evaluator_;
116      SelectionManager seleMan_;
117      bool usePeriodicBoundaryConditions_;
118 +    bool outputTemp_;
119 +    bool outputVx_;
120 +    bool outputVy_;
121      bool output3DTemp_;
122 +    bool outputRotTemp_;
123 +    // James put this in.
124 +    bool outputDen_;
125 +    bool outputVz_;
126      int nBins_; /**< The number of bins to divide the simulation box into.  */
127      /*!
128        The middle bin for the RNEMD method. midBin_ = nBins_/2;
# Line 116 | Line 134 | namespace OpenMD {
134      RealType zShift_;
135      RealType exchangeTime_;
136      RealType targetFlux_;
137 +    RealType targetJzKE_;
138 +    RealType targetJzpx_;
139 +    RealType targetJzpy_;
140 +    RealType targetJzpz_;
141 +    RealType targetJzpz2_;
142 +    Vector3d jzp_, njzp_;
143      RealType exchangeSum_;
144      int failTrialCount_;
145      int failRootCount_;
146      ofstream rnemdLog_;
147 <    // keeps track of what's being averaged
148 <    vector<RealType> valueHist_;
149 <    vector<int> valueCount_, xyzTempCount_;
147 >    int logFrameCount_;
148 >    // James added denLog, vzzLog
149 >    ofstream tempLog_, vxzLog_, vyzLog_, denLog_, vzzLog_, denLog2_;
150 >    ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_;
151 >    // keeps track of what's being averaged James added DenHist, pzzHist
152 >    vector<RealType> tempHist_, pxzHist_, pyzHist_, mHist_, DenHist_, pzzHist_, DenHist2_;
153 >    vector<RealType> xTempHist_, yTempHist_, zTempHist_, rotTempHist_;
154      // keeps track of the number of degrees of freedom being averaged
155 <    vector<RealType> xTempHist_, yTempHist_, zTempHist_;
156 <    ofstream xTempLog_, yTempLog_, zTempLog_;
155 >    //vector<int> pxzCount_, pyzCount_;
156 >    vector<int> tempCount_, xyzTempCount_, rotTempCount_;
157    };
158  
159   }

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