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Comparing branches/development/src/integrators/RNEMD.hpp (file contents):
Revision 1722 by gezelter, Thu May 24 14:23:40 2012 UTC vs.
Revision 1730 by gezelter, Wed May 30 17:19:13 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 85 | Line 86 | namespace OpenMD {
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 118 | Line 120 | namespace OpenMD {
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 133 | Line 138 | namespace OpenMD {
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 tempLog_, vxzLog_, vyzLog_;
147 <    ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_;
148 <    // keeps track of what's being averaged
149 <    vector<RealType> tempHist_, pxzHist_, pyzHist_, mHist_;
146 >    ofstream rnemdLog_;
147 >    int logFrameCount_;
148 >    // James added denLog, vzzLog
149 >    ofstream tempLog_, vxzLog_, vyzLog_, denLog_, vzzLog_, denLog2_;
150 >    ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_, AhLog_;
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<int> pxzCount_, pyzCount_;
156      vector<int> tempCount_, xyzTempCount_, rotTempCount_;
157 +    RealType Asum_, Jsum_, AhCount_, runTime_, statusTime_;
158 +    int Numcount_;
159 +    bool outputAh_;
160    };
161  
162   }

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