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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 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 55 | Line 56
56   #include "selection/SelectionManager.hpp"
57   #include <iostream>
58  
59 + using namespace std;
60   namespace OpenMD {
61  
62    /**
# Line 69 | 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 76 | Line 79 | namespace OpenMD {
79        exchangeTime_ = exchangeTime;
80      }
81      void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
82 <    RealType get_RNEMD_exchange_total() { return exchangeSum_; }
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:
93  
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      
110      SimInfo* info_;
111      RandNumGen* randNumGen_;
112 <    std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
112 >    map<string, RNEMDTypeEnum> stringToEnumMap_;
113      RNEMDTypeEnum rnemdType_;
114 <    std::string rnemdObjectSelection_;
114 >    string rnemdObjectSelection_;
115      SelectionEvaluator evaluator_;
116      SelectionManager seleMan_;
117      bool usePeriodicBoundaryConditions_;
118 <    int nBins_;
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;
129 >      Depending on the setting of the flux, this box should contain the minimum energy (temperature)
130 >      within the simulation.
131 >    */
132      int midBin_;
133 <    int rnemdLogWidth_;
133 >    int rnemdLogWidth_; /**< Number of elements to print out in logs */
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 <    std::ofstream rnemdLog_;
147 <    // keeps track of what's being averaged
148 <    std::vector<RealType> valueHist_;
149 <    std::vector<int> valueCount_;
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_;
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 <    std::vector<RealType> xTempHist_, yTempHist_, zTempHist_;
156 <    std::ofstream xTempLog_, yTempLog_, zTempLog_;
155 >    //vector<int> pxzCount_, pyzCount_;
156 >    vector<int> tempCount_, xyzTempCount_, rotTempCount_;
157    };
158  
159   }

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 1728 by jmarr, Wed May 30 16:07:03 2012 UTC

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