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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.
branches/development/src/rnemd/RNEMD.hpp (file contents), Revision 1773 by gezelter, Tue Aug 7 18:26:40 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]  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 58 | Line 59 | namespace OpenMD {
59   using namespace std;
60   namespace OpenMD {
61  
61 –  /**
62 –   * @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
63 –   * @todo document
64 –   */
62    class RNEMD {
63    public:
64      RNEMD(SimInfo* info);
# Line 69 | Line 66 | namespace OpenMD {
66      
67      void doRNEMD();
68      void doSwap();
69 <    void doScale();
70 <    void doShiftScale();
69 >    void doNIVS();
70 >    void doVSS();
71      void collectData();
72      void getStarted();
73 <    void getStatus();
74 <    void set_RNEMD_exchange_time(RealType exchangeTime) {
75 <      exchangeTime_ = exchangeTime;
76 <    }
77 <    void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
78 <    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_; }
73 >    bool inSlabA(Vector3d pos);
74 >    bool inSlabB(Vector3d pos);
75 >    void parseOutputFileFormat(const std::string& format);
76 >    void writeOutputFile();
77 >    void writeReal(int index, unsigned int bin);
78 >    void writeVector(int index, unsigned int bin);
79  
80    private:
81  
82 <    enum RNEMDTypeEnum {
83 <      rnemdKineticSwap,
84 <      rnemdKineticScale,
85 <      rnemdKineticScaleVAM,
86 <      rnemdKineticScaleAM,
97 <      rnemdPxScale,
98 <      rnemdPyScale,
99 <      rnemdPzScale,
100 <      rnemdPx,
101 <      rnemdPy,
102 <      rnemdPz,
103 <      rnemdShiftScaleV,
104 <      rnemdShiftScaleVAM,
105 <      rnemdUnknown
82 >    enum RNEMDMethod {
83 >      rnemdSwap,
84 >      rnemdNIVS,
85 >      rnemdVSS,
86 >      rnemdUnkownMethod
87      };
88 +    enum RNEMDFluxType {
89 +      rnemdKE,       // translational kinetic energy flux
90 +      rnemdRotKE,    // rotational kinetic energy flux
91 +      rnemdFullKE,   // full kinetic energy flux
92 +      rnemdPx,       // flux of momentum along x axis
93 +      rnemdPy,       // flux of momentum along y axis
94 +      rnemdPz,       // flux of momentum along z axis
95 +      rnemdPvector,  // flux of momentum vector
96 +      rnemdKePx,     // flux of translational KE and x-momentum
97 +      rnemdKePy,     // flux of translational KE and y-momentum
98 +      rnemdKePvector, // full combo platter
99 +      rnemdUnknownFluxType
100 +    };
101 +
102 +    enum OutputFields {
103 +      BEGININDEX = 0,
104 +      Z = BEGININDEX,
105 +      TEMPERATURE,
106 +      VELOCITY,
107 +      DENSITY,
108 +      ENDINDEX
109 +    };
110 +
111 +    struct OutputData {
112 +      string title;
113 +      string units;
114 +      string dataType;
115 +      vector<Accumulator*> accumulator;
116 +    };
117 +
118 +    typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
119 +    typedef map<string, OutputFields> OutputMapType;
120      
121      SimInfo* info_;
122 <    RandNumGen* randNumGen_;
123 <    map<string, RNEMDTypeEnum> stringToEnumMap_;
124 <    RNEMDTypeEnum rnemdType_;
122 >
123 >    map<string, RNEMDMethod> stringToMethod_;
124 >    map<string, RNEMDFluxType> stringToFluxType_;
125 >    RNEMDMethod rnemdMethod_;
126 >    RNEMDFluxType rnemdFluxType_;
127      string rnemdObjectSelection_;
128      SelectionEvaluator evaluator_;
129      SelectionManager seleMan_;
130      bool usePeriodicBoundaryConditions_;
131 <    bool outputTemp_;
132 <    bool outputVx_;
133 <    bool outputVy_;
134 <    bool output3DTemp_;
135 <    bool outputRotTemp_;
136 <    int nBins_; /**< The number of bins to divide the simulation box into.  */
137 <    /*!
138 <      The middle bin for the RNEMD method. midBin_ = nBins_/2;
139 <      Depending on the setting of the flux, this box should contain the minimum energy (temperature)
140 <      within the simulation.
141 <    */
142 <    int midBin_;
143 <    int rnemdLogWidth_; /**< Number of elements to print out in logs */
144 <    RealType zShift_;
131 >    int nBins_;
132 >    RealType slabWidth_;
133 >    RealType slabACenter_;
134 >    RealType slabBCenter_;
135 >
136 >    RealType kineticFlux_;        // target or desired *flux*
137 >    Vector3d momentumFluxVector_; // target or desired *flux*
138 >
139 >    RealType kineticTarget_;     // target or desired one-time exchange energy
140 >    Vector3d momentumTarget_;    // target or desired one-time exchange momentum
141 >
142 >    RealType kineticExchange_;    // actual exchange energy (running total)
143 >    Vector3d momentumExchange_;   // actual exchange momentum (running total)
144 >
145      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 tempLog_, vxzLog_, vyzLog_;
141 –    ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_;
142 –    // keeps track of what's being averaged
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<int> pxzCount_, pyzCount_;
147 –    vector<int> tempCount_, xyzTempCount_, rotTempCount_;
148 –  };
146  
147 +    RealType targetJzpz2_;
148 +
149 +    unsigned int trialCount_;
150 +    unsigned int failTrialCount_;
151 +    unsigned int failRootCount_;
152 +
153 +    string rnemdFileName_;
154 +    ofstream rnemdFile_;
155 +
156 +    RealType runTime_, statusTime_;
157 +
158 +    vector<OutputData> data_;
159 +    OutputBitSet outputMask_;
160 +    OutputMapType outputMap_;
161 +
162 +  };
163   }
164   #endif //INTEGRATORS_RNEMD_HPP

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