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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 1776 by gezelter, Thu Aug 9 15:52:59 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; }
79 <    void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
80 <    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 >    void writeRealStdDev(int index, unsigned int bin);
80 >    void writeVectorStdDev(int index, unsigned int bin);
81  
82    private:
83  
84 <    enum RNEMDTypeEnum {
85 <      rnemdKineticSwap,
86 <      rnemdKineticScale,
87 <      rnemdKineticScaleVAM,
88 <      rnemdKineticScaleAM,
97 <      rnemdPxScale,
98 <      rnemdPyScale,
99 <      rnemdPzScale,
100 <      rnemdPx,
101 <      rnemdPy,
102 <      rnemdPz,
103 <      rnemdShiftScaleV,
104 <      rnemdShiftScaleVAM,
105 <      rnemdUnknown
84 >    enum RNEMDMethod {
85 >      rnemdSwap,
86 >      rnemdNIVS,
87 >      rnemdVSS,
88 >      rnemdUnkownMethod
89      };
90 +    enum RNEMDFluxType {
91 +      rnemdKE,       // translational kinetic energy flux
92 +      rnemdRotKE,    // rotational kinetic energy flux
93 +      rnemdFullKE,   // full kinetic energy flux
94 +      rnemdPx,       // flux of momentum along x axis
95 +      rnemdPy,       // flux of momentum along y axis
96 +      rnemdPz,       // flux of momentum along z axis
97 +      rnemdPvector,  // flux of momentum vector
98 +      rnemdKePx,     // flux of translational KE and x-momentum
99 +      rnemdKePy,     // flux of translational KE and y-momentum
100 +      rnemdKePvector, // full combo platter
101 +      rnemdUnknownFluxType
102 +    };
103 +
104 +    enum OutputFields {
105 +      BEGININDEX = 0,
106 +      Z = BEGININDEX,
107 +      TEMPERATURE,
108 +      VELOCITY,
109 +      DENSITY,
110 +      ENDINDEX
111 +    };
112 +
113 +    struct OutputData {
114 +      string title;
115 +      string units;
116 +      string dataType;
117 +      vector<Accumulator*> accumulator;
118 +    };
119 +
120 +    typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
121 +    typedef map<string, OutputFields> OutputMapType;
122      
123      SimInfo* info_;
124 <    RandNumGen* randNumGen_;
125 <    map<string, RNEMDTypeEnum> stringToEnumMap_;
126 <    RNEMDTypeEnum rnemdType_;
124 >
125 >    map<string, RNEMDMethod> stringToMethod_;
126 >    map<string, RNEMDFluxType> stringToFluxType_;
127 >    RNEMDMethod rnemdMethod_;
128 >    RNEMDFluxType rnemdFluxType_;
129      string rnemdObjectSelection_;
130      SelectionEvaluator evaluator_;
131      SelectionManager seleMan_;
132      bool usePeriodicBoundaryConditions_;
133 <    bool outputTemp_;
134 <    bool outputVx_;
135 <    bool outputVy_;
136 <    bool output3DTemp_;
137 <    bool outputRotTemp_;
138 <    int nBins_; /**< The number of bins to divide the simulation box into.  */
139 <    /*!
140 <      The middle bin for the RNEMD method. midBin_ = nBins_/2;
141 <      Depending on the setting of the flux, this box should contain the minimum energy (temperature)
142 <      within the simulation.
143 <    */
144 <    int midBin_;
145 <    int rnemdLogWidth_; /**< Number of elements to print out in logs */
146 <    RealType zShift_;
133 >    int nBins_;
134 >    RealType slabWidth_;
135 >    RealType slabACenter_;
136 >    RealType slabBCenter_;
137 >
138 >    RealType kineticFlux_;        // target or desired *flux*
139 >    Vector3d momentumFluxVector_; // target or desired *flux*
140 >
141 >    RealType kineticTarget_;     // target or desired one-time exchange energy
142 >    Vector3d momentumTarget_;    // target or desired one-time exchange momentum
143 >
144 >    RealType kineticExchange_;    // actual exchange energy (running total)
145 >    Vector3d momentumExchange_;   // actual exchange momentum (running total)
146 >
147      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 –  };
148  
149 +    RealType targetJzpz2_;
150 +
151 +    unsigned int trialCount_;
152 +    unsigned int failTrialCount_;
153 +    unsigned int failRootCount_;
154 +
155 +    string rnemdFileName_;
156 +    ofstream rnemdFile_;
157 +
158 +    RealType runTime_, statusTime_;
159 +
160 +    vector<OutputData> data_;
161 +    OutputBitSet outputMask_;
162 +    OutputMapType outputMap_;
163 +    Accumulator* areaAccumulator_;
164 +    bool doRNEMD_;
165 +
166 +  };
167   }
168   #endif //INTEGRATORS_RNEMD_HPP

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