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root/OpenMD/trunk/src/rnemd/RNEMD.hpp
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branches/development/src/integrators/RNEMD.hpp (file contents), Revision 1730 by gezelter, Wed May 30 17:19:13 2012 UTC vs.
trunk/src/rnemd/RNEMD.hpp (file contents), Revision 1903 by gezelter, Tue Jul 16 18:58:08 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 59 | Line 59 | namespace OpenMD {
59   using namespace std;
60   namespace OpenMD {
61  
62 –  /**
63 –   * @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
64 –   * @todo document
65 –   */
62    class RNEMD {
63    public:
64      RNEMD(SimInfo* info);
65 <    virtual ~RNEMD();
65 >    ~RNEMD();
66      
67      void doRNEMD();
68 <    void doSwap();
69 <    void doScale();
70 <    void doShiftScale();
68 >    void doSwap(SelectionManager& smanA, SelectionManager& smanB);
69 >    void doNIVS(SelectionManager& smanA, SelectionManager& smanB);
70 >    void doVSS(SelectionManager& smanA, SelectionManager& smanB);
71 >    RealType getDividingArea();
72      void collectData();
73      void getStarted();
74 <    void getStatus();
75 <    void set_RNEMD_exchange_time(RealType exchangeTime) {
76 <      exchangeTime_ = exchangeTime;
77 <    }
78 <    void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
79 <    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_; }
74 >    void parseOutputFileFormat(const std::string& format);
75 >    void writeOutputFile();
76 >    void writeReal(int index, unsigned int bin);
77 >    void writeVector(int index, unsigned int bin);
78 >    void writeRealStdDev(int index, unsigned int bin);
79 >    void writeVectorStdDev(int index, unsigned int bin);
80  
81    private:
82  
83 <    enum RNEMDTypeEnum {
84 <      rnemdKineticSwap,
85 <      rnemdKineticScale,
86 <      rnemdKineticScaleVAM,
87 <      rnemdKineticScaleAM,
99 <      rnemdPxScale,
100 <      rnemdPyScale,
101 <      rnemdPzScale,
102 <      rnemdPx,
103 <      rnemdPy,
104 <      rnemdPz,
105 <      rnemdShiftScaleV,
106 <      rnemdShiftScaleVAM,
107 <      rnemdUnknown
83 >    enum RNEMDMethod {
84 >      rnemdSwap,
85 >      rnemdNIVS,
86 >      rnemdVSS,
87 >      rnemdUnkownMethod
88      };
89 +    enum RNEMDFluxType {
90 +      rnemdKE,       // translational kinetic energy flux
91 +      rnemdRotKE,    // rotational kinetic energy flux
92 +      rnemdFullKE,   // full kinetic energy flux
93 +      rnemdPx,       // flux of momentum along x axis
94 +      rnemdPy,       // flux of momentum along y axis
95 +      rnemdPz,       // flux of momentum along z axis
96 +      rnemdPvector,  // flux of momentum vector
97 +      rnemdLx,       // flux of angular momentum along x axis
98 +      rnemdLy,       // flux of angular momentum along y axis
99 +      rnemdLz,       // flux of angular momentum along z axis
100 +      rnemdLvector,  // flux of angular momentum vector
101 +      rnemdKePx,     // flux of translational KE and x-momentum
102 +      rnemdKePy,     // flux of translational KE and y-momentum
103 +      rnemdKePvector, // full combo flying platter
104 +      rnemdKeLx,     // flux of translational KE and x-angular momentum
105 +      rnemdKeLy,     // flux of translational KE and y-angular momentum
106 +      rnemdKeLz,     // flux of translational KE and z-angular momentum
107 +      rnemdKeLvector, // full combo spinning platter
108 +      rnemdUnknownFluxType
109 +    };
110 +
111 +    enum OutputFields {
112 +      BEGININDEX = 0,
113 +      Z = BEGININDEX,
114 +      R,
115 +      TEMPERATURE,
116 +      VELOCITY,
117 +      ANGULARVELOCITY,
118 +      DENSITY,
119 +      ENDINDEX
120 +    };
121 +
122 +    struct OutputData {
123 +      string title;
124 +      string units;
125 +      string dataType;
126 +      vector<BaseAccumulator*> accumulator;
127 +    };
128 +
129 +    typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
130 +    typedef map<string, OutputFields> OutputMapType;
131      
132      SimInfo* info_;
133 <    RandNumGen* randNumGen_;
134 <    map<string, RNEMDTypeEnum> stringToEnumMap_;
135 <    RNEMDTypeEnum rnemdType_;
133 >
134 >    map<string, RNEMDMethod> stringToMethod_;
135 >    map<string, RNEMDFluxType> stringToFluxType_;
136 >    RNEMDMethod rnemdMethod_;
137 >    RNEMDFluxType rnemdFluxType_;
138 >
139 >    // object selection for specifying a particular species:
140      string rnemdObjectSelection_;
141      SelectionEvaluator evaluator_;
142      SelectionManager seleMan_;
143 +
144 +    // Geometric selections for the two regions for the exchange:
145 +    string selectionA_;
146 +    SelectionEvaluator evaluatorA_;
147 +    SelectionManager seleManA_;
148 +    string selectionB_;
149 +    SelectionEvaluator evaluatorB_;
150 +    SelectionManager seleManB_;
151 +    SelectionManager commonA_;
152 +    SelectionManager commonB_;
153 +    bool hasSelectionA_;
154 +    bool hasSelectionB_;                      
155 +    bool hasSphereBRadius_;
156 +
157      bool usePeriodicBoundaryConditions_;
158 <    bool outputTemp_;
159 <    bool outputVx_;
160 <    bool outputVy_;
161 <    bool output3DTemp_;
162 <    bool outputRotTemp_;
163 <    // James put this in.
164 <    bool outputDen_;
165 <    bool outputVz_;
166 <    int nBins_; /**< The number of bins to divide the simulation box into.  */
167 <    /*!
168 <      The middle bin for the RNEMD method. midBin_ = nBins_/2;
169 <      Depending on the setting of the flux, this box should contain the minimum energy (temperature)
170 <      within the simulation.
171 <    */
172 <    int midBin_;
173 <    int rnemdLogWidth_; /**< Number of elements to print out in logs */
174 <    RealType zShift_;
158 >    bool hasDividingArea_;
159 >    RealType dividingArea_;
160 >
161 >    int nBins_;
162 >    RealType binWidth_;
163 >    RealType slabWidth_;
164 >    RealType slabACenter_;
165 >    RealType slabBCenter_;
166 >    RealType sphereARadius_;
167 >    RealType sphereBRadius_;
168 >    RealType areaA_;
169 >    bool AisHull_;
170 >    RealType areaB_;
171 >    bool BisHull_;
172 >
173 >    Vector3d coordinateOrigin_;
174 >
175 >    RealType kineticFlux_;        // target or desired *flux*
176 >    Vector3d momentumFluxVector_; // target or desired *flux*
177 >    Vector3d angularMomentumFluxVector_; // target or desired *flux*
178 >
179 >    RealType kineticTarget_;     // target or desired one-time exchange energy
180 >    Vector3d momentumTarget_;    // target or desired one-time exchange momentum
181 >    Vector3d angularMomentumTarget_; // target or desired one-time
182 >                                     // exchange angular momentum
183 >
184 >    RealType kineticExchange_;    // actual exchange energy (running total)
185 >    Vector3d momentumExchange_;   // actual exchange momentum (running total)
186 >    Vector3d angularMomentumExchange_; // actual exchange momentum
187 >                                       // (running total)
188      RealType exchangeTime_;
189 <    RealType targetFlux_;
137 <    RealType targetJzKE_;
138 <    RealType targetJzpx_;
139 <    RealType targetJzpy_;
140 <    RealType targetJzpz_;
189 >
190      RealType targetJzpz2_;
142 –    Vector3d jzp_, njzp_;
143 –    RealType exchangeSum_;
144 –    int failTrialCount_;
145 –    int failRootCount_;
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 –  };
191  
192 +    unsigned int trialCount_;
193 +    unsigned int failTrialCount_;
194 +    unsigned int failRootCount_;
195 +
196 +    string rnemdFileName_;
197 +    ofstream rnemdFile_;
198 +
199 +    RealType runTime_, statusTime_;
200 +
201 +    vector<OutputData> data_;
202 +    OutputBitSet outputMask_;
203 +    OutputMapType outputMap_;
204 +    Accumulator* areaAccumulator_;
205 +    bool doRNEMD_;
206 +    bool hasData_;
207 +
208 +  };
209   }
210   #endif //INTEGRATORS_RNEMD_HPP

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