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Comparing:
trunk/src/integrators/RNEMD.hpp (file contents), Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
branches/development/src/rnemd/RNEMD.hpp (file contents), Revision 1774 by gezelter, Wed Aug 8 16:03:02 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  
60 –  /**
61 –   * @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
62 –   * @todo document
63 –   */
62    class RNEMD {
63    public:
64      RNEMD(SimInfo* info);
# Line 68 | Line 66 | namespace OpenMD {
66      
67      void doRNEMD();
68      void doSwap();
69 <    void doScale();
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 <    RealType get_RNEMD_exchange_total() { return exchangeSum_; }
79 <    void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
80 <    void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
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 <      rnemdPxScale,
88 <      rnemdPyScale,
90 <      rnemdPzScale,
91 <      rnemdPx,
92 <      rnemdPy,
93 <      rnemdPz,
94 <      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 <    std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
126 <    RNEMDTypeEnum rnemdType_;
127 <    std::string rnemdObjectSelection_;
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 <    int nBins_;
134 <    int midBin_;
135 <    int rnemdLogWidth_;
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_;
109 –    RealType targetFlux_;
110 –    RealType exchangeSum_;
111 –    int failTrialCount_;
112 –    int failRootCount_;
113 –    std::ofstream rnemdLog_;
114 –    // keeps track of what's being averaged
115 –    std::vector<RealType> valueHist_;
116 –    std::vector<int> valueCount_;
117 –    // keeps track of the number of degrees of freedom being averaged
118 –    std::vector<RealType> xTempHist_, yTempHist_, zTempHist_;
119 –    std::ofstream xTempLog_, yTempLog_, zTempLog_;
120 –  };
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 +
165 +  };
166   }
167   #endif //INTEGRATORS_RNEMD_HPP

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