FluctuatingNRSolver.h

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/*
 * University of Illinois Open Source License
 * Copyright 2010-2018 Luthey-Schulten Group,
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 * Developed by: Luthey-Schulten Group
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 * Author(s): Elijah Roberts
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#ifndef LM_CME_FLUCTUATINGNRSOLVER_H_
#define LM_CME_FLUCTUATINGNRSOLVER_H_
 
#include <map>
#include <list>
#include <string>
#include "cme/NextReactionSolver.h"
#include "rng/RandomGenerator.h"
 
using std::map;
using std::list;
using std::string;
using lm::main::ResourceAllocator;
using lm::reaction::ReactionQueue;
using lm::rng::RandomGenerator;
 
namespace lm {
namespace cme {
 
class FluctuatingNRSolver : public NextReactionSolver
{
protected:
    struct OUPropensityArgs : public PropensityArgs
    {
        OUPropensityArgs(void * basePropensityFunction, void * basePropensityFunctionArgs, double * noisyK, double noisyKInitialValue, uint oui, double noiseVariance, double noiseTau, RandomGenerator * rng) :basePropensityFunction(basePropensityFunction),basePropensityFunctionArgs(basePropensityFunctionArgs),noisyK(noisyK),noisyKInitialValue(noisyKInitialValue),oui(oui),noiseVariance(noiseVariance),noiseTau(noiseTau),noise(0.0),lastOUJumpNumber(0),previousTime(0.0),rng(rng),rngNext(TUNE_LOCAL_RNG_CACHE_SIZE) {}
        void * basePropensityFunction;
        void * basePropensityFunctionArgs;
        double * noisyK;
        double noisyKInitialValue;
        uint oui;
        double noiseVariance;
        double noiseTau;
        double noise;
        uint lastOUJumpNumber;
        double previousTime;
        RandomGenerator * rng;
        double normRngValues[TUNE_LOCAL_RNG_CACHE_SIZE];
        int rngNext;
    };
 
public:
    FluctuatingNRSolver();
    virtual ~FluctuatingNRSolver();
    virtual void setReactionModel(lm::io::ReactionModel * rm);
    virtual void buildModel(const uint numberSpecies, const uint numberReactions, const uint * initialSpeciesCounts, const uint * reactionType, const double * k, const int * S, const uint * D, const uint kCols=1);
    virtual void buildModel(const uint numberSpecies, const uint numberReactions, const uint * initialSpeciesCounts, const uint * reactionType, const double * K, const int * S, const uint * D, const double * nvar, const double * ntau, const double noiseRecalcFraction, const uint kCols=1);
 
protected:
    virtual void destroyModel();
    static double ouPropensity(double time, uint * speciesCounts, void * pargs);
};
 
}
}
 
#endif