GillespieDSolver.h

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/*
 * University of Illinois Open Source License
 * Copyright 2010-2018 Luthey-Schulten Group,
 * All rights reserved.
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 * Developed by: Luthey-Schulten Group
 *               University of Illinois at Urbana-Champaign
 *               http://www.scs.uiuc.edu/~schulten
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 * - Redistributions of source code must retain the above copyright notice, 
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 * Author(s): Elijah Roberts
 */
 
#ifndef LM_CME_GILLESPIEDSOLVER_H_
#define LM_CME_GILLESPIEDSOLVER_H_
 
#include <map>
#include <list>
#include <string>
#include "cme/CMESolver.h"
#include "FirstPassageTimes.pb.h"
#include "core/ResourceAllocator.h"
#include "rng/RandomGenerator.h"
 
using std::map;
using std::list;
using std::string;
using lm::main::ResourceAllocator;
using lm::rng::RandomGenerator;
 
namespace lm {
namespace cme {
 
class GillespieDSolver : public CMESolver
{
public:
    GillespieDSolver();
    virtual ~GillespieDSolver();
    virtual bool needsReactionModel() {return true;}
    virtual bool needsDiffusionModel()  {return false;}
    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 generateTrajectory();
 
protected:
    virtual void destroyModel();
    inline void updateAllPropensities(double time);
    inline void updatePropensities(double time, uint r);
 
protected:
    double * propensities;
 
protected:
    virtual int hookSimulation(double time);
    virtual int onBeginTrajectory();
    virtual int onEndTrajectory();
};
 
}
}
 
#endif