NextSubvolumeSolver.h

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/*
 * University of Illinois Open Source License
 * Copyright 2011-2018 Luthey-Schulten Group,
 * All rights reserved.
 * 
 * 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_RDME_NEXTSUBVOLUMESOLVER_H_
#define LM_RDME_NEXTSUBVOLUMESOLVER_H_
 
#include "rdme/Lattice.h"
#include "rdme/RDMESolver.h"
#include "reaction/ReactionQueue.h"
 
using lm::rdme::RDMESolver;
using lm::reaction::ReactionQueue;
 
 
namespace lm {
 
namespace io {
class Lattice;
class SpeciesCounts;
}
namespace rdme {
 
class ByteLattice;
 
class NextSubvolumeSolver : public RDMESolver
{
public:
    NextSubvolumeSolver();
    NextSubvolumeSolver(RandomGenerator::Distributions neededDists);
    virtual ~NextSubvolumeSolver();
    virtual bool needsReactionModel() {return true;}
    virtual bool needsDiffusionModel()  {return true;}
    virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true);
    virtual void generateTrajectory();
 
protected:
    virtual void allocateModel(uint numberSpecies, uint numberReactions);
    virtual void destroyModel();
    virtual void destroyDiffusionModel();
    virtual void checkSpeciesCountsAgainstLattice();
    virtual void writeLatticeData(double time, ByteLattice * lattice, lm::io::Lattice * latticeDataSet);
    virtual void recordSpeciesCounts(double time, lm::io::SpeciesCounts * speciesCountsDataSet);
    virtual void writeSpeciesCounts(lm::io::SpeciesCounts * speciesCountsDataSet);
    virtual int updateAllSubvolumePropensities(si_time_t time, int rngNext, double * expRngValues);
    virtual int updateSubvolumePropensity(si_time_t time, lattice_size_t s, int rngNext, double * expRngValues);
    virtual double calculateSubvolumePropensity(si_time_t time, lattice_size_t s);
    virtual int performSubvolumeReaction(si_time_t time, lattice_size_t s, int rngNext, double * uniRngValues, bool * affectedNeighbor, lattice_size_t * neighborSubvolume);
    virtual void updateCurrentSubvolumeSpeciesCounts(uint r);
 
 
    virtual void  updateSpeciesCountsForSubvolume(lattice_size_t subvolume);
    void updateSubvolumeWithSpeciesCounts(lattice_size_t subvolume);
    void addParticles(lattice_size_t subvolume, particle_t particle, uint count);
 
protected:
    lattice_size_t numberSubvolumes;
    double * reactionPropensities;
    double latticeSpacingSquared;
    ReactionQueue * reactionQueue;
    uint * currentSubvolumeSpeciesCounts;                           // numberSpecies
};
 
}
}
 
#endif