RDMESolver.h

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/*
 * University of Illinois Open Source License
 * Copyright 2011-2018 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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 * of the Software, and to permit persons to whom the Software is furnished to 
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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_RDMESOLVER_H_
#define LM_RDME_RDMESOLVER_H_
 
#include "cme/CMESolver.h"
#include "DiffusionModel.pb.h"
#include "rdme/Lattice.h"
 
using lm::cme::CMESolver;
using lm::io::DiffusionModel;
using lm::rdme::Lattice;
 
namespace lm {
namespace rdme {
 
class RDMESolver : public CMESolver
{
public:
    RDMESolver(RandomGenerator::Distributions neededDists);
    virtual ~RDMESolver();
    virtual void setDiffusionModel(DiffusionModel * dm, const uint8_t * lattice, size_t latticeSize, const uint8_t * latticeSites, size_t latticeSitesSize);
    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, const unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true);
 
protected:
    virtual void allocateDiffusionModel(uint numberSiteTypesA, 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);
    virtual void allocateLattice(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);
    virtual void setLatticeData(const uint8_t* latticeData);
    virtual void setLatticeSitesData(const uint8_t* latticeSitesData);
    virtual void destroyDiffusionModel();
 
protected:
    uint numberSiteTypes;
    double * DF;                            // diffusion matrix: numberSpecies x numberSiteTypes x numberSiteTypes
    uint * RL;                                // reaction location matrix: numberReactions x numberSiteTypes
    Lattice * lattice;
};
 
}
}
 
#endif