- Generated by
1.14.0
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Lattice Microbes 2.5
This is for whole cell modeling
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This is the complete list of members for MpdRdmeSolver, including all inherited members.
| allocateLattice(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) | MpdRdmeSolver | protectedvirtual |
| 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) | MpdRdmeSolver | virtual |
| buildModel(const uint numberSpeciesA, const uint numberReactionsA, const uint *initialSpeciesCountsA, const uint *reactionTypeA, const double *kA, const int *SA, const uint *DA, const uint kCols=1) | MpdRdmeSolver | virtual |
| calculateReactionLaunchParameters(unsigned int *gridXSize, dim3 *gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockYSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize) | MpdRdmeSolver | protectedvirtual |
| calculateXLaunchParameters(unsigned int *gridXSize, dim3 *gridSize, dim3 *threadBlockSize, const unsigned int maxXBlockSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize) | MpdRdmeSolver | protectedvirtual |
| calculateYLaunchParameters(unsigned int *gridXSize, dim3 *gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockYSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize) | MpdRdmeSolver | protectedvirtual |
| calculateZLaunchParameters(unsigned int *gridXSize, dim3 *gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockZSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize) | MpdRdmeSolver | protectedvirtual |
| computePropensities() | MpdRdmeSolver | protectedvirtual |
| copyModelsToDevice() | MpdRdmeSolver | protectedvirtual |
| cudaOverflowList | MpdRdmeSolver | protected |
| cudaStream | MpdRdmeSolver | protected |
| firstOrder | MpdRdmeSolver | protected |
| firstOrderSize | MpdRdmeSolver | protected |
| generateTrajectory() | MpdRdmeSolver | virtual |
| getTimestepSeed(uint32_t timestep, uint32_t substep) | MpdRdmeSolver | protectedvirtual |
| hookCheckSimulation(double time, CudaByteLattice *lattice) | MpdRdmeSolver | protectedvirtual |
| hookSimulation(double time, CudaByteLattice *lattice) | MpdRdmeSolver | protectedvirtual |
| initialize(unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources) | MpdRdmeSolver | virtual |
| model_reactionRates | MpdRdmeSolver | protected |
| MpdRdmeSolver() | MpdRdmeSolver | |
| needsDiffusionModel() | MpdRdmeSolver | inlinevirtual |
| needsReactionModel() | MpdRdmeSolver | inlinevirtual |
| onBeginTrajectory(CudaByteLattice *lattice) | MpdRdmeSolver | protectedvirtual |
| onEndTrajectory(CudaByteLattice *lattice) | MpdRdmeSolver | protectedvirtual |
| onWriteLattice(double time, CudaByteLattice *lattice) | MpdRdmeSolver | protectedvirtual |
| overflow_handling | MpdRdmeSolver | protected |
| overflowListUses | MpdRdmeSolver | protected |
| overflowTimesteps | MpdRdmeSolver | protected |
| propFirstOrder | MpdRdmeSolver | protected |
| propSecondOrder | MpdRdmeSolver | protected |
| propZeroOrder | MpdRdmeSolver | protected |
| reactionModelModified | MpdRdmeSolver | protected |
| recordSpeciesCounts(double time, CudaByteLattice *lattice, lm::io::SpeciesCounts *speciesCountsDataSet) | MpdRdmeSolver | protectedvirtual |
| runTimestep(CudaByteLattice *lattice, uint32_t timestep) | MpdRdmeSolver | protectedvirtual |
| secondOrder | MpdRdmeSolver | protected |
| secondOrderSize | MpdRdmeSolver | protected |
| seed | MpdRdmeSolver | protected |
| setReactionRate(unsigned int rxid, float rate) | MpdRdmeSolver | virtual |
| tau | MpdRdmeSolver | protected |
| writeLatticeData(double time, CudaByteLattice *lattice, lm::io::Lattice *latticeDataSet) | MpdRdmeSolver | protectedvirtual |
| writeLatticeSites(double time, CudaByteLattice *lattice) | MpdRdmeSolver | protectedvirtual |
| writeSpeciesCounts(lm::io::SpeciesCounts *speciesCountsDataSet) | MpdRdmeSolver | protectedvirtual |
| zeroOrder | MpdRdmeSolver | protected |
| zeroOrderSize | MpdRdmeSolver | protected |
| ~MpdRdmeSolver() | MpdRdmeSolver | virtual |
1.14.0