- 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 lm::rdme::MGPUMpdRdmeSolver, including all inherited members.
| addToParameterTrackingList(pair< string, double * >parameter) | lm::cme::CMESolver | virtual |
| aggcopy_r_pack | lm::rdme::MGPUMpdRdmeSolver | protected |
| aggcopy_x_unpack | lm::rdme::MGPUMpdRdmeSolver | protected |
| 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) | lm::rdme::RDMESolver | protectedvirtual |
| 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) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| allocateModel(uint numberSpecies, uint numberReactions) | lm::cme::CMESolver | 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) | lm::rdme::MGPUMpdRdmeSolver | 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) | lm::rdme::MGPUMpdRdmeSolver | virtual |
| calculateReactionLaunchParameters(dim3 *gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockYSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| calculateXLaunchParameters(dim3 *gridSize, dim3 *threadBlockSize, const unsigned int maxXBlockSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| calculateYLaunchParameters(dim3 *gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockYSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| calculateZLaunchParameters(dim3 *gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockZSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| CMESolver(RandomGenerator::Distributions neededDists) | lm::cme::CMESolver | |
| competitiveMMPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| computePropensities() | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| copyModelsToDevice(int gpu) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| current_timestep | lm::rdme::MGPUMpdRdmeSolver | protected |
| D | lm::cme::CMESolver | protected |
| dependentReactions | lm::cme::CMESolver | protected |
| dependentSpecies | lm::cme::CMESolver | protected |
| dependentSpeciesChange | lm::cme::CMESolver | protected |
| destroyDiffusionModel() | lm::rdme::RDMESolver | protectedvirtual |
| destroyModel() | lm::cme::CMESolver | protectedvirtual |
| DF | lm::rdme::RDMESolver | protected |
| firstOrder | lm::rdme::MGPUMpdRdmeSolver | protected |
| firstOrderPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| firstOrderSize | lm::rdme::MGPUMpdRdmeSolver | protected |
| fptTrackedSpecies | lm::cme::CMESolver | protected |
| generateTrajectory() | lm::rdme::MGPUMpdRdmeSolver | virtual |
| getReactionRateConstantsView(int reactionNumber, double **rates, int *rateConstantCount) | lm::cme::CMESolver | virtual |
| getSpeciesCountView(uint **counts, int *number) | lm::cme::CMESolver | virtual |
| getTimestepSeed(uint32_t timestep, uint32_t substep) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| gpu_worker_thread(void *arg) | lm::rdme::MGPUMpdRdmeSolver | friend |
| handle_all_overflows() | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| handle_overflows(int gpu, void *hptr, void *dptr, int ts) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| hookCheckSimulation(double time, ByteLattice *lattice) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| hookSimulation(double time, ByteLattice *lattice) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| lm::rdme::RDMESolver::hookSimulation(double time) | lm::cme::CMESolver | protectedvirtual |
| initialize(unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources) | lm::rdme::MGPUMpdRdmeSolver | virtual |
| initialize_decomposition() | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| initialSpeciesCounts | lm::cme::CMESolver | protected |
| kHillPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| kHillTransportPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| lattice | lm::rdme::RDMESolver | protected |
| mapper | lm::rdme::MGPUMpdRdmeSolver | protected |
| MESolver() | lm::me::MESolver | |
| MGPUMpdRdmeSolver() | lm::rdme::MGPUMpdRdmeSolver | |
| michaelisMentenPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| model_D1 | lm::rdme::MGPUMpdRdmeSolver | protected |
| model_D2 | lm::rdme::MGPUMpdRdmeSolver | protected |
| model_reactionOrders | lm::rdme::MGPUMpdRdmeSolver | protected |
| model_reactionRates | lm::rdme::MGPUMpdRdmeSolver | protected |
| model_reactionSites | lm::rdme::MGPUMpdRdmeSolver | protected |
| model_RL | lm::rdme::MGPUMpdRdmeSolver | protected |
| model_S | lm::rdme::MGPUMpdRdmeSolver | protected |
| model_T | lm::rdme::MGPUMpdRdmeSolver | protected |
| neededDists | lm::cme::CMESolver | protected |
| needsDiffusionModel() | lm::rdme::MGPUMpdRdmeSolver | inlinevirtual |
| needsReactionModel() | lm::rdme::MGPUMpdRdmeSolver | inlinevirtual |
| noncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| numberDependentReactions | lm::cme::CMESolver | protected |
| numberDependentSpecies | lm::cme::CMESolver | protected |
| numberFptTrackedSpecies | lm::cme::CMESolver | protected |
| numberReactions | lm::cme::CMESolver | protected |
| numberSiteTypes | lm::rdme::RDMESolver | protected |
| numberSpecies | lm::cme::CMESolver | protected |
| numberSpeciesLimits | lm::cme::CMESolver | protected |
| numberSpeciesToTrack | lm::cme::CMESolver | protected |
| onBeginTrajectory() | lm::cme::CMESolver | protectedvirtual |
| onEndTrajectory() | lm::cme::CMESolver | protectedvirtual |
| overflow_barrier | lm::rdme::MGPUMpdRdmeSolver | protected |
| overflow_handling | lm::rdme::MGPUMpdRdmeSolver | protected |
| overflowListUses | lm::rdme::MGPUMpdRdmeSolver | protected |
| overflowTimesteps | lm::rdme::MGPUMpdRdmeSolver | protected |
| parameters | lm::cme::CMESolver | protected |
| printPerfInterval | lm::rdme::MGPUMpdRdmeSolver | protected |
| propensityArgs | lm::cme::CMESolver | protected |
| propensityFunctionArgs | lm::cme::CMESolver | protected |
| propensityFunctions | lm::cme::CMESolver | protected |
| queueRecordedParameters(bool flush=false) | lm::cme::CMESolver | protectedvirtual |
| RDMESolver(RandomGenerator::Distributions neededDists) | lm::rdme::RDMESolver | |
| reachedSpeciesLimit() | lm::cme::CMESolver | inlineprotected |
| reactionModelModified | lm::rdme::MGPUMpdRdmeSolver | protected |
| reactionTypes | lm::cme::CMESolver | protected |
| recordParameters(double nextRecordTime, double recordInterval, double simulationTime) | lm::cme::CMESolver | protectedvirtual |
| recordSpeciesCounts(double time, ByteLattice *lattice, lm::io::SpeciesCounts *speciesCountsDataSet) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| replicate | lm::cme::CMESolver | protected |
| resources | lm::rdme::MGPUMpdRdmeSolver | protected |
| RL | lm::rdme::RDMESolver | protected |
| rng | lm::cme::CMESolver | protected |
| run_next_timestep(int gpu, uint32_t timestep) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| run_thread(int) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| S | lm::cme::CMESolver | protected |
| secondOrder | lm::rdme::MGPUMpdRdmeSolver | protected |
| secondOrderPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| secondOrderSelfPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| secondOrderSize | lm::rdme::MGPUMpdRdmeSolver | protected |
| seed | lm::rdme::MGPUMpdRdmeSolver | protected |
| setDiffusionModel(DiffusionModel *dm, const uint8_t *lattice, size_t latticeSize, const uint8_t *latticeSites, size_t latticeSitesSize) | lm::rdme::RDMESolver | virtual |
| setFptTrackingList(list< uint > speciesList) | lm::cme::CMESolver | virtual |
| setLatticeData(const uint8_t *latticeData) | lm::rdme::RDMESolver | protectedvirtual |
| setLatticeSitesData(const uint8_t *latticeSitesData) | lm::rdme::RDMESolver | protectedvirtual |
| setModelPropensityFunction(uint reaction, double(*propensityFunction)(double time, uint *speciesCounts, void *args), void *propensityFunctionArg) | lm::cme::CMESolver | virtual |
| setReactionModel(lm::io::ReactionModel *reactionModel) | lm::cme::CMESolver | virtual |
| setReactionRate(unsigned int rxid, float rate) | lm::rdme::MGPUMpdRdmeSolver | virtual |
| setReactionRateCME(unsigned int reactionId, double rate) | lm::cme::CMESolver | virtual |
| setSpeciesLowerLimit(uint species, uint limit) | lm::cme::CMESolver | virtual |
| setSpeciesUpperLimit(uint species, uint limit) | lm::cme::CMESolver | virtual |
| setupModelsOnDevice(int gpu) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| simulation_barrier | lm::rdme::MGPUMpdRdmeSolver | protected |
| speciesCounts | lm::cme::CMESolver | protected |
| speciesLimits | lm::cme::CMESolver | protected |
| start_barrier | lm::rdme::MGPUMpdRdmeSolver | protected |
| start_threads() | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| stop_barrier | lm::rdme::MGPUMpdRdmeSolver | protected |
| stop_threads() | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| tau | lm::rdme::MGPUMpdRdmeSolver | protected |
| threads | lm::rdme::MGPUMpdRdmeSolver | protected |
| timesteps_to_run | lm::rdme::MGPUMpdRdmeSolver | protected |
| trackedParameters | lm::cme::CMESolver | protected |
| uncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| updateSpeciesCounts(uint r) | lm::cme::CMESolver | inlineprotected |
| use_spin_barrier | lm::rdme::MGPUMpdRdmeSolver | protected |
| writeLatticeData(double time, ByteLattice *lattice, lm::io::Lattice *latticeDataSet) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| writeLatticeSites(double time, ByteLattice *lattice) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| writeSpeciesCounts(lm::io::SpeciesCounts *speciesCountsDataSet) | lm::rdme::MGPUMpdRdmeSolver | protectedvirtual |
| zeroOrder | lm::rdme::MGPUMpdRdmeSolver | protected |
| zeroOrderSize | lm::rdme::MGPUMpdRdmeSolver | protected |
| zerothOrderHeavisidePropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| zerothOrderPropensity(double time, uint *speciesCounts, void *pargs) | lm::cme::CMESolver | protectedstatic |
| ~CMESolver() | lm::cme::CMESolver | virtual |
| ~MESolver() | lm::me::MESolver | virtual |
| ~MGPUMpdRdmeSolver() | lm::rdme::MGPUMpdRdmeSolver | virtual |
| ~RDMESolver() | lm::rdme::RDMESolver | virtual |
1.14.0