Lattice Microbes 2.5
This is for whole cell modeling
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lm::rdme::MGPUIntMpdRdmeSolver Member List

This is the complete list of members for lm::rdme::MGPUIntMpdRdmeSolver, including all inherited members.

addToParameterTrackingList(pair< string, double * >parameter)lm::cme::CMESolvervirtual
aggcopy_r_packlm::rdme::MGPUIntMpdRdmeSolverprotected
aggcopy_x_unpacklm::rdme::MGPUIntMpdRdmeSolverprotected
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::RDMESolverprotectedvirtual
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::MGPUIntMpdRdmeSolverprotectedvirtual
allocateModel(uint numberSpecies, uint numberReactions)lm::cme::CMESolverprotectedvirtual
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::MGPUIntMpdRdmeSolvervirtual
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::MGPUIntMpdRdmeSolvervirtual
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::MGPUIntMpdRdmeSolverprotectedvirtual
calculateXLaunchParameters(dim3 *gridSize, dim3 *threadBlockSize, const unsigned int maxXBlockSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
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::MGPUIntMpdRdmeSolverprotectedvirtual
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::MGPUIntMpdRdmeSolverprotectedvirtual
CMESolver(RandomGenerator::Distributions neededDists)lm::cme::CMESolver
competitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
computePropensities()lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
copyModelsToDevice(int gpu)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
current_timesteplm::rdme::MGPUIntMpdRdmeSolverprotected
Dlm::cme::CMESolverprotected
dependentReactionslm::cme::CMESolverprotected
dependentSpecieslm::cme::CMESolverprotected
dependentSpeciesChangelm::cme::CMESolverprotected
destroyDiffusionModel()lm::rdme::RDMESolverprotectedvirtual
destroyModel()lm::cme::CMESolverprotectedvirtual
DFlm::rdme::RDMESolverprotected
firstOrderlm::rdme::MGPUIntMpdRdmeSolverprotected
firstOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
firstOrderSizelm::rdme::MGPUIntMpdRdmeSolverprotected
fptTrackedSpecieslm::cme::CMESolverprotected
generateTrajectory()lm::rdme::MGPUIntMpdRdmeSolvervirtual
getReactionRateConstantsView(int reactionNumber, double **rates, int *rateConstantCount)lm::cme::CMESolvervirtual
getSpeciesCountView(uint **counts, int *number)lm::cme::CMESolvervirtual
getTimestepSeed(uint32_t timestep, uint32_t substep)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
gpu_worker_thread_int(void *arg)lm::rdme::MGPUIntMpdRdmeSolverfriend
handle_all_overflows()lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
handle_overflows(int gpu, void *hptr, void *dptr, int ts)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
hookCheckSimulation(double time, CudaIntLattice *lattice)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
hookSimulation(double time, CudaIntLattice *lattice)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
lm::rdme::RDMESolver::hookSimulation(double time)lm::cme::CMESolverprotectedvirtual
initialize(unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources)lm::rdme::MGPUIntMpdRdmeSolvervirtual
initialize_decomposition()lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
initialSpeciesCountslm::cme::CMESolverprotected
kHillPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
kHillTransportPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
latticelm::rdme::RDMESolverprotected
mapperlm::rdme::MGPUIntMpdRdmeSolverprotected
MESolver()lm::me::MESolver
MGPUIntMpdRdmeSolver()lm::rdme::MGPUIntMpdRdmeSolver
michaelisMentenPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
model_D1lm::rdme::MGPUIntMpdRdmeSolverprotected
model_D2lm::rdme::MGPUIntMpdRdmeSolverprotected
model_reactionOrderslm::rdme::MGPUIntMpdRdmeSolverprotected
model_reactionRateslm::rdme::MGPUIntMpdRdmeSolverprotected
model_reactionSiteslm::rdme::MGPUIntMpdRdmeSolverprotected
model_RLlm::rdme::MGPUIntMpdRdmeSolverprotected
model_Slm::rdme::MGPUIntMpdRdmeSolverprotected
model_Tlm::rdme::MGPUIntMpdRdmeSolverprotected
neededDistslm::cme::CMESolverprotected
needsDiffusionModel()lm::rdme::MGPUIntMpdRdmeSolverinlinevirtual
needsReactionModel()lm::rdme::MGPUIntMpdRdmeSolverinlinevirtual
noncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
numberDependentReactionslm::cme::CMESolverprotected
numberDependentSpecieslm::cme::CMESolverprotected
numberFptTrackedSpecieslm::cme::CMESolverprotected
numberReactionslm::cme::CMESolverprotected
numberSiteTypeslm::rdme::RDMESolverprotected
numberSpecieslm::cme::CMESolverprotected
numberSpeciesLimitslm::cme::CMESolverprotected
numberSpeciesToTracklm::cme::CMESolverprotected
onBeginTrajectory()lm::cme::CMESolverprotectedvirtual
onEndTrajectory()lm::cme::CMESolverprotectedvirtual
overflow_barrierlm::rdme::MGPUIntMpdRdmeSolverprotected
overflow_handlinglm::rdme::MGPUIntMpdRdmeSolverprotected
overflowListUseslm::rdme::MGPUIntMpdRdmeSolverprotected
overflowTimestepslm::rdme::MGPUIntMpdRdmeSolverprotected
parameterslm::cme::CMESolverprotected
printPerfIntervallm::rdme::MGPUIntMpdRdmeSolverprotected
propensityArgslm::cme::CMESolverprotected
propensityFunctionArgslm::cme::CMESolverprotected
propensityFunctionslm::cme::CMESolverprotected
queueRecordedParameters(bool flush=false)lm::cme::CMESolverprotectedvirtual
RDMESolver(RandomGenerator::Distributions neededDists)lm::rdme::RDMESolver
reachedSpeciesLimit()lm::cme::CMESolverinlineprotected
reactionModelModifiedlm::rdme::MGPUIntMpdRdmeSolverprotected
reactionTypeslm::cme::CMESolverprotected
recordParameters(double nextRecordTime, double recordInterval, double simulationTime)lm::cme::CMESolverprotectedvirtual
recordSpeciesCounts(double time, CudaIntLattice *lattice, lm::io::SpeciesCounts *speciesCountsDataSet)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
replicatelm::cme::CMESolverprotected
resourceslm::rdme::MGPUIntMpdRdmeSolverprotected
RLlm::rdme::RDMESolverprotected
rnglm::cme::CMESolverprotected
run_next_timestep(int gpu, uint32_t timestep)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
run_thread(int)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
Slm::cme::CMESolverprotected
secondOrderlm::rdme::MGPUIntMpdRdmeSolverprotected
secondOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
secondOrderSelfPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
secondOrderSizelm::rdme::MGPUIntMpdRdmeSolverprotected
seedlm::rdme::MGPUIntMpdRdmeSolverprotected
setDiffusionModel(DiffusionModel *dm, const uint8_t *lattice, size_t latticeSize, const uint8_t *latticeSites, size_t latticeSitesSize)lm::rdme::RDMESolvervirtual
setFptTrackingList(list< uint > speciesList)lm::cme::CMESolvervirtual
setLatticeData(const uint8_t *latticeData)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
setLatticeSitesData(const uint8_t *latticeSitesData)lm::rdme::RDMESolverprotectedvirtual
setModelPropensityFunction(uint reaction, double(*propensityFunction)(double time, uint *speciesCounts, void *args), void *propensityFunctionArg)lm::cme::CMESolvervirtual
setReactionModel(lm::io::ReactionModel *reactionModel)lm::cme::CMESolvervirtual
setReactionRate(unsigned int rxid, float rate)lm::rdme::MGPUIntMpdRdmeSolvervirtual
setReactionRateCME(unsigned int reactionId, double rate)lm::cme::CMESolvervirtual
setSpeciesLowerLimit(uint species, uint limit)lm::cme::CMESolvervirtual
setSpeciesUpperLimit(uint species, uint limit)lm::cme::CMESolvervirtual
setupModelsOnDevice(int gpu)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
simulation_barrierlm::rdme::MGPUIntMpdRdmeSolverprotected
speciesCountslm::cme::CMESolverprotected
speciesLimitslm::cme::CMESolverprotected
start_barrierlm::rdme::MGPUIntMpdRdmeSolverprotected
start_threads()lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
stop_barrierlm::rdme::MGPUIntMpdRdmeSolverprotected
stop_threads()lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
taulm::rdme::MGPUIntMpdRdmeSolverprotected
threadslm::rdme::MGPUIntMpdRdmeSolverprotected
timesteps_to_runlm::rdme::MGPUIntMpdRdmeSolverprotected
trackedParameterslm::cme::CMESolverprotected
uncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
updateSpeciesCounts(uint r)lm::cme::CMESolverinlineprotected
use_spin_barrierlm::rdme::MGPUIntMpdRdmeSolverprotected
writeLatticeData(double time, CudaIntLattice *lattice, lm::io::Lattice *latticeDataSet)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
writeLatticeSites(double time, CudaIntLattice *lattice)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
writeSpeciesCounts(lm::io::SpeciesCounts *speciesCountsDataSet)lm::rdme::MGPUIntMpdRdmeSolverprotectedvirtual
zeroOrderlm::rdme::MGPUIntMpdRdmeSolverprotected
zeroOrderSizelm::rdme::MGPUIntMpdRdmeSolverprotected
zerothOrderHeavisidePropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
zerothOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
~CMESolver()lm::cme::CMESolvervirtual
~MESolver()lm::me::MESolvervirtual
~MGPUIntMpdRdmeSolver()lm::rdme::MGPUIntMpdRdmeSolvervirtual
~RDMESolver()lm::rdme::RDMESolvervirtual