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

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

addToParameterTrackingList(pair< string, double * >parameter)lm::cme::CMESolvervirtual
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::MpdRdmeSolverExtendedvirtual
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::MpdRdmeSolverExtendedvirtual
buildModel(const uint numberSpeciesA, const uint numberReactionsA, const uint *initialSpeciesCountsA, const uint *reactionTypesA, const double *KA, const int *SA, const uint *DA, const uint kCols)lm::MpdRdmeSolverExtendedvirtual
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)lm::rdme::MpdRdmeSolverprotectedvirtual
calculateXLaunchParameters(unsigned int *gridXSize, dim3 *gridSize, dim3 *threadBlockSize, const unsigned int maxXBlockSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize)lm::rdme::MpdRdmeSolverprotectedvirtual
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)lm::rdme::MpdRdmeSolverprotectedvirtual
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)lm::rdme::MpdRdmeSolverprotectedvirtual
CMESolver(RandomGenerator::Distributions neededDists)lm::cme::CMESolver
competitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
computePropensities()lm::rdme::MpdRdmeSolverprotectedvirtual
copyModelsToDevice()lm::rdme::MpdRdmeSolverprotectedvirtual
copyParticleSizesToDevice()lm::MpdRdmeSolverExtendedprotected
copyReactionDataToDevice()lm::MpdRdmeSolverExtendedprotected
cudaOverflowListlm::rdme::MpdRdmeSolverprotected
cudaStreamlm::rdme::MpdRdmeSolverprotected
Dlm::cme::CMESolverprotected
dependentReactionslm::cme::CMESolverprotected
dependentSpecieslm::cme::CMESolverprotected
dependentSpeciesChangelm::cme::CMESolverprotected
destroyDiffusionModel()lm::rdme::RDMESolverprotectedvirtual
destroyModel()lm::cme::CMESolverprotectedvirtual
deviceReactionLocationMatrixlm::MpdRdmeSolverExtendedprotected
deviceReactionMatrixlm::MpdRdmeSolverExtendedprotected
DFlm::rdme::RDMESolverprotected
enableParticleSizeChecking(bool enable)lm::MpdRdmeSolverExtended
firstOrderlm::rdme::MpdRdmeSolverprotected
firstOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
firstOrderSizelm::rdme::MpdRdmeSolverprotected
fptTrackedSpecieslm::cme::CMESolverprotected
generateSizeAwareTrajectory()lm::MpdRdmeSolverExtendedprotected
generateTrajectory()lm::MpdRdmeSolverExtendedvirtual
getParticleSize(particle_t particleType) constlm::MpdRdmeSolverExtended
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::MpdRdmeSolverprotectedvirtual
hookCheckSimulation(double time, CudaByteLattice *lattice)lm::rdme::MpdRdmeSolverprotectedvirtual
hookSimulation(double time, CudaByteLattice *lattice)lm::rdme::MpdRdmeSolverprotectedvirtual
lm::rdme::RDMESolver::hookSimulation(double time)lm::cme::CMESolverprotectedvirtual
hostParticleSizeslm::MpdRdmeSolverExtendedprotected
initialize(unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources)lm::rdme::MpdRdmeSolvervirtual
initializeFastSizeChecking()lm::MpdRdmeSolverExtended
initializeParticleSizes()lm::MpdRdmeSolverExtendedprotected
initialSpeciesCountslm::cme::CMESolverprotected
isFastSizeCheckingEnabled() constlm::MpdRdmeSolverExtendedinline
kHillPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
kHillTransportPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
latticelm::rdme::RDMESolverprotected
MESolver()lm::me::MESolver
michaelisMentenPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
model_reactionRateslm::rdme::MpdRdmeSolverprotected
MpdRdmeSolver()lm::rdme::MpdRdmeSolver
MpdRdmeSolverExtended()lm::MpdRdmeSolverExtended
neededDistslm::cme::CMESolverprotected
needsDiffusionModel()lm::rdme::MpdRdmeSolverinlinevirtual
needsReactionModel()lm::rdme::MpdRdmeSolverinlinevirtual
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
numParticleTypeslm::MpdRdmeSolverExtendedprotected
onBeginTrajectory(CudaByteLattice *lattice)lm::rdme::MpdRdmeSolverprotectedvirtual
lm::rdme::RDMESolver::onBeginTrajectory()lm::cme::CMESolverprotectedvirtual
onEndTrajectory(CudaByteLattice *lattice)lm::rdme::MpdRdmeSolverprotectedvirtual
lm::rdme::RDMESolver::onEndTrajectory()lm::cme::CMESolverprotectedvirtual
onWriteLattice(double time, CudaByteLattice *lattice)lm::rdme::MpdRdmeSolverprotectedvirtual
overflow_handlinglm::rdme::MpdRdmeSolverprotected
overflowListUseslm::rdme::MpdRdmeSolverprotected
overflowTimestepslm::rdme::MpdRdmeSolverprotected
parameterslm::cme::CMESolverprotected
particleSizeEnabledlm::MpdRdmeSolverExtendedprotected
particleSizesInitializedlm::MpdRdmeSolverExtendedprotected
printConstraintViolations() constlm::MpdRdmeSolverExtended
propensityArgslm::cme::CMESolverprotected
propensityFunctionArgslm::cme::CMESolverprotected
propensityFunctionslm::cme::CMESolverprotected
propFirstOrderlm::rdme::MpdRdmeSolverprotected
propSecondOrderlm::rdme::MpdRdmeSolverprotected
propZeroOrderlm::rdme::MpdRdmeSolverprotected
queueRecordedParameters(bool flush=false)lm::cme::CMESolverprotectedvirtual
RDMESolver(RandomGenerator::Distributions neededDists)lm::rdme::RDMESolver
reachedSpeciesLimit()lm::cme::CMESolverinlineprotected
reactionModelModifiedlm::rdme::MpdRdmeSolverprotected
reactionTypeslm::cme::CMESolverprotected
recordParameters(double nextRecordTime, double recordInterval, double simulationTime)lm::cme::CMESolverprotectedvirtual
recordSpeciesCounts(double time, CudaByteLattice *lattice, lm::io::SpeciesCounts *speciesCountsDataSet)lm::rdme::MpdRdmeSolverprotectedvirtual
replicatelm::cme::CMESolverprotected
resourceslm::cme::CMESolverprotected
RLlm::rdme::RDMESolverprotected
rnglm::cme::CMESolverprotected
runSizeAwareTimestep(lm::rdme::CudaByteLatticeExtended *lattice, uint32_t timestep)lm::MpdRdmeSolverExtendedprotected
runStandardTimestep(lm::rdme::CudaByteLatticeExtended *lattice, uint32_t timestep)lm::MpdRdmeSolverExtendedprotected
runTimestep(CudaByteLattice *lattice, uint32_t timestep)lm::MpdRdmeSolverExtendedvirtual
Slm::cme::CMESolverprotected
secondOrderlm::rdme::MpdRdmeSolverprotected
secondOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
secondOrderSelfPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
secondOrderSizelm::rdme::MpdRdmeSolverprotected
seedlm::rdme::MpdRdmeSolverprotected
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::RDMESolverprotectedvirtual
setLatticeSitesData(const uint8_t *latticeSitesData)lm::rdme::RDMESolverprotectedvirtual
setModelPropensityFunction(uint reaction, double(*propensityFunction)(double time, uint *speciesCounts, void *args), void *propensityFunctionArg)lm::cme::CMESolvervirtual
setParticleSizes(const uint32_t *sizes, uint32_t numTypes)lm::MpdRdmeSolverExtended
setReactionModel(lm::io::ReactionModel *reactionModel)lm::cme::CMESolvervirtual
setReactionRate(unsigned int rxid, float rate)lm::rdme::MpdRdmeSolvervirtual
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
speciesCountslm::cme::CMESolverprotected
speciesLimitslm::cme::CMESolverprotected
taulm::rdme::MpdRdmeSolverprotected
trackedParameterslm::cme::CMESolverprotected
uncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
updateSpeciesCounts(uint r)lm::cme::CMESolverinlineprotected
useFastSizeAwareDiffusion(bool enable)lm::MpdRdmeSolverExtended
useFastSizeKernels_lm::MpdRdmeSolverExtendedprotected
validateConstraints() constlm::MpdRdmeSolverExtended
writeLatticeData(double time, CudaByteLattice *lattice, lm::io::Lattice *latticeDataSet)lm::rdme::MpdRdmeSolverprotectedvirtual
writeLatticeSites(double time, CudaByteLattice *lattice)lm::rdme::MpdRdmeSolverprotectedvirtual
writeSpeciesCounts(lm::io::SpeciesCounts *speciesCountsDataSet)lm::rdme::MpdRdmeSolverprotectedvirtual
zeroOrderlm::rdme::MpdRdmeSolverprotected
zeroOrderSizelm::rdme::MpdRdmeSolverprotected
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
~MpdRdmeSolver()lm::rdme::MpdRdmeSolvervirtual
~MpdRdmeSolverExtended()lm::MpdRdmeSolverExtendedvirtual
~RDMESolver()lm::rdme::RDMESolvervirtual