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

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

addParticles(lattice_size_t subvolume, particle_t particle, uint count)lm::rdme::NextSubvolumeSolverprotected
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, unsigned int bytes_per_particle, si_dist_t latticeSpacing)lm::rdme::RDMESolverprotectedvirtual
allocateModel(uint numberSpecies, uint numberReactions)lm::rdme::NextSubvolumeSolverprotectedvirtual
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, unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t *latticeData, const uint8_t *latticeSitesData, bool rowMajorData=true)lm::rdme::NextSubvolumeSolvervirtual
buildModel(const uint numberSpecies, const uint numberReactions, const uint *initialSpeciesCounts, const uint *reactionTypesA, const double *k, const int *S, const uint *D, const uint kCols=1)lm::cme::CMESolvervirtual
calculateSubvolumePropensity(si_time_t time, lattice_size_t s)lm::rdme::NextSubvolumeSolverprotectedvirtual
checkSpeciesCountsAgainstLattice()lm::rdme::NextSubvolumeSolverprotectedvirtual
CMESolver(RandomGenerator::Distributions neededDists)lm::cme::CMESolver
competitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
currentSubvolumeSpeciesCountslm::rdme::NextSubvolumeSolverprotected
Dlm::cme::CMESolverprotected
dependentReactionslm::cme::CMESolverprotected
dependentSpecieslm::cme::CMESolverprotected
dependentSpeciesChangelm::cme::CMESolverprotected
destroyDiffusionModel()lm::rdme::NextSubvolumeSolverprotectedvirtual
destroyModel()lm::rdme::NextSubvolumeSolverprotectedvirtual
DFlm::rdme::RDMESolverprotected
firstOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
fptTrackedSpecieslm::cme::CMESolverprotected
generateTrajectory()lm::rdme::NextSubvolumeSolvervirtual
getReactionRateConstantsView(int reactionNumber, double **rates, int *rateConstantCount)lm::cme::CMESolvervirtual
getSpeciesCountView(uint **counts, int *number)lm::cme::CMESolvervirtual
hookSimulation(double time)lm::cme::CMESolverprotectedvirtual
initialize(unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources)lm::cme::CMESolvervirtual
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
latticeSpacingSquaredlm::rdme::NextSubvolumeSolverprotected
MESolver()lm::me::MESolver
michaelisMentenPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
neededDistslm::cme::CMESolverprotected
needsDiffusionModel()lm::rdme::NextSubvolumeSolverinlinevirtual
needsReactionModel()lm::rdme::NextSubvolumeSolverinlinevirtual
NextSubvolumeSolver()lm::rdme::NextSubvolumeSolver
NextSubvolumeSolver(RandomGenerator::Distributions neededDists)lm::rdme::NextSubvolumeSolver
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
numberSubvolumeslm::rdme::NextSubvolumeSolverprotected
onBeginTrajectory()lm::cme::CMESolverprotectedvirtual
onEndTrajectory()lm::cme::CMESolverprotectedvirtual
parameterslm::cme::CMESolverprotected
performSubvolumeReaction(si_time_t time, lattice_size_t s, int rngNext, double *uniRngValues, bool *affectedNeighbor, lattice_size_t *neighborSubvolume)lm::rdme::NextSubvolumeSolverprotectedvirtual
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
reactionPropensitieslm::rdme::NextSubvolumeSolverprotected
reactionQueuelm::rdme::NextSubvolumeSolverprotected
reactionTypeslm::cme::CMESolverprotected
recordParameters(double nextRecordTime, double recordInterval, double simulationTime)lm::cme::CMESolverprotectedvirtual
recordSpeciesCounts(double time, lm::io::SpeciesCounts *speciesCountsDataSet)lm::rdme::NextSubvolumeSolverprotectedvirtual
replicatelm::cme::CMESolverprotected
resourceslm::cme::CMESolverprotected
RLlm::rdme::RDMESolverprotected
rnglm::cme::CMESolverprotected
Slm::cme::CMESolverprotected
secondOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
secondOrderSelfPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
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
setReactionModel(lm::io::ReactionModel *reactionModel)lm::cme::CMESolvervirtual
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
trackedParameterslm::cme::CMESolverprotected
uncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
updateAllSubvolumePropensities(si_time_t time, int rngNext, double *expRngValues)lm::rdme::NextSubvolumeSolverprotectedvirtual
updateCurrentSubvolumeSpeciesCounts(uint r)lm::rdme::NextSubvolumeSolverprotectedvirtual
updateSpeciesCounts(uint r)lm::cme::CMESolverinlineprotected
updateSpeciesCountsForSubvolume(lattice_size_t subvolume)lm::rdme::NextSubvolumeSolverprotectedvirtual
updateSubvolumePropensity(si_time_t time, lattice_size_t s, int rngNext, double *expRngValues)lm::rdme::NextSubvolumeSolverprotectedvirtual
updateSubvolumeWithSpeciesCounts(lattice_size_t subvolume)lm::rdme::NextSubvolumeSolverprotected
writeLatticeData(double time, ByteLattice *lattice, lm::io::Lattice *latticeDataSet)lm::rdme::NextSubvolumeSolverprotectedvirtual
writeSpeciesCounts(lm::io::SpeciesCounts *speciesCountsDataSet)lm::rdme::NextSubvolumeSolverprotectedvirtual
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
~NextSubvolumeSolver()lm::rdme::NextSubvolumeSolvervirtual
~RDMESolver()lm::rdme::RDMESolvervirtual