Lattice Microbes 2.5
This is for whole cell modeling
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lm::io::hdf5::SimulationFile Member List

This is the complete list of members for lm::io::hdf5::SimulationFile, including all inherited members.

appendDsToGroup(H5MetaData *header, byte *data)lm::io::hdf5::SimulationFileprotected
appendLattice(unsigned int replicate, lm::io::Lattice *lattice, byte *latticeData, size_t latticeDataSize)lm::io::hdf5::SimulationFilevirtual
appendLattice_U32LE(unsigned int replicate, lm::io::Lattice *lattice, uint32_t *latticeData, size_t latticeDataSize)lm::io::hdf5::SimulationFilevirtual
appendParameterValues(unsigned int replicate, lm::io::ParameterValues *parameterValues)lm::io::hdf5::SimulationFilevirtual
appendSites(unsigned int replicate, lm::io::Lattice *lattice, uint8_t *siteData, size_t siteDataSize)lm::io::hdf5::SimulationFilevirtual
appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts *speciesCounts)lm::io::hdf5::SimulationFilevirtual
appendToDataset(H5MetaData *header, byte *data)lm::io::hdf5::SimulationFileprotected
arbitraryH5(byte *ptr)lm::io::hdf5::SimulationFilevirtual
arbitraryH5Lookup(byte *in, byte *&out, size_t &out_sz)lm::io::hdf5::SimulationFilevirtual
checkpoint()lm::io::hdf5::SimulationFilevirtual
close()lm::io::hdf5::SimulationFilevirtual
closeAllReplicates()lm::io::hdf5::SimulationFilevirtual
closeReplicate(unsigned int replicate)lm::io::hdf5::SimulationFilevirtual
closeReplicateHandles(ReplicateHandles *handles)lm::io::hdf5::SimulationFileprotectedvirtual
create(const string filename)lm::io::hdf5::SimulationFilestatic
create(const char *filename)lm::io::hdf5::SimulationFilestatic
create(const string filename, unsigned int numberSpecies)lm::io::hdf5::SimulationFilestatic
create(const char *filename, unsigned int numberSpecies)lm::io::hdf5::SimulationFilestatic
create(const char *filename, bool initializeModel, unsigned int numberSpecies=0)lm::io::hdf5::SimulationFilestatic
createReplicateHandles(string replicateString)lm::io::hdf5::SimulationFileprotectedvirtual
CURRENT_VERSIONlm::io::hdf5::SimulationFilestatic
filelm::io::hdf5::SimulationFileprotected
filenamelm::io::hdf5::SimulationFileprotected
flush()lm::io::hdf5::SimulationFilevirtual
getDiffusionModel(lm::io::DiffusionModel *diffusionModel)lm::io::hdf5::SimulationFilevirtual
getDiffusionModelLattice(lm::io::DiffusionModel *diffusionModel, byte *lattice, size_t latticeMaxSize, byte *latticeSites, size_t latticeSitesMaxSize)lm::io::hdf5::SimulationFilevirtual
getDiffusionModelLattice(lm::io::DiffusionModel *diffusionModel, lm::rdme::Lattice *lattice)lm::io::hdf5::SimulationFilevirtual
getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice *lattice)lm::io::hdf5::SimulationFilevirtual
getLatticeTimes(unsigned int replicate)lm::io::hdf5::SimulationFilevirtual
getParameter(string key, string defaultValue="")lm::io::hdf5::SimulationFilevirtual
getParameters()lm::io::hdf5::SimulationFilevirtual
getParticleCounts(unsigned int replicate, unsigned int latticeIndex)lm::io::hdf5::SimulationFile
getReactionModel(lm::io::ReactionModel *reactionModel)lm::io::hdf5::SimulationFilevirtual
getSiteTypeNames()lm::io::hdf5::SimulationFile
getSpatialModel(lm::io::SpatialModel *model)lm::io::hdf5::SimulationFilevirtual
getSpeciesCounts(unsigned int replicate)lm::io::hdf5::SimulationFile
getSpeciesCountTimes(unsigned int replicate)lm::io::hdf5::SimulationFile
getSpeciesNames()lm::io::hdf5::SimulationFile
isValidFile(const string filename)lm::io::hdf5::SimulationFilestatic
isValidFile(const char *filename)lm::io::hdf5::SimulationFilestatic
loadModel()lm::io::hdf5::SimulationFileprotectedvirtual
loadParameters()lm::io::hdf5::SimulationFileprotectedvirtual
makeNewDataset(H5MetaData *header, byte *data)lm::io::hdf5::SimulationFileprotected
MAX_REACTION_RATE_CONSTANTSlm::io::hdf5::SimulationFilestatic
MAX_SHAPE_PARAMETERSlm::io::hdf5::SimulationFilestatic
MIN_VERSIONlm::io::hdf5::SimulationFilestatic
modelGrouplm::io::hdf5::SimulationFileprotected
modelLoadedlm::io::hdf5::SimulationFileprotected
numberSpecieslm::io::hdf5::SimulationFileprotected
open()lm::io::hdf5::SimulationFileprotectedvirtual
openGroups()lm::io::hdf5::SimulationFileprotectedvirtual
openReplicate(unsigned int replicate)lm::io::hdf5::SimulationFilevirtual
openReplicateHandles(unsigned int replicate)lm::io::hdf5::SimulationFileprotectedvirtual
openReplicateslm::io::hdf5::SimulationFileprotected
parameterMaplm::io::hdf5::SimulationFileprotected
parametersGrouplm::io::hdf5::SimulationFileprotected
parseParameter(hid_t location_id, const char *attr_name, const H5A_info_t *ainfo, void *op_data)lm::io::hdf5::SimulationFileprotectedstatic
readAttr(H5Lookup *req, byte *&data, size_t &sz)lm::io::hdf5::SimulationFileprotected
readDataset(H5Lookup *req, byte *&data, size_t &sz)lm::io::hdf5::SimulationFileprotected
replicateExists(unsigned int replicate)lm::io::hdf5::SimulationFilevirtual
setDiffusionModel(lm::io::DiffusionModel *diffusionModel)lm::io::hdf5::SimulationFilevirtual
setDiffusionModelLattice(lm::io::DiffusionModel *m, uint8_t *lattice, uint8_t *latticeSites)lm::io::hdf5::SimulationFilevirtual
setDiffusionModelLattice(lm::io::DiffusionModel *m, uint32_t *lattice, uint8_t *latticeSites)lm::io::hdf5::SimulationFilevirtual
setDiffusionModelLattice(lm::io::DiffusionModel *m, lm::rdme::ByteLattice *lattice)lm::io::hdf5::SimulationFilevirtual
setDiffusionModelLattice(lm::io::DiffusionModel *m, lm::rdme::IntLattice *lattice)lm::io::hdf5::SimulationFilevirtual
setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes *speciesCounts)lm::io::hdf5::SimulationFilevirtual
setParameter(string key, string value)lm::io::hdf5::SimulationFilevirtual
setReactionModel(lm::io::ReactionModel *reactionModel)lm::io::hdf5::SimulationFilevirtual
setSpatialModel(lm::io::SpatialModel *model)lm::io::hdf5::SimulationFilevirtual
SimulationFile(const string filename)lm::io::hdf5::SimulationFile
SimulationFile(const char *filename)lm::io::hdf5::SimulationFile
simulationsGrouplm::io::hdf5::SimulationFileprotected
versionlm::io::hdf5::SimulationFileprotected
write3DLattice_U8LE(const char *path, uint8_t *data, unsigned int x, unsigned int y, unsigned int z)lm::io::hdf5::SimulationFileprotected
writeParticleLattice_U32LE(hid_t handle, const char *path, unsigned int *data, unsigned int x, unsigned int y, unsigned int z, unsigned int w)lm::io::hdf5::SimulationFileprotected
writeParticleLattice_U8LE(const char *path, uint8_t *data, unsigned int x, unsigned int y, unsigned int z, unsigned int w)lm::io::hdf5::SimulationFileprotected
~SimulationFile()lm::io::hdf5::SimulationFilevirtual