Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 12345]

Ndoxy2swig
CDoxy2SWIG
NjLM
NAnalysis
CLatticeAnalysisMixin
CTrajAnalysisMixin
NBaseTypes
CNamespace
CSimObj
CSimObjs
NCME
CCMESimulation	A CME simulation that contains reactions and species
NColorGen
CColorGen
NImageAnalysis
CSvgContext
NJupyterDisplay
C_Report
CFileJupyterMixin
CJupyterDisplayMixin
NLmInteract
CLmReadMixin
CLmWriteMixin
NLMLogger
CNullHandler
NParticleSizeSupport
CParticleSizeError
CParticleSizeMixin
CParticleSizeValidator
NRDME
CFile
CSim
CSpatialModel
NRDMEExtended
CFileExtended
CSimExtended
CSpatialModelExtended
NRegionBuilder
CRegionBuilder
NSolvers
CConstBoundaryConc
NTypes
CBuilderReaction
CBuilderRegion
CBuilderSpecies
CDiffusionConst
CRateConst
CReaction
CRegion
CSpecies
CTrajRegion
CTrajSpecies
Nlm
Nbuilder
Cbounding_box	The bounds for a shape represented as a rectangular box
CCapsule	A Shape representing a cylinder with hemispherical ends
CCapsuleShell	A capsule shell Shape with a hollow inside
CCone	A Shape that represents a Cone
CCuboid	A cube-like Shape
CCylinder	A Shape representing a cylinder
CDifference	A Shape that represents a Difference between the first and second object
CEllipse
CHemisphere	A hemisphere Shape
CIntersection	A Shape that represents a Intersection of two shapes
CLatticeBuilder	A class that defines regions of a lattice based on a set of geometries defined by shapes. It also allows packing different types of particles into different regions
CParticlePlacement	A representation of a placement operation that needs to occur (i.e. where to place (siteType), what to place (particleType) and how many (count))
Cmatrix	A matrix used for rotations
CMesh	A Shape that represents a mesh
Cpoint	Type to store a position in space
CShape	Abstract base class for all the shapes in Lattice Microbes simulation builder
CSphere	A Shape that represents a Sphere
CTorus	A Shape that represents a Torus
CUnion	A Shape that represents a Union between two shapes
CUnionSet	A Shape that represents a Union of many shapes
Cvector	A vector which points in a direction
Ncme
CCMESolver
CCompetitiveMMPropensityArgs
CFirstOrderPropensityArgs
CFPTTracking
CKHillPropensityArgs
CKHillTransportPropensityArgs
CMichaelisMentenPropensityArgs
CNoncompetitiveMMPropensityArgs
CPropensityArgs
CSecondOrderPropensityArgs
CSecondOrderSelfPropensityArgs
CSpeciesLimit
CTrackedParameter
CUncompetitiveMMPropensityArgs
CZerothOrderHeavisidePropensityArgs
CZerothOrderPropensityArgs
CFluctuatingNRSolver
COUPropensityArgs
CGillespieDSolver
CHillSwitch
CLacHillSwitch
CNextReactionSolver
CSelfRegulatingGeneSwitch
COUKHillPropensityArgs
CTwoStateExpression
CTwoStateHillLoopSwitch
CTwoStateHillSwitch
CKHillPropensityArgs
Nio
Nhdf5
CHDF5Exception	Exception due to a failure in writing the HDF5 file
CIOException	Exception when input or output fails
CSimulationFile	A representation of the simulation that is used to input or output from an HDF5 file
CReplicateHandles	A handle for the different replicates that may be stored in the HDF5 file
CSimulationParameters
Nmain
CCheckpointSignaler	A type of worker thread that checkpoints at a specified interval
CDataOutputQueue	A queue class that writes out data in the order it is recieved
CDataSet	A set of data in the form of bytes to be written to disk
CLocalDataOutputWorker	A class that handles output on a particular core
CMPIRemoteDataOutputQueue	A DataOutputQueue that works for MPI jobs across various different nodes that outputs only on the "master" thread
CReplicateRunner	A thread that launches all the various replicates requested
CResourceAllocator	An object that tracks the available resources for the main simulation runner
CComputeResources	A representation for the resources for a given node
CSignalHandler	A thread safe Worker thread type that captures SIG* type signals over the various threads
Nme
CMESolver	An abstract base class for all Master Equation solvers, this is essentially a representation of "the simulation instance"
CMESolverFactory	A factory object used to create Master Equation simulation instances
Nrdme
CByteLattice	A Lattice that is based on packed bytes of memory, i.e. one byte per lattice site to hold particles
CByteLatticeExtended	Extended ByteLattice with particle size awareness
CCudaByteLattice
CCudaByteLatticeExtended	CUDA-accelerated extended ByteLattice with particle size awareness
CCudaIntLattice
Cgpu_worker_thread_int_params
Cgpu_worker_thread_params
CIntLattice	A Lattice that is based on one particle per word, with sites strided per particle
CIntMpdRdmeSolver
CIntMpdRdmeSolverExtended
CInvalidParticleException	InvalidArgException for when a particle is
CInvalidSiteException	InvalidArgException for when an index into the lattice is out of bound or does not exist
CLattice	Base class for lattice type objects
CMGPUIntMpdRdmeSolver
CMGPUMpdRdmeSolver
CMpdRdmeSolver
CMpdTestHarness
CMPIMpdRdmeSolver
CNextSubvolumeSolver
CParticleSizeException	Exception thrown when particle size constraints are violated
CParticleSizeManager	Manages particle sizes and validates site occupancy constraints
CRDMESolver
Nreaction
CReactionQueue	A queue that contains information on reaction events
CReactionEvent	Definition of a reaction event with the time to reaction and the propensity for the reaction to occur
Nrng
CRandomGenerator	Base class for random number generators in Lattice Microbes
CXORShift	A random number generator that works for a grid based on the index
CXORWow
Nthread
CPthreadException	An Exception class for handling pthread exceptions
CThread	A base class wrapping pthreads
CWorker	An actual worker Thread that runs a simulation replicate
CWorkerManager	A singleton manager that creates and manages workers that run on a processing node
CCommandLineArgumentException	Exception from a command line argument
CCUDA
CCUDADriverException
CCUDAException
CException	Base class for exceptions
CInvalidArgException	Exception for an argument to a function
CIOException	Exception when input or output fails
CMpdRdmeSolverExtended
CMPI	Handles the MPI capabilities and properties of the simulation
CMPIException	An Exception thrown when an MPI call fails
CPrint	Print messages to the console at varying levels of verbosity
NpyLM
NCME
CCMESimulation	A CME simulation that contains reactions and species
NLMLogger
CNullHandler
NRDME
CIntRDMESimulation
CRDMERegion
CRDMESimulation
NpySTDLM
NCellArranger
CCellArranger
CLooseGridArranger
CRandomArranger
CRandomSphericalArranger
CTightGridArranger
NCells
CBoxCell
CCapsuleCell
CCapsuleShellCell
CCellShape
CSphereCell
NDistributions
CParticleGenerator
CCMESolver
CCompetitiveMMPropensityArgs
CFirstOrderPropensityArgs
CFPTTracking
CKHillPropensityArgs
CKHillTransportPropensityArgs
CMichaelisMentenPropensityArgs
CNoncompetitiveMMPropensityArgs
CPropensityArgs
CSecondOrderPropensityArgs
CSecondOrderSelfPropensityArgs
CSpeciesLimit
CTrackedParameter
CUncompetitiveMMPropensityArgs
CZerothOrderHeavisidePropensityArgs
CZerothOrderPropensityArgs
CCudaByteLattice
CCudaByteLatticeExtended	CUDA-accelerated extended ByteLattice with particle size awareness
CException	Base class for exceptions
Cgpu_info
CH5Lookup
CH5MetaData
CIOException	Exception when input or output fails
CLattice	Base class for lattice type objects
Clattice_coord_t	Type to store a lattice coordinate
CMESolver	An abstract base class for all Master Equation solvers, this is essentially a representation of "the simulation instance"
CMESolverFactory	A factory object used to create Master Equation simulation instances
CMpdRdmeSolver
CMultiGPUMapper
Cneighbor_buffer
Cparticle_loc_t	Type to store a particle and position
CPrint	Print messages to the console at varying levels of verbosity
CPthreadException	An Exception class for handling pthread exceptions
CRandomGenerator	Base class for random number generators in Lattice Microbes
CRDMESolver
CReactionQueue	A queue that contains information on reaction events
CReactionEvent	Definition of a reaction event with the time to reaction and the propensity for the reaction to occur
CReplicateRunner	A thread that launches all the various replicates requested
CResourceAllocator	An object that tracks the available resources for the main simulation runner
CComputeResources	A representation for the resources for a given node
CsegmentDescriptor
CSimulationFile	A representation of the simulation that is used to input or output from an HDF5 file
CReplicateHandles	A handle for the different replicates that may be stored in the HDF5 file
CWorker	An actual worker Thread that runs a simulation replicate
CWorkerManager	A singleton manager that creates and manages workers that run on a processing node
CZDivMPIGPUMapper
CZDivMultiGPUMapper