File List

Here is a list of all files with brief descriptions:

[detail level 12345]

Lattice-Microbes
src
builder
Capsule.cpp
Capsule.h
CapsuleShell.cpp
CapsuleShell.h
Cone.cpp
Cone.h
Cuboid.cpp
Cuboid.h
Cylinder.cpp
Cylinder.h
Difference.cpp
Difference.h
Ellipse.cpp
Ellipse.h
Hemisphere.cpp
Hemisphere.h
Intersection.cpp
Intersection.h
LatticeBuilder.cpp
LatticeBuilder.h
Mesh.cpp
Mesh.h
Shape.cpp
Shape.h
Sphere.cpp
Sphere.h
Torus.cpp
Torus.h
Union.cpp
Union.h
UnionSet.cpp
UnionSet.h
cmd
common.cpp
common.h
lm_python.cpp
lm_sbml_import.cpp
lm_setdm.cpp
lm_setp.cpp
lm_setrm.cpp
Main-MPMPD.cpp
MainMPI.cpp
MainSA.cpp
cme
CMESolver.cpp
CMESolver.h
FluctuatingNRSolver.cpp
FluctuatingNRSolver.h
GillespieDSolver.cpp
GillespieDSolver.h
HillSwitch.cpp
HillSwitch.h
LacHillSwitch.cpp
LacHillSwitch.h
NextReactionSolver.cpp
NextReactionSolver.h
SelfRegulatingGeneSwitch.cpp
SelfRegulatingGeneSwitch.h
TwoStateExpression.cpp
TwoStateExpression.h
TwoStateHillLoopSwitch.cpp
TwoStateHillLoopSwitch.h
TwoStateHillSwitch.cpp
TwoStateHillSwitch.h
core
CheckpointSignaler.cpp
CheckpointSignaler.h
DataOutputQueue.cpp
DataOutputQueue.h
Exceptions.h
Globals.cpp
Globals.h
LocalDataOutputWorker.cpp
LocalDataOutputWorker.h
Math.h
MPIRemoteDataOutputQueue.cpp
MPIRemoteDataOutputQueue.h
Print.cpp
Print.h
ReplicateRunner.cpp
ReplicateRunner.h
ResourceAllocator.cpp
ResourceAllocator.h
runSimulation.cpp
runSimulation.h
SignalHandler.cpp
SignalHandler.h
Timer.h
Types.h
util.cpp
util.h
cuda
constant.cu
constant.cuh
ldg.h
lm_cuda.cu
lm_cuda.h
particle_size_kernels.cu
particle_size_kernels.cuh
doc
conf.py
doxy2swig.py
io
ArbitraryH5.h
lm_hdf5.h
SimulationFile.cpp
SimulationFile.h
SimulationFile_create.cpp
SimulationParameters.cpp
SimulationParameters.h
jlm
jLM
__init__.py
Analysis.py
BaseTypes.py
CME.py
CMEPostProcessing.py
ColorGen.py
DisplayUtils.py
ImageAnalysis.py
JupyterDisplay.py
LmInteract.py
LMLogger.py
ParticleSizeSupport.py
RDME.py
RDMEExtended.py
RegionBuilder.py
Solvers.py
Template.py
TexFmt.py
Types.py
units.py
lptf
Profile.h
Profile_NVTX.h
ProfileCodes.h
me
MESolver.cpp
MESolver.h
MESolverFactory.cpp
MESolverFactory.h
mpi
lm_mpi.cpp
lm_mpi.h
pylm
pyLM
__init__.py
CME.py
ipyInterface.py
LMLogger.py
RDME.py
units.py
pySTDLM
__init__.py
CellArranger.py
Cells.py
CmdUtils.py
Distributions.py
NetworkVisualization.py
OnTheFly.py
PostProcessing.py
SBMLReader.py
StandardCells.py
StandardReactions.py
StandardReactionSystems.py
rdme
dev
bit_packed_diffusion_1d_dev.cu
byte_diffusion_1d_dev.cu
byte_diffusion_1d_mgpu_dev.cu
byte_diffusion_1d_size_dev.cu
byte_diffusion_2d_dev.cu
byte_diffusion_3dw_dev.cu
byte_reaction_dev.cu
lattice_sim_1d_dev.cu
lattice_sim_2d_dev.cu
lattice_sim_3d_dev.cu
lattice_sim_3dw_dev.cu
mpd_size_kernels.cu
word_diffusion_1d_dev.cu
word_reaction_dev.cu
xor_random_dev.cu
GPUMapper
MultiGPUMapper.cu
MultiGPUMapper.h
osx_barrier.cu
osx_barrier.h
SegmentDescriptor.h
ZDivMPIGPUMapper.cu
ZDivMPIGPUMapper.h
ZDivMultiGPUMapper.cu
ZDivMultiGPUMapper.h
ByteLattice.cpp
ByteLattice.h
ByteLatticeExtended.cpp
ByteLatticeExtended.h
CudaByteLattice.cu
CudaByteLattice.h
CudaByteLatticeExtended.cu
CudaByteLatticeExtended.h
CudaIntLattice.cu
CudaIntLattice.h
IntLattice.cpp
IntLattice.h
IntMpdRdmeSolver.cu
IntMpdRdmeSolver.h
IntMpdRdmeSolverExtended.cu
IntMpdRdmeSolverExtended.h
Lattice.cpp
Lattice.h
MGPUIntMpdRdmeSolver.cu
MGPUIntMpdRdmeSolver.h
MGPUMpdRdmeSolver.cu
MGPUMpdRdmeSolver.h
MpdRdmeSolver.cu
MpdRdmeSolver.h
MpdRdmeSolverExtended.cu
MpdRdmeSolverExtended.h
MpdTestHarness.cu
MpdTestHarness.h
MPIMpdRdmeSolver.cu
MPIMpdRdmeSolver.h
NextSubvolumeSolver.cpp
NextSubvolumeSolver.h
ParticleSizeManager.cpp
ParticleSizeManager.h
RDMESolver.cpp
RDMESolver.h
reaction
ReactionQueue.h
rng
RandomGenerator.cpp
RandomGenerator.h
XORShift.cpp
XORShift.h
XORWow.cu
XORWow.h
swig
embed_lm_dot_py.py
thread
Thread.cpp
Thread.h
Worker.cpp
Worker.h
WorkerManager.cpp
WorkerManager.h
vmd
lmplugin.cpp
lmplugin_backup.cpp