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

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

addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) overridelm::rdme::CudaByteLatticeExtendedvirtual
addParticle(lattice_size_t index, particle_t particle) overridelm::rdme::CudaByteLatticeExtendedvirtual
addParticleGPU(lattice_size_t subvolume, particle_t particle)lm::rdme::CudaByteLatticeExtendedprotected
addParticleWithSizeCheck(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle)lm::rdme::CudaByteLatticeExtendedvirtual
addParticleWithSizeCheck(lattice_size_t subvolume, particle_t particle)lm::rdme::CudaByteLatticeExtendedvirtual
allocateCudaMemory() overridelm::rdme::CudaByteLatticeExtendedprotectedvirtual
allocateMemory()lm::rdme::ByteLatticeprotectedvirtual
ByteLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite)lm::rdme::ByteLattice
ByteLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite)lm::rdme::ByteLattice
canAddParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) constlm::rdme::CudaByteLatticeExtended
canAddParticle(lattice_size_t subvolume, particle_t particle) constlm::rdme::CudaByteLatticeExtended
canAddParticleGPU(lattice_size_t subvolume, particle_t particle) constlm::rdme::CudaByteLatticeExtendedprotected
copyFromGPU() overridelm::rdme::CudaByteLatticeExtendedvirtual
copyNativeToRowMajorByte(void *destBuffer, void *sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, uint particlesPerSite, size_t bufferSize)lm::rdme::ByteLatticestatic
copyRowMajorByteToNative(void *destBuffer, void *sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, uint particlesPerSite, size_t bufferSize)lm::rdme::ByteLatticestatic
copySites(void *destBuffer, size_t latticeSize)lm::rdme::ByteLattice
copySitesNativeToRowMajorByte(void *destBuffer, void *sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, size_t bufferSize)lm::rdme::ByteLatticestatic
copySitesRowMajorByteToNative(void *destBuffer, void *sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, size_t bufferSize)lm::rdme::ByteLatticestatic
copyToGPU() overridelm::rdme::CudaByteLatticeExtendedvirtual
CudaByteLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite)lm::rdme::CudaByteLattice
CudaByteLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite)lm::rdme::CudaByteLattice
CudaByteLatticeExtended(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite, bool enableSizeChecking=true)lm::rdme::CudaByteLatticeExtended
CudaByteLatticeExtended(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite, bool enableSizeChecking=true)lm::rdme::CudaByteLatticeExtended
cudaParticleslm::rdme::CudaByteLatticeprotected
cudaParticlesCurrentlm::rdme::CudaByteLatticeprotected
cudaParticleSizes_lm::rdme::CudaByteLatticeExtendedprotected
cudaParticleSizesSize_lm::rdme::CudaByteLatticeExtendedprotected
cudaParticlesSizelm::rdme::CudaByteLatticeprotected
cudaSiteSizes_lm::rdme::CudaByteLatticeExtendedprotected
cudaSiteSizesCurrent_lm::rdme::CudaByteLatticeExtendedprotected
cudaSiteSizesSize_lm::rdme::CudaByteLatticeExtendedprotected
cudaSiteTypeslm::rdme::CudaByteLatticeprotected
cudaSiteTypesSizelm::rdme::CudaByteLatticeprotected
deallocateCudaMemory() overridelm::rdme::CudaByteLatticeExtendedprotectedvirtual
deallocateMemory()lm::rdme::ByteLatticeprotectedvirtual
findParticles(particle_t minParticleType, particle_t maxParticleType)lm::rdme::ByteLatticevirtual
getGPUMemoryDest()lm::rdme::CudaByteLatticevirtual
getGPUMemoryParticleSizes()lm::rdme::CudaByteLatticeExtendedvirtual
getGPUMemorySiteSizes()lm::rdme::CudaByteLatticeExtendedvirtual
getGPUMemorySiteTypes()lm::rdme::CudaByteLatticevirtual
getGPUMemorySizeDest()lm::rdme::CudaByteLatticeExtendedvirtual
getGPUMemorySizeLattice()lm::rdme::CudaByteLatticeExtendedvirtual
getGPUMemorySrc()lm::rdme::CudaByteLatticevirtual
getLatticeMemorySize() constlm::rdme::ByteLatticevirtual
getMaxOccupancy() constlm::rdme::ByteLatticevirtual
getMaxParticle() constlm::rdme::ByteLatticevirtual
getMaxSiteType() constlm::rdme::ByteLatticevirtual
getNearbySites(lattice_size_t xc, lattice_size_t yc, lattice_size_t zc, uint minDistance, uint maxDistance)lm::rdme::Lattice
getNeighboringSites(lattice_size_t index, lattice_size_t *neighboringIndices)lm::rdme::ByteLatticevirtual
getNumberSites() constlm::rdme::Latticevirtual
getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) constlm::rdme::ByteLatticevirtual
getOccupancy(lattice_size_t subvolume) constlm::rdme::ByteLatticevirtual
getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) constlm::rdme::ByteLatticevirtual
getParticle(lattice_size_t subvolume, site_size_t particleIndex) constlm::rdme::ByteLatticevirtual
getParticleCounts()lm::rdme::ByteLatticevirtual
getParticleLatticeView(uint8_t **particleLattice, int *Nw, int *Nz, int *Ny, int *Nx, int *Np)lm::rdme::CudaByteLatticevirtual
getParticleMemorySize() constlm::rdme::CudaByteLatticeinlinevirtual
getParticlesAtSite(lattice_size_t subvolume, particle_t *particles, site_size_t maxCount) constlm::rdme::CudaByteLatticeExtendedprotected
getParticleSize(particle_t particleType) constlm::rdme::CudaByteLatticeExtended
getParticleSizeManager() constlm::rdme::CudaByteLatticeExtended
getParticlesMemory()lm::rdme::ByteLatticeprotectedvirtual
getSiteLatticeView(uint8_t **siteLattice, int *Nz, int *Ny, int *Nx)lm::rdme::CudaByteLatticevirtual
getSitesMemory()lm::rdme::ByteLatticeprotectedvirtual
getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) constlm::rdme::ByteLatticevirtual
getSiteType(lattice_size_t subvolume) constlm::rdme::ByteLatticevirtual
getSize() constlm::rdme::Latticevirtual
getSizeBasedOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) constlm::rdme::CudaByteLatticeExtended
getSizeBasedOccupancy(lattice_size_t subvolume) constlm::rdme::CudaByteLatticeExtended
getSizeBasedOccupancyStats() constlm::rdme::CudaByteLatticeExtended
getSpacing() constlm::rdme::Latticevirtual
getXSize() constlm::rdme::Latticevirtual
getYSize() constlm::rdme::Latticevirtual
getZSize() constlm::rdme::Latticevirtual
initializeGPUSiteSizes()lm::rdme::CudaByteLatticeExtendedprotected
isGPUMemorySynchedlm::rdme::CudaByteLatticeprotected
isGPUParticleSizesSynched_lm::rdme::CudaByteLatticeExtendedprotected
isGPUSiteSizesSynched_lm::rdme::CudaByteLatticeExtendedprotected
isSizeCheckingEnabled() constlm::rdme::CudaByteLatticeExtended
Lattice(lattice_coord_t size, si_dist_t spacing)lm::rdme::Lattice
Lattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing)lm::rdme::Lattice
lm::MpdRdmeSolverExtended classlm::rdme::CudaByteLatticeExtendedfriend
maxSiteCapacity_lm::rdme::CudaByteLatticeExtendedprotected
nativeSerialize(void *destBuffer, void *lattice, size_t latticeSize)lm::rdme::ByteLatticestatic
nativeSerializeSites(void *destBuffer, void *lattice, size_t latticeSize)lm::rdme::ByteLatticestatic
numberSiteslm::rdme::Latticeprotected
particleslm::rdme::ByteLatticeprotected
print() constlm::rdme::Latticevirtual
recalculateAllSiteSizes()lm::rdme::CudaByteLatticeExtendedprotected
removeAllParticles() overridelm::rdme::CudaByteLatticeExtendedvirtual
removeParticleGPU(lattice_size_t subvolume, particle_t particle)lm::rdme::CudaByteLatticeExtendedprotected
removeParticles(lattice_size_t x, lattice_size_t y, lattice_size_t z) overridelm::rdme::CudaByteLatticeExtendedvirtual
removeParticles(lattice_size_t index) overridelm::rdme::CudaByteLatticeExtendedvirtual
rowMajorByteSerialize(void *destBuffer, void *lattice, size_t bufferSize)lm::rdme::Latticestatic
rowMajorByteSerializeSites(void *destBuffer, void *lattice, size_t bufferSize)lm::rdme::Latticestatic
rowMajorIntSerialize(void *destBuffer, void *lattice, size_t bufferSize)lm::rdme::Latticestatic
setFromRowMajorByteData(void *buffer, size_t bufferSize)lm::rdme::CudaByteLatticevirtual
setParticleSize(particle_t particleType, uint32_t size)lm::rdme::CudaByteLatticeExtended
setSitesFromRowMajorByteData(void *buffer, size_t bufferSize)lm::rdme::ByteLatticevirtual
setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site)lm::rdme::CudaByteLatticevirtual
setSiteType(lattice_size_t index, site_t site)lm::rdme::CudaByteLatticevirtual
setSizeCheckingEnabled(bool enable)lm::rdme::CudaByteLatticeExtended
siteSizes_lm::rdme::CudaByteLatticeExtendedprotected
siteTypeslm::rdme::ByteLatticeprotected
sizelm::rdme::Latticeprotected
sizeCheckingEnabled_lm::rdme::CudaByteLatticeExtendedprotected
sizeManager_lm::rdme::CudaByteLatticeExtendedprotected
spacinglm::rdme::Latticeprotected
swapSizeSrcDest()lm::rdme::CudaByteLatticeExtendedvirtual
swapSrcDest()lm::rdme::CudaByteLatticevirtual
syncSiteSizesFromGPU()lm::rdme::CudaByteLatticeExtended
updateGPUSiteSizes()lm::rdme::CudaByteLatticeExtended
updateSiteSize(lattice_size_t subvolume, particle_t particle, bool adding)lm::rdme::CudaByteLatticeExtendedprotected
validateSizeConstraints() constlm::rdme::CudaByteLatticeExtended
wordsPerSitelm::rdme::ByteLatticeprotected
~ByteLattice()lm::rdme::ByteLatticevirtual
~CudaByteLattice()lm::rdme::CudaByteLatticevirtual
~CudaByteLatticeExtended()lm::rdme::CudaByteLatticeExtendedvirtual
~Lattice()lm::rdme::Latticevirtual