- s -
- saveComputeMap()
: ComputeMap
- saveComputeMapChanges()
: WorkDistrib
- saveForce()
: Sequencer
, HomePatch
- saveMolDataPointers()
: Node
- savePatchMap()
: WorkDistrib
- saveResults()
: ComputeFmmSerial
, ComputeGBISser
, ComputeMsm
, ComputeMsmSerial
, ComputeQM
, ComputeExt
- saveTotalForces()
: ComputeGlobal
- scalable_group_coms()
: colvarproxy_namd
- scale()
: Lattice
, Matrix4
- Scale()
: AVector
- scalePositionsVelocities()
: Sequencer
- scaleVelocities()
: Sequencer
- scan()
: PDBData
- script_obj_to_str()
: colvarproxy_namd
- script_obj_to_str_vector()
: colvarproxy_namd
- scriptBarrier()
: Node
- scriptParam()
: Node
- scriptSet()
: SimParameters
- ScriptTcl()
: ScriptTcl
- segmentname()
: PDBAtom
- select()
: ComputeNonbondedUtil
, ComputePmeUtil
- send()
: BroadcastMgr
- send_all_ungrid()
: PmeZPencil
- send_contributeHostDeviceLDB()
: WorkDistrib
- send_energies()
: GlobalMasterIMD
- send_fcoords()
: GlobalMasterIMD
- send_GoMolecule()
: Molecule
- send_initHostDeviceLDB()
: WorkDistrib
- send_Molecule()
: Molecule
- send_Parameters()
: Parameters
- send_setDeviceLDBParams()
: WorkDistrib
- send_SimParameters()
: SimParameters
- send_subset_trans()
: PmeZPencil
, PmeYPencil
- send_subset_ungrid()
: PmeZPencil
- send_subset_untrans()
: PmeYPencil
, PmeXPencil
- send_trans()
: PmeZPencil
, PmeYPencil
- send_ungrid()
: PmeZPencil
- send_untrans()
: PmeYPencil
, PmeXPencil
- sendAssignPatchesOnPe()
: ComputeMgr
- sendAtoms()
: PatchMgr
- sendAtomsToHomePatchProcs()
: ParallelIOMgr
- sendAtomsToNeighbor()
: ComputePmeCUDADevice
- sendAtomsToNeighbors()
: ComputePmeCUDADevice
- sendBuildCudaExclusions()
: ComputeMgr
- sendBuildCudaForceTable()
: ComputeMgr
- sendBuildMICForceTable()
: ComputeMgr
- sendCharge()
: msm::PatchData
- sendChargeC1Hermite()
: msm::PatchData
- sendChargeGridReady()
: ComputePmeMgr
- sendCheckpointAck()
: PatchMgr
- sendCheckpointLoad()
: PatchMgr
- sendCheckpointReq()
: Node
, PatchMgr
- sendCheckpointStore()
: PatchMgr
- sendCollectLoads()
: LdbCoordinator
- sendComputeDPMEData()
: ComputeMgr
- sendComputeDPMEResults()
: ComputeMgr
- sendComputeEwaldData()
: ComputeMgr
- sendComputeEwaldResults()
: ComputeMgr
- sendComputeGlobalConfig()
: ComputeMgr
- sendComputeGlobalData()
: ComputeMgr
- sendComputeGlobalResults()
: ComputeMgr
- sendComputeMap()
: WorkDistrib
- sendCreateNonbondedCUDASlave()
: ComputeMgr
- sendCreateNonbondedMICSlave()
: ComputeMgr
- sendData()
: ComputePmeMgr
- sendDataHelper()
: ComputePmeMgr
, NodePmeMgr
- sendDataPart()
: ComputePmeMgr
- sendDataStream()
: CollectionMgr
- sendDownPotential()
: MsmBlock
, MsmC1HermiteBlock
- sendEnableEarlyExit()
: Node
- sendEnableExitScheduler()
: Node
- sendExchangeMsg()
: PatchMgr
- sendExchangeReq()
: PatchMgr
- sendFinishPatchesOnPe()
: ComputeMgr
- sendFinishPatchOnPe()
: ComputeMgr
- sendFinishReductions()
: ComputeMgr
- sendForcesToNeighbors()
: ComputePmeCUDADevice
- sendForcesToPatch()
: ComputePmeCUDADevice
- sendLaunchWork()
: ComputeMgr
- sendMessage()
: Communicate
- sendMessageEnqueueWork()
: ComputeMgr
- sendMICPEData()
: ComputeMgr
- sendMigrationMsgs()
: PatchMgr
- sendMovePatches()
: PatchMgr
- sendNodeAwareSpanningTree()
: HomePatch
, ProxyMgr
- sendNodeAwareSpanningTreeToHomePatch()
: ProxyMgr
- sendNonbondedCUDASlaveEnqueue()
: ComputeMgr
- sendNonbondedCUDASlaveEnqueuePatch()
: ComputeMgr
- sendNonbondedCUDASlaveReady()
: ComputeMgr
- sendNonbondedCUDASlaveSkip()
: ComputeMgr
- sendNonbondedMICSlaveEnqueue()
: ComputeMgr
- sendNonbondedMICSlaveReady()
: ComputeMgr
- sendNonbondedMICSlaveSkip()
: ComputeMgr
- sendOneHomePatch()
: PatchMgr
- sendOpenBoxesOnPe()
: ComputeMgr
- sendPatch()
: MsmBlock
, MsmC1HermiteBlock
- sendPatchMap()
: WorkDistrib
- sendPencils()
: ComputePmeMgr
- sendPencilsHelper()
: ComputePmeMgr
, NodePmeMgr
- sendPencilsPart()
: ComputePmeMgr
- sendProxies()
: HomePatch
, ProxyMgr
- sendProxyAll()
: ProxyMgr
- sendProxyData()
: ProxyMgr
- sendProxyList()
: NodeProxyMgr
- sendProxyListInfo()
: NodeProxyMgr
- sendResult()
: ProxyMgr
- sendResults()
: ProxyMgr
- sendSkipPatchesOnPe()
: ComputeMgr
- sendSpanningTree()
: HomePatch
, ProxyMgr
- sendSpanningTrees()
: ProxyMgr
- sendSpanningTreeToHomePatch()
: ProxyMgr
- sendTrans()
: ComputePmeMgr
- sendTransBarrier()
: ComputePmeMgr
- sendTransSubset()
: ComputePmeMgr
- sendUngrid()
: ComputePmeMgr
- sendUngridSubset()
: ComputePmeMgr
- sendUnregisterBoxesOnPe()
: ComputeMgr
- sendUntrans()
: ComputePmeMgr
- sendUntransSubset()
: ComputePmeMgr
- sendUpCharge()
: MsmBlock
, MsmC1HermiteBlock
- sendYieldDevice()
: ComputeMgr
- sequence()
: Compute
- Sequencer()
: Sequencer
- serialnumber()
: PDBAtom
- Set()
: AVector
- set()
: StringList
, Lattice
, C1Vector
, C1Matrix
, msm::IndexRange
, msm::GridFixed< T, N >
, msm::Grid< T >
, msm::FoldFactor
, ParseOptions
, Vector
- set_all_gridvals()
: GridforceGrid
, GridforceFullMainGrid
, GridforceLiteGrid
- set_all_positions()
: PDB
- set_grid()
: GridforceFullBaseGrid
, GridforceLiteGrid
- set_gridfrc_grid()
: Molecule
- set_num_atoms()
: PmeRealSpace
- set_qm_replaceAll()
: Molecule
- set_scale()
: GridforceGrid
, GridforceFullBaseGrid
, GridforceFullMainGrid
, GridforceLiteGrid
- set_transrate()
: IMDOutput
- set_unit_system()
: colvarproxy_namd
- setall()
: ResizeArray< T >
- setBFactorData()
: Molecule
- setBlockSize()
: ObjectArena< Type >
- SetBound()
: ARestraint
, ABoundPosRestraint
, ABoundDistRestraint
, ABoundAngleRestraint
- setbounds()
: msm::IndexRange
, msm::GridFixed< T, N >
, msm::Grid< T >
- setcolumn()
: eABF
- setCompute()
: ComputeExtMgr
, ComputeFmmSerialMgr
, ComputeGBISserMgr
, ComputeMsmMgr
, ComputeMsmSerialMgr
, ComputeQMMgr
- setDataPtrsYZX()
: CudaPmeTranspose
- setDataPtrsZXY()
: CudaPmeTranspose
- setDeviceLDBParams()
: WorkDistrib
- setEmpty()
: TupleSignature
- setGBISIntrinsicRadii()
: HomePatch
- setGpuIsMine()
: DeviceCUDA
- SetGroup()
: ARestraint
- SetGroups()
: ARestraint
- setHomePatchFixedAtomNum()
: PatchMgr
- setIndexValue()
: Pairlists
- SetIntervalAngle()
: ARestraint
, ABoundDiheRestraint
- SetKf()
: ARestraint
- SetLambdaKf()
: ALambdaControl
, ARestraint
, ARestraintManager
- SetLambdaRef()
: ALambdaControl
, ARestraint
, ARestraintManager
- SetLambdas()
: ARestraintManager
- setLattice()
: GlobalMaster
, PatchMgr
- setLcpoType()
: HomePatch
- SetLowerAngle()
: ARestraint
, ABoundDiheRestraint
- setmax()
: msm::Array< T >
- setMergeGrids()
: DeviceCUDA
- setMessage()
: DataMessage
- setMgr()
: ComputeMsm
, ComputePme
- setNewNode()
: ComputeMap
- setNewNumPartitions()
: ComputeMap
- setNext()
: Entry< Elem >
, EntryGlob< Elem >
- setNode()
: ComputeMap
- SetNumAccumSteps()
: ALambdaControl
- SetNumEquilSteps()
: ALambdaControl
- setNumFixedAtoms()
: Patch
- setNumPartitions()
: ComputeMap
- setNumPatches()
: Compute
- SetNumPrintSteps()
: ALambdaControl
- SetNumRepeats()
: ALambdaControl
- SetNumSteps()
: ALambdaControl
- setOccupancyData()
: Molecule
- setOffsets()
: TupleSignature
, ExclusionSignature
- setPatchMapArrived()
: WorkDistrib
- setPencilProxy()
: ComputePmeCUDADevice
- setPlugin()
: PluginIOMgr
- setProxyTreeBranchFactor()
: ProxyMgr
- setRecvSpanning()
: ProxyMgr
- SetRefAngle()
: ABoundAngleRestraint
, AFixedDiheRestraint
, AFixedAngleRestraint
, ARestraint
- SetRefDist()
: ARestraint
, ABoundPosRestraint
, AFixedDistRestraint
, ABoundDistRestraint
- SetRefPos()
: ARestraint
, ABoundPosRestraint
, AFixedPosRestraint
- setReplicaDcdIndex()
: Output
- setSafeNoDestruction()
: UniqueSetRaw< Elem >
- setScript()
: Node
- setSendSpanning()
: ProxyMgr
- setSpanningTree()
: ProxyPatch
- SetStartAngle()
: ARestraint
, AForcingDiheRestraint
, AForcingAngleRestraint
- SetStartDist()
: ARestraint
, AForcingDistRestraint
- SetStartPos()
: ARestraint
, AForcingPosRestraint
- SetStartStep()
: ALambdaControl
- SetStopAngle()
: ARestraint
, AForcingDiheRestraint
, AForcingAngleRestraint
- SetStopDist()
: ARestraint
, AForcingDistRestraint
- SetStopPos()
: AForcingPosRestraint
, ARestraint
- SetStopStep()
: ALambdaControl
- SetTask()
: ALambdaControl
- setTileListVirialEnergyGBISLength()
: CudaTileListKernel
- setTileListVirialEnergyLength()
: CudaTileListKernel
- setup()
: colvarproxy_namd
, MsmGridCutoffKernel< Vtype, Mtype >
- setup_hgrid_1d()
: ComputeMsmMgr
- setup_periodic_blocksize()
: ComputeMsmMgr
- setupAngleValues()
: ComputeBondedCUDAKernel
- setupBondValues()
: ComputeBondedCUDAKernel
- setupCrosstermValues()
: ComputeBondedCUDAKernel
- setupDihedralValues()
: ComputeBondedCUDAKernel
- setupIDWS()
: SimParameters
- setupImproperValues()
: ComputeBondedCUDAKernel
- setupPencils()
: ComputePmeCUDAMgr
- SetUpperAngle()
: ABoundDiheRestraint
, ARestraint
- setupSections()
: MsmBlock
, MsmC1HermiteBlock
- setupStencils()
: MsmBlockKernel< Vtype, Mtype >
- setupWeights()
: MsmGridCutoffKernel< Vtype, Mtype >
- shared()
: ResizeArray< T >
- shuffleNext()
: GBISResults< 2 >
, GBISInput< 2 >
, GBISResults< 1 >
, GBISResults< 3 >
, GBISInput< 1 >
, GBISInput< 3 >
- sign()
: ComputeMsmMgr
- SimParameters()
: SimParameters
- SimpleBroadcastObject()
: SimpleBroadcastObject< T >
- size()
: UniqueSet< Elem >
, HashPool< T >
, AngleTable
, DihedralTable
, ResizeArray< T >
, UniqueSetRaw< Elem >
, AtomTable
, BondTable
- sizeGrid()
: PatchMap
- skip()
: Box< Owner, Data >
, ComputeNonbondedMIC
, PmePencilXYZ
, Random
, ComputeNonbondedCUDA
, PmePencilZ
, ComputePmeCUDAMgr
- skipPatchesOnPe()
: CudaComputeNonbonded
- skipWork()
: LdbCoordinator
- solve()
: PmeKSpaceCompute
, CudaPmeKSpaceCompute
- sort()
: SortableResizeArray< Type >
, SortedArray< Type >
- SortableResizeArray()
: SortableResizeArray< Type >
- sortAndSplit()
: TopoManagerWrapper
- SortedArray()
: SortedArray< Type >
- sortExclOffset()
: ExclSigInfo
- sortop_base()
: sortop_base
- sortop_x()
: sortop_x
- sortop_y()
: sortop_y
- sortop_z()
: sortop_z
- sortPmePes()
: WorkDistrib
- sortTupleSigIndices()
: AtomSigInfo
- split()
: Random
- splitComputes()
: ComputeMgr
, NamdHybridLB
- splitComputes2()
: ComputeMgr
- splitting()
: ComputeMsmMgr
- spreadCharge()
: PmeRealSpaceCompute
, ComputePmeCUDADevice
, CudaPmeRealSpaceCompute
- sprint()
: PDBAtom
, PDBUnknown
, PDBData
- sprintcol()
: PDBData
- square()
: ComputeNonbondedUtil
- star()
: floatcomplex
- startHPM()
: Node
- startNextRoundOutputForce()
: CollectionMaster
- startNextRoundOutputPos()
: CollectionMaster
- startNextRoundOutputVel()
: CollectionMaster
- startup()
: Node
- startWork()
: LdbCoordinator
- staticCompare()
: HashPoolAdaptorT< T >
, ProxyUsageKey
- staticHash()
: ProxyUsageKey
, HashPoolAdaptorT< T >
- staticMigrateFn()
: LdbCoordinator
- staticQueryEstLoadFn()
: LdbCoordinator
- staticReceiveAtSync()
: LdbCoordinator
- staticResumeFromSync()
: LdbCoordinator
- staticStatsFn()
: LdbCoordinator
- status()
: NamdState
, UniqueSetIter< Type >
- stencil_1d()
: ComputeMsmMgr
- stencil_1d_c1hermite()
: ComputeMsmMgr
- stochRescaleCoefficient()
: Controller
- stochRescaleVelocities()
: Controller
, Sequencer
- stopHPM()
: Node
- storeCompute()
: ComputeMap
- storePmeForceMsg()
: ComputePmeCUDA
- storeQMRes()
: ComputeQMMgr
- Strategy()
: NamdCentLB
- strategy()
: Rebalancer
- StringList()
: StringList
- submit()
: SubmitReduction
- submitCollections()
: Sequencer
- submitData()
: CollectionMgr::CollectVectorSequence
, CollectionMaster::CollectVectorSequence
, CollectProxyVectorSequence
- submitForces()
: CollectionMgr
- submitHalfstep()
: Sequencer
- submitLoadStats()
: HomePatch
- submitMinimizeReductions()
: Sequencer
- submitMomentum()
: Sequencer
- submitPositions()
: CollectionMgr
- submitPressureProfileData()
: ComputeNonbondedUtil
- submitReductionData()
: DihedralElem
, AngleElem
, TholeElem
, ImproperElem
, AnisoElem
, CrosstermElem
, BondElem
, ComputeNonbondedUtil
, ExclElem
, GromacsPairElem
- submitReductions()
: PmePencilZ
, Sequencer
, ComputePmeMgr
, PmePencilXYZ
- submitVelocities()
: CollectionMgr
- subscribe()
: BroadcastMgr
- subtractVirialContrib()
: ComputeMsmMgr
- Sum_dU_dLambdas()
: ARestraintManager
- sum_of_squared_gaussians()
: Random
- sumReducedPotential()
: MsmBlock
, MsmC1HermiteBlock
- suspend()
: BackEnd
, Sequencer
- suspendFor()
: BroadcastClient
- swap()
: ResizeArray< T >
- symmetric()
: Tensor
- Sync()
: Sync
- sync()
: CkPrintf_stringbuf