Here is a list of all class members with links to the classes they belong to:
- s -
- s_edge
: ComputeMsmMgr
- SALT
: PDBAtom
- saveComputeMap()
: ComputeMap
- saveComputeMapChanges()
: WorkDistrib
- saved_lattice
: ComputePmeMgr
- saved_sequence
: ComputePmeMgr
- saveForce()
: Sequencer
, HomePatch
- saveMolDataPointers()
: Node
- savePairlists
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
, nonbonded
, Flags
- savePatchMap()
: WorkDistrib
- saveResults()
: ComputeFmmSerial
, ComputeGBISser
, ComputeMsm
, ComputeMsmSerial
, ComputeQM
, ComputeExt
- saveTotalForces()
: ComputeGlobal
- scalable_group_coms()
: colvarproxy_namd
- scale
: ExclElem
, TholeElem
, GridforceFullBaseGrid
, GridforceLiteGrid
, CudaBond
, CudaAngle
, CudaDihedral
, CudaCrossterm
, Lattice
, Matrix4
- SCALE
: PDBData
- Scale()
: AVector
- scale
: AngleElem
, AnisoElem
, BondElem
, CrosstermElem
, DihedralElem
, GromacsPairElem
, ImproperElem
- scale14
: ComputeNonbondedUtil
, SimParameters
- scale_d2V
: GridforceFullSubGrid
- scale_d3V
: GridforceFullSubGrid
- scale_dV
: GridforceFullSubGrid
- scalePositionsVelocities()
: Sequencer
- scaleVelocities()
: Sequencer
- scaling
: ComputeNonbondedUtil
, GBISParam< 2 >
- scan()
: PDBData
- SceeScaleFactor
: AmberParm7Reader::Ambertoppar
- SCHAIN
: PDBAtom
- ScnbScaleFactor
: AmberParm7Reader::Ambertoppar
- scor_table
: ComputeNonbondedUtil
- Screen
: AmberParm7Reader::Ambertoppar
- script_obj_to_str()
: colvarproxy_namd
- script_obj_to_str_vector()
: colvarproxy_namd
- scriptArg1
: SimParameters
- scriptArg2
: SimParameters
- scriptArg3
: SimParameters
- scriptArg4
: SimParameters
- scriptArg5
: SimParameters
- scriptBarrier
: ControllerBroadcasts
, Node
- scriptIntArg1
: SimParameters
- scriptIntArg2
: SimParameters
- scriptParam()
: Node
- scriptSet()
: SimParameters
- scriptStringArg1
: SimParameters
- scriptStringArg2
: SimParameters
- ScriptTcl
: Controller
, NamdState
, ScriptTcl
- sdScaling
: SimParameters
- second
: intpair
- secProc
: QMGrpCalcMsg
- secProcOn
: QMGrpCalcMsg
- segid
: refSelStr
- segmentname()
: PDBAtom
- segname
: seg_resid
- segName
: qmSolvData
- segNameIdx
: BasicAtomInfo
, OutputAtomRecord::shortVals
- select()
: ComputeNonbondedUtil
, ComputePmeUtil
- selectConstraintsOn
: SimParameters
- SELEMENT
: PDBAtom
- selfOn
: ComputePmeUtil
- send
: msm::PatchDiagram
, BroadcastMgr
- send_all_ungrid()
: PmeZPencil
- send_contributeHostDeviceLDB()
: WorkDistrib
- send_energies()
: GlobalMasterIMD
- send_fcoords()
: GlobalMasterIMD
- send_GoMolecule()
: Molecule
- send_initHostDeviceLDB()
: WorkDistrib
- send_Molecule()
: Molecule
- send_order
: PmePencil< T >
- 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
- sendAcross
: msm::BlockDiagram
- sendAssignPatchesOnPe()
: ComputeMgr
- sendAtoms()
: PatchMgr
- sendAtomsThread
: ParallelIOMgr
- sendAtomsToHomePatchProcs()
: ParallelIOMgr
- sendAtomsToNeighbor()
: ComputePmeCUDADevice
- sendAtomsToNeighbors()
: ComputePmeCUDADevice
- sendbcast
: DataExchanger
- 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
- sendDataHelper_errors
: ComputePmeMgr
- sendDataHelper_lattice
: ComputePmeMgr
- sendDataHelper_sequence
: ComputePmeMgr
- sendDataHelper_sourcepe
: ComputePmeMgr
- sendDataPart()
: ComputePmeMgr
- sendDataStream()
: CollectionMgr
- sendDown
: msm::BlockDiagram
- 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
: msm::BlockDiagram
, 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
- sendUp
: msm::BlockDiagram
- sendUpCharge()
: MsmBlock
, MsmC1HermiteBlock
- sendYieldDevice()
: ComputeMgr
- SEPTIC
: ComputeMsmMgr
- SEPTIC3
: ComputeMsmMgr
- seq
: CollectVectorMsg
, CollectionMaster::CollectVectorInstance
, CollectVectorVarMsg
, CollectionMgr::CollectVectorInstance
, ComputeGlobalResultsMsg
, CollectProxyVectorInstance
- seqnum
: GridMsg
- SEQRES
: PDBData
- sequence
: GBISCoordMsg
, msm::PatchData
, MsmGridCutoffKernel< Vtype, Mtype >
, MsmBlockKernel< Vtype, Mtype >
, GBISParamStruct
, PmeGridMsg
, PmeTransMsg
, ComputePmeMgr::cuda_submit_charges_args
, PmePencil< T >
, Flags
, Compute
- sequenceNumber
: ReductionSubmitMsg
, ReductionSetData
- Sequencer
: HomePatch
, Sequencer
- sequencerThreads
: LdbCoordinator
- serialnumber()
: PDBAtom
- set()
: msm::IndexRange
, msm::GridFixed< T, N >
, msm::Grid< T >
, msm::FoldFactor
, ParseOptions
, Vector
- Set()
: AVector
- set()
: StringList
, Lattice
, C1Vector
, C1Matrix
- 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
- SetEqual
: AVector
- 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()
: ARestraint
, AFixedAngleRestraint
, ABoundAngleRestraint
, AFixedDiheRestraint
- SetRefDist()
: ARestraint
, ABoundPosRestraint
, AFixedDistRestraint
, ABoundDistRestraint
- SetRefPos()
: ARestraint
, AFixedPosRestraint
, ABoundPosRestraint
- setReplicaDcdIndex()
: Output
- setSafeNoDestruction()
: UniqueSetRaw< Elem >
- setScript()
: Node
- setSendSpanning()
: ProxyMgr
- setSpanningTree()
: ProxyPatch
- SetStartAngle()
: ARestraint
, AForcingAngleRestraint
, AForcingDiheRestraint
- SetStartDist()
: ARestraint
, AForcingDistRestraint
- SetStartPos()
: ARestraint
, AForcingPosRestraint
- SetStartStep()
: ALambdaControl
- SetStopAngle()
: ARestraint
, AForcingAngleRestraint
, AForcingDiheRestraint
- SetStopDist()
: ARestraint
, AForcingDistRestraint
- SetStopPos()
: ARestraint
, AForcingPosRestraint
- SetStopStep()
: ALambdaControl
- SetTask()
: ALambdaControl
- setTileListVirialEnergyGBISLength()
: CudaTileListKernel
- setTileListVirialEnergyLength()
: CudaTileListKernel
- settleList
: HomePatch
- 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()
: ARestraint
, ABoundDiheRestraint
- setupSections()
: MsmBlock
, MsmC1HermiteBlock
- setupStencils()
: MsmBlockKernel< Vtype, Mtype >
- setupWeights()
: MsmGridCutoffKernel< Vtype, Mtype >
- SFOOT
: PDBAtom
- sglower
: ComputeMsmMgr
- sh
: MoaData
- shared()
: ResizeArray< T >
- SHEET
: PDBData
- shuffleNext()
: GBISResults< 3 >
, GBISResults< 1 >
, GBISInput< 1 >
, GBISInput< 2 >
, GBISResults< 2 >
, GBISInput< 3 >
- shx
: ComputeMsmMgr
, TileListVirialEnergy
- shx_1
: ComputeMsmMgr
- shy
: ComputeMsmMgr
, TileListVirialEnergy
- shy_1
: ComputeMsmMgr
- shz
: TileListVirialEnergy
, ComputeMsmMgr
- shz_1
: ComputeMsmMgr
- SIGATM
: PDBData
- sigma
: vdw_val
, vdw_params
- sigma14
: vdw_params
, vdw_val
- sigmaRep
: go_val
- sign()
: ComputeMsmMgr
- SIGUIJ
: PDBData
- SimParameters
: Output
, SimParameters
- simParameters
: nonbonded
, Node
- simParams
: Controller
- simparams
: colvarproxy_namd
- simParams
: Sequencer
- SimpleBroadcastObject()
: SimpleBroadcastObject< T >
- simulatedNodeSize
: SimParameters
- simulatedPEs
: SimParameters
- simulateInitialMapping
: SimParameters
- singleTopology
: SimParameters
- SINSERT
: PDBAtom
- SITE
: PDBData
- size()
: AtomTable
, GridforceFullBaseGrid
, ImproperElem
, CollectVectorVarMsg
, AngleElem
, AnisoElem
, BondElem
, CrosstermElem
, DihedralElem
, GromacsPairElem
, ExclElem
, TholeElem
, DataMessage
, GridforceLiteGrid
, qmSolvData
, HashPool< T >
, BondTable
, AngleTable
, DihedralTable
, ResizeArray< T >
, UniqueSet< Elem >
, UniqueSetRaw< Elem >
- size1
: PmeKSpaceCompute
- size2
: PmeKSpaceCompute
- size3
: PmeKSpaceCompute
- size_nopad
: GridforceFullBaseGrid
- sizeGrid()
: PatchMap
- sizeList
: MovePatchAtomsMsg
- sizes
: ProxyTree
- skip()
: ComputeNonbondedMIC
, Box< Owner, Data >
, ComputeNonbondedCUDA
, ComputePmeCUDAMgr
, PmePencilXYZ
, PmePencilZ
, Random
- skipPatchesOnPe()
: CudaComputeNonbonded
- skipWork()
: LdbCoordinator
- slave
: ComputeNonbondedCUDA::patch_record
- slaveIndex
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- slavePes
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- slaves
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- sldata
: ParseOptions::DataElement
- slow
: Results
- slow_forces
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- slow_forces_size
: ComputeNonbondedCUDA
- slow_table
: ComputeNonbondedUtil
- slowForce
: GBISForceMsg
- slowFreq
: Controller
, Sequencer
- slowVirialIndex_XX
: ComputeBondedCUDAKernel
- slowVirialIndex_XY
: ComputeBondedCUDAKernel
- slowVirialIndex_XZ
: ComputeBondedCUDAKernel
- slowVirialIndex_YX
: ComputeBondedCUDAKernel
- slowVirialIndex_YY
: ComputeBondedCUDAKernel
- slowVirialIndex_YZ
: ComputeBondedCUDAKernel
- slowVirialIndex_ZX
: ComputeBondedCUDAKernel
- slowVirialIndex_ZY
: ComputeBondedCUDAKernel
- slowVirialIndex_ZZ
: ComputeBondedCUDAKernel
- slptr
: ParseOptions::DataElement
- smax
: ComputeMsmMgr
, MsmInitMsg
- SMDDir
: SimParameters
- SMDFile
: SimParameters
- SMDk
: SimParameters
- SMDk2
: SimParameters
- SMDOn
: SimParameters
- SMDOutputFreq
: SimParameters
- SMDVel
: SimParameters
- smin
: ComputeMsmMgr
, MsmInitMsg
- smooth2_avg
: ControllerState
- smooth2_avg2
: Controller
- smoothDist
: GBISParam< 2 >
- SNAME
: PDBAtom
- SOCC
: PDBAtom
- sock
: GlobalMasterIMD
- Solty
: parm
, AmberParm7Reader::Ambertoppar
- soluteScalingAll
: SimParameters
- soluteScalingFactor
: SimParameters
- soluteScalingFactorCharge
: SimParameters
- soluteScalingFactorVdw
: SimParameters
- soluteScalingOn
: SimParameters
- solve()
: CudaPmeKSpaceCompute
, PmeKSpaceCompute
- solvent_dielectric
: SimParameters
- sort()
: SortableResizeArray< Type >
, SortedArray< Type >
, SortableResizeArray< Type >
- SortableResizeArray()
: SortableResizeArray< Type >
- SortableResizeArray< Elem >
: ResizeArrayRaw< Type >
- sortAndSplit()
: TopoManagerWrapper
- sortdims
: TopoManagerWrapper::pe_sortop_topo
- SortedArray()
: SortedArray< Type >
- SortedArray< Elem >
: ResizeArrayRaw< Type >
- sortExclOffset()
: ExclSigInfo
- sortop_base()
: sortop_base
- sortop_x()
: sortop_x
- sortop_y()
: sortop_y
- sortop_z()
: sortop_z
- sortOrder
: CompAtomExt
- sortPmePes()
: WorkDistrib
- sortTupleSigIndices()
: AtomSigInfo
- sortValue
: __sort_entry
- SOURCE
: PDBData
- sourceNode
: MsmSerialCoordMsg
, FmmSerialCoordMsg
, PmeTransMsg
, ReductionRegisterMsg
, ReductionSubmitMsg
, ExtCoordMsg
, PmeGridMsg
, QMPntChrgMsg
, QMCoordMsg
, GBISCoordMsg
, PmeUntransMsg
- specialTracing
: Node
- sphericalBCexp1
: SimParameters
- sphericalBCexp2
: SimParameters
- sphericalBCk1
: SimParameters
- sphericalBCk2
: SimParameters
- sphericalBCOn
: SimParameters
- sphericalBCr1
: SimParameters
- sphericalBCr2
: SimParameters
- sphericalCenter
: SimParameters
- sphericalConstraintsOn
: SimParameters
- sphericalConstrCenter
: SimParameters
- Split
: ComputeMsmMgr
- split()
: Random
, NL_Msm_t
, ComputeMsmMgr
- splitComputes()
: ComputeMgr
, NamdHybridLB
- splitComputes2()
: ComputeMgr
- splitPatch
: SimParameters
- splitting()
: ComputeMsmMgr
- spos
: pe_sortop_coord_y
, pe_sortop_coord_x
- spreadCharge()
: ComputePmeCUDADevice
, PmeRealSpaceCompute
, CudaPmeRealSpaceCompute
- sprint()
: PDBUnknown
, PDBData
, PDBAtom
- sprintcol()
: PDBData
- SPRSDE
: PDBData
- sptr
: ParseOptions::DataElement
- square()
: ComputeNonbondedUtil
- src
: DataMessage
- srcPart
: ReplicaDcdDataMsg
, DataMessage
, ReplicaDcdInitMsg
- srcPatchID
: MigrateAtomsMsg
, MigrateAtomsCombinedMsg
- srcRank
: ClusterSizeMsg
, ClusterCoorMsg
- srcY
: PmeAtomPencilMsg
, PmeForcePencilMsg
- srcZ
: PmeAtomPencilMsg
, PmeForcePencilMsg
- SRESNAME
: PDBAtom
- SRESSEQ
: PDBAtom
- srx_x
: ComputeMsmMgr
- srx_y
: ComputeMsmMgr
- srx_z
: ComputeMsmMgr
- sry_x
: ComputeMsmMgr
- sry_y
: ComputeMsmMgr
- sry_z
: ComputeMsmMgr
- srz_x
: ComputeMsmMgr
- srz_y
: ComputeMsmMgr
- srz_z
: ComputeMsmMgr
- ss_index
: Molecule
- ss_num_vdw_params
: Molecule
- ss_vdw_type
: Molecule
- SSBOND
: PDBData
- SSEGNAME
: PDBAtom
- SSERIAL
: PDBAtom
- sSet
: OutputAtomRecord
- star()
: floatcomplex
- Start
: PDBAtom
- start
: PmeGridMsg
- startHPM()
: Node
- startNextRoundOutputForce()
: CollectionMaster
- startNextRoundOutputPos()
: CollectionMaster
- startNextRoundOutputVel()
: CollectionMaster
- startPE
: LocalLBInfoMsg
- startup()
: Node
- startWork()
: LdbCoordinator
- state
: Controller
, Controller::checkpoint
, Node
- staticAtomAssignment
: SimParameters
- staticCompare()
: HashPoolAdaptorT< T >
, ProxyUsageKey
- staticHash()
: ProxyUsageKey
, HashPoolAdaptorT< T >
- staticMigrateFn()
: LdbCoordinator
- staticQueryEstLoadFn()
: LdbCoordinator
- staticReceiveAtSync()
: LdbCoordinator
- staticResumeFromSync()
: LdbCoordinator
- staticStatsFn()
: LdbCoordinator
- statsOn
: SimParameters
- status()
: NamdState
, UniqueSetIter< Type >
, atom_constants
, AtomCstInfo
, CollectVectorVarMsg
, FullAtom
- STEMPF
: PDBAtom
- stencil
: InterpParams_t
- stencil_1d()
: ComputeMsmMgr
- stencil_1d_c1hermite()
: ComputeMsmMgr
- step
: GlobalMaster
, ComputeLCPO
, Flags
, ComputeNonbondedCUDA
, nonbonded
, ComputeNonbondedMIC
, ComputeGlobalDataMsg
- stepInFullRun
: Controller
- stepsPerCycle
: SimParameters
- stepsPerLdbCycle
: LdbCoordinator
- stirAxis
: SimParameters
- stirFilename
: SimParameters
- stirK
: SimParameters
- stirOn
: SimParameters
- stirPivot
: SimParameters
- stirStartingTheta
: SimParameters
- stirVel
: SimParameters
- stochRescale_count
: Controller
, Sequencer
- stochRescaleCoefficient()
: Controller
, ControllerBroadcasts
- stochRescaleFreq
: SimParameters
- stochRescaleHeat
: SimParameters
- stochRescaleOn
: SimParameters
- stochRescalePeriod
: SimParameters
- stochRescaleTemp
: SimParameters
- stochRescaleTimefactor
: Controller
- stochRescaleVelocities()
: Sequencer
, Controller
- stopHPM()
: Node
- storeCompute()
: ComputeMap
- storeComputeMap
: SimParameters
- storePmeForceMsg()
: ComputePmeCUDA
- storeQMRes()
: ComputeQMMgr
- strainRate
: SimParameters
- strainRate2
: SimParameters
- strainRate_old
: Controller
- strategy()
: Rebalancer
- Strategy()
: NamdCentLB
- strategyName
: CollectLoadsMsg
, Rebalancer
- stream
: InitDeviceMsg2
- String
: AmberParm7Reader::FortranData
- STRING
: ParseOptions::DataElement
- String
: AmberParm7Reader::FortranData
- STRINGLIST
: ParseOptions::DataElement
- StringList()
: StringList
- STYPE
: PDBAtom
- subcube_total
: NL_Msm_t
- subgrid
: MsmBlockKernel< Vtype, Mtype >
, ComputeMsmMgr
, msm::PatchData
- subgrid_c1hermite
: msm::PatchData
, ComputeMsmMgr
- subgridIdx
: GridforceFullSubGrid
- subgrids
: GridforceFullBaseGrid
- subgrids_flat
: GridforceFullMainGrid
- submit()
: SubmitReduction
- submit_reduction
: Controller
- submitCollections()
: Sequencer
- submitData()
: CollectionMaster::CollectVectorSequence
, CollectionMgr::CollectVectorSequence
, CollectProxyVectorSequence
- submitForces()
: CollectionMgr
- submitHalfstep()
: Sequencer
- submitLoadStats
: Flags
, HomePatch
- submitMinimizeReductions()
: Sequencer
- submitMomentum()
: Sequencer
- submitPositions()
: CollectionMgr
- submitPressureProfileData()
: ComputeNonbondedUtil
- SubmitReduction
: ReductionMgr
- submitReductionData()
: AngleElem
, GromacsPairElem
, TholeElem
, CrosstermElem
, ComputeNonbondedUtil
, ImproperElem
, AnisoElem
, BondElem
, ExclElem
, DihedralElem
- submitReductions()
: PmePencilZ
, ComputePmeMgr
, Sequencer
, PmePencilXYZ
- submitsRecorded
: ReductionSetData
- submitsRegistered
: ReductionSet
- submitVelocities()
: CollectionMgr
- subscribe()
: BroadcastMgr
- subtractVirialContrib()
: ComputeMsmMgr
- Sum_dU_dLambdas()
: ARestraintManager
- sum_of_squared_gaussians()
: Random
- sumReducedPotential()
: MsmBlock
, MsmC1HermiteBlock
- sumx
: eABF1D
- sumx2
: eABF1D
- surface_tension
: SimParameters
- surfaceTensionTarget
: SimParameters
- suspend()
: BackEnd
, Sequencer
- suspended
: BroadcastClient
- suspendFor()
: BroadcastClient
- suspiciousAlchBonds
: Molecule
- swap
: msm::Array< T >
, ResizeArray< T >
- swdist
: QMGrpCalcMsg
- switching
: QMGrpCalcMsg
- switchingActive
: SimParameters
- switchingDist
: SimParameters
- switchOn
: ComputeNonbondedUtil
- switchOn2
: ComputeNonbondedUtil
- switchOn_1
: ComputeNonbondedUtil
- switchOn_f
: ComputeNonbondedUtil
- switchType
: QMGrpCalcMsg
- SX
: PDBAtom
- sx_shx
: ComputeMsmMgr
- SY
: PDBAtom
- sy_shy
: ComputeMsmMgr
- symmetric
: Tensor
- symmetryFile
: SimParameters
- symmetryFirstFullStep
: SimParameters
- symmetryFirstStep
: SimParameters
- symmetryk
: SimParameters
- symmetrykfile
: SimParameters
- symmetryLastFullStep
: SimParameters
- symmetryLastStep
: SimParameters
- symmetryMatrixFile
: SimParameters
- symmetryOn
: SimParameters
- symmetryScaleForces
: SimParameters
- Sync()
: Sync
- sync
: BOCgroup
, CkPrintf_stringbuf
- SZ
: PDBAtom
- sz_shz
: ComputeMsmMgr