- s -
- s_edge
: ComputeMsmMgr
- saved_lattice
: ComputePmeMgr
- saved_sequence
: ComputePmeMgr
- savePairlists
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
, nonbonded
, Flags
- scale
: AngleElem
, TholeElem
, GridforceFullBaseGrid
, AnisoElem
, GridforceLiteGrid
, CudaBond
, BondElem
, CudaAngle
, CudaDihedral
, CrosstermElem
, CudaCrossterm
, DihedralElem
, GromacsPairElem
, ImproperElem
, ExclElem
- scale14
: ComputeNonbondedUtil
, SimParameters
- scale_d2V
: GridforceFullSubGrid
- scale_d3V
: GridforceFullSubGrid
- scale_dV
: GridforceFullSubGrid
- scaling
: ComputeNonbondedUtil
, GBISParam< 2 >
- SceeScaleFactor
: AmberParm7Reader::Ambertoppar
- ScnbScaleFactor
: AmberParm7Reader::Ambertoppar
- scor_table
: ComputeNonbondedUtil
- Screen
: AmberParm7Reader::Ambertoppar
- scriptArg1
: SimParameters
- scriptArg2
: SimParameters
- scriptArg3
: SimParameters
- scriptArg4
: SimParameters
- scriptArg5
: SimParameters
- scriptBarrier
: ControllerBroadcasts
- scriptIntArg1
: SimParameters
- scriptIntArg2
: SimParameters
- scriptStringArg1
: SimParameters
- scriptStringArg2
: SimParameters
- sdScaling
: SimParameters
- second
: intpair
- secProc
: QMGrpCalcMsg
- secProcOn
: QMGrpCalcMsg
- segid
: refSelStr
- segname
: seg_resid
- segName
: qmSolvData
- segNameIdx
: BasicAtomInfo
, OutputAtomRecord::shortVals
- selectConstraintsOn
: SimParameters
- selfOn
: ComputePmeUtil
- send
: msm::PatchDiagram
- send_order
: PmePencil< T >
- sendAcross
: msm::BlockDiagram
- sendAtomsThread
: ParallelIOMgr
- sendbcast
: DataExchanger
- sendDataHelper_errors
: ComputePmeMgr
- sendDataHelper_lattice
: ComputePmeMgr
- sendDataHelper_sequence
: ComputePmeMgr
- sendDataHelper_sourcepe
: ComputePmeMgr
- sendDown
: msm::BlockDiagram
- sendPatch
: msm::BlockDiagram
- sendUp
: msm::BlockDiagram
- seq
: CollectVectorMsg
, CollectionMaster::CollectVectorInstance
, CollectVectorVarMsg
, CollectionMgr::CollectVectorInstance
, ComputeGlobalResultsMsg
, CollectProxyVectorInstance
- seqnum
: GridMsg
- sequence
: GBISCoordMsg
, msm::PatchData
, MsmGridCutoffKernel< Vtype, Mtype >
, MsmBlockKernel< Vtype, Mtype >
, GBISParamStruct
, PmeGridMsg
, PmeTransMsg
, ComputePmeMgr::cuda_submit_charges_args
, PmePencil< T >
, Flags
- sequenceNumber
: ReductionSubmitMsg
, ReductionSetData
- sequencerThreads
: LdbCoordinator
- settleList
: HomePatch
- sglower
: ComputeMsmMgr
- sh
: MoaData
- shx
: ComputeMsmMgr
, TileListVirialEnergy
- shx_1
: ComputeMsmMgr
- shy
: ComputeMsmMgr
, TileListVirialEnergy
- shy_1
: ComputeMsmMgr
- shz
: ComputeMsmMgr
, TileListVirialEnergy
- shz_1
: ComputeMsmMgr
- sigma
: vdw_params
, vdw_val
- sigma14
: vdw_params
, vdw_val
- sigmaRep
: go_val
- simParameters
: nonbonded
, Node
- simparams
: colvarproxy_namd
- simParams
: Controller
, Sequencer
- simulatedNodeSize
: SimParameters
- simulatedPEs
: SimParameters
- simulateInitialMapping
: SimParameters
- singleTopology
: SimParameters
- size
: CollectVectorVarMsg
, DataMessage
, GridforceFullBaseGrid
, GridforceLiteGrid
, qmSolvData
- size1
: PmeKSpaceCompute
- size2
: PmeKSpaceCompute
- size3
: PmeKSpaceCompute
- size_nopad
: GridforceFullBaseGrid
- sizeList
: MovePatchAtomsMsg
- sizes
: ProxyTree
- slave
: ComputeNonbondedCUDA::patch_record
- slaveIndex
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- slavePes
: ComputeNonbondedMIC
, ComputeNonbondedCUDA
- slaves
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- sldata
: ParseOptions::DataElement
- slow_forces
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- slow_forces_size
: ComputeNonbondedCUDA
- slow_table
: ComputeNonbondedUtil
- slowForce
: GBISForceMsg
- slowFreq
: Controller
, Sequencer
- 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 >
- sock
: GlobalMasterIMD
- Solty
: parm
, AmberParm7Reader::Ambertoppar
- soluteScalingAll
: SimParameters
- soluteScalingFactor
: SimParameters
- soluteScalingFactorCharge
: SimParameters
- soluteScalingFactorVdw
: SimParameters
- soluteScalingOn
: SimParameters
- solvent_dielectric
: SimParameters
- sortdims
: TopoManagerWrapper::pe_sortop_topo
- sortOrder
: CompAtomExt
- sortValue
: __sort_entry
- sourceNode
: FmmSerialCoordMsg
, ReductionRegisterMsg
, PmeTransMsg
, ExtCoordMsg
, GBISCoordMsg
, MsmSerialCoordMsg
, PmeGridMsg
, PmeUntransMsg
, QMCoordMsg
, QMPntChrgMsg
, ReductionSubmitMsg
- specialTracing
: Node
- sphericalBCexp1
: SimParameters
- sphericalBCexp2
: SimParameters
- sphericalBCk1
: SimParameters
- sphericalBCk2
: SimParameters
- sphericalBCOn
: SimParameters
- sphericalBCr1
: SimParameters
- sphericalBCr2
: SimParameters
- sphericalCenter
: SimParameters
- sphericalConstraintsOn
: SimParameters
- sphericalConstrCenter
: SimParameters
- split
: ComputeMsmMgr
, NL_Msm_t
- splitPatch
: SimParameters
- spos
: pe_sortop_coord_y
, pe_sortop_coord_x
- sptr
: ParseOptions::DataElement
- src
: DataMessage
- srcPart
: DataMessage
, ReplicaDcdInitMsg
, ReplicaDcdDataMsg
- srcPatchID
: MigrateAtomsMsg
, MigrateAtomsCombinedMsg
- srcRank
: ClusterSizeMsg
, ClusterCoorMsg
- srcY
: PmeAtomPencilMsg
, PmeForcePencilMsg
- srcZ
: PmeAtomPencilMsg
, PmeForcePencilMsg
- 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
- sSet
: OutputAtomRecord
- start
: PmeGridMsg
- startPE
: LocalLBInfoMsg
- state
: Controller
, Node
, Controller::checkpoint
- staticAtomAssignment
: SimParameters
- statsOn
: SimParameters
- status
: AtomCstInfo
, FullAtom
, CollectVectorVarMsg
, atom_constants
- stencil
: InterpParams_t
- step
: ComputeGlobalDataMsg
, Flags
, nonbonded
, ComputeNonbondedCUDA
, ComputeLCPO
, ComputeNonbondedMIC
, GlobalMaster
- 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
: ControllerBroadcasts
- stochRescaleFreq
: SimParameters
- stochRescaleHeat
: SimParameters
- stochRescaleOn
: SimParameters
- stochRescalePeriod
: SimParameters
- stochRescaleTemp
: SimParameters
- stochRescaleTimefactor
: Controller
- storeComputeMap
: SimParameters
- strainRate
: SimParameters
- strainRate2
: SimParameters
- strainRate_old
: Controller
- strategyName
: CollectLoadsMsg
, Rebalancer
- stream
: InitDeviceMsg2
- String
: AmberParm7Reader::FortranData
- subcube_total
: NL_Msm_t
- subgrid
: ComputeMsmMgr
, msm::PatchData
, MsmBlockKernel< Vtype, Mtype >
- subgrid_c1hermite
: ComputeMsmMgr
, msm::PatchData
- subgridIdx
: GridforceFullSubGrid
- subgrids
: GridforceFullBaseGrid
- subgrids_flat
: GridforceFullMainGrid
- submit_reduction
: Controller
- submitLoadStats
: Flags
- submitsRecorded
: ReductionSetData
- submitsRegistered
: ReductionSet
- sumx
: eABF1D
- sumx2
: eABF1D
- surface_tension
: SimParameters
- surfaceTensionTarget
: SimParameters
- suspended
: BroadcastClient
- suspiciousAlchBonds
: Molecule
- swdist
: QMGrpCalcMsg
- switching
: QMGrpCalcMsg
- switchingActive
: SimParameters
- switchingDist
: SimParameters
- switchOn
: ComputeNonbondedUtil
- switchOn2
: ComputeNonbondedUtil
- switchOn_1
: ComputeNonbondedUtil
- switchOn_f
: ComputeNonbondedUtil
- switchType
: QMGrpCalcMsg
- sx_shx
: ComputeMsmMgr
- sy_shy
: ComputeMsmMgr
- symmetryFile
: SimParameters
- symmetryFirstFullStep
: SimParameters
- symmetryFirstStep
: SimParameters
- symmetryk
: SimParameters
- symmetrykfile
: SimParameters
- symmetryLastFullStep
: SimParameters
- symmetryLastStep
: SimParameters
- symmetryMatrixFile
: SimParameters
- symmetryOn
: SimParameters
- symmetryScaleForces
: SimParameters
- sync
: BOCgroup
- sz_shz
: ComputeMsmMgr