- r -
- rand_gaussian()
: colvarproxy_namd
- Random()
: AVector
, Random
- range()
: ParseOptions
- rattle1()
: Sequencer
, HomePatch
- rattle1old()
: HomePatch
- rattle2()
: HomePatch
- read_alch_unpert_angles()
: Molecule
- read_alch_unpert_bonds()
: Molecule
- read_alch_unpert_dihedrals()
: Molecule
- read_charmm_parameter_file()
: Parameters
- read_ener_table()
: Parameters
- read_energy_type()
: Parameters
- read_energy_type_bothcubspline()
: Parameters
- read_energy_type_cubspline()
: Parameters
- read_fortran_12I6()
: parm
- read_go_file()
: Molecule
- read_parameter_file()
: Parameters
- read_parm()
: Molecule
, Parameters
- readExtendedSystem()
: SimParameters
- readfile()
: eABF
, eABF1D
- readHeader()
: GridforceFullBaseGrid
- readparm()
: parm
- readPerAtomInfo()
: ParallelIOMgr
- readSubgridHierarchy()
: GridforceFullBaseGrid
- ready()
: CollectionMaster::CollectVectorInstance
- reallocate_forceSOA()
: CudaComputeNonbondedKernel
- reassignVelocities()
: Controller
, Sequencer
- rebalance()
: LdbCoordinator
- rebalanceLoad()
: Controller
, Sequencer
- Rebalancer()
: Rebalancer
- RecBisection()
: RecBisection
- receive_GoMolecule()
: Molecule
- receive_Molecule()
: Molecule
- receive_Parameters()
: Parameters
- receive_SimParameters()
: SimParameters
- receiveAll()
: ProxyPatch
- receiveData()
: ProxyPatch
- receiveDataStream()
: CollectionMaster
- receiveForces()
: CollectionMaster
, ParallelIOMgr
- receiveOutputForceReady()
: CollectionMaster
- receiveOutputPosReady()
: CollectionMaster
- receiveOutputVelReady()
: CollectionMaster
- receivePositions()
: CollectionMaster
, ParallelIOMgr
- receivePressure()
: Controller
- receiveResult()
: HomePatch
- receiveResults()
: HomePatch
- receiveVelocities()
: CollectionMaster
, ParallelIOMgr
- recv_grid()
: PmeZPencil
- recv_trans()
: PmeYPencil
, PmeXPencil
- recv_untrans()
: PmeZPencil
, PmeYPencil
- recvAck()
: ComputePmeMgr
- recvArrays()
: ComputePmeMgr
- recvAssignPatchesOnPe()
: ComputeMgr
- recvAtomFiler()
: ComputePmeCUDAMgr
- recvAtoms()
: ComputePmeCUDADevice
, ComputePmeCUDAMgr
, PatchMgr
- recvAtomsCntPerPatch()
: ParallelIOMgr
- recvAtomsFromNeighbor()
: ComputePmeCUDADevice
- recvAtomsMGrp()
: ParallelIOMgr
- recvAtomsToHomePatchProcs()
: ParallelIOMgr
- recvBroadcast()
: BroadcastMgr
- recvBuildCudaExclusions()
: ComputeMgr
- recvBuildCudaForceTable()
: ComputeMgr
- recvBuildMICForceTable()
: ComputeMgr
- recvChargeGridReady()
: ComputePmeMgr
- recvCheckpointAck()
: Controller
, HomePatch
, Node
, PatchMgr
- recvCheckpointLoad()
: HomePatch
, PatchMgr
- recvCheckpointReq()
: Controller
, HomePatch
, Node
, PatchMgr
- recvCheckpointStore()
: HomePatch
, PatchMgr
- recvClusterCoor()
: ParallelIOMgr
- recvClusterSize()
: ParallelIOMgr
- recvComputeConsForceMsg()
: ComputeMgr
- recvComputeDPMEData()
: ComputeMgr
- recvComputeDPMEResults()
: ComputeMgr
- recvComputeEwaldData()
: ComputeMgr
- recvComputeEwaldResults()
: ComputeMgr
- recvComputeGlobalConfig()
: ComputeMgr
- recvComputeGlobalData()
: ComputeMgr
- recvComputeGlobalResults()
: ComputeMgr
- recvComputeMapChanges()
: WorkDistrib
- recvCoord()
: ComputeExtMgr
, ComputeFmmSerialMgr
, ComputeGBISserMgr
, ComputeMsmSerialMgr
- recvCreateNonbondedCUDASlave()
: ComputeMgr
- recvCreateNonbondedMICSlave()
: ComputeMgr
- recvData()
: ComputeEwald
, GlobalMasterServer
, ProxyMgr
- recvDevices()
: ComputePmeCUDAMgr
- recvEnableEarlyExit()
: Node
- recvEnableExitScheduler()
: Node
- recvExchangeMsg()
: HomePatch
, PatchMgr
- recvExchangeReq()
: HomePatch
, PatchMgr
- recvFinalClusterCoor()
: ParallelIOMgr
- recvFinalClusterSize()
: ParallelIOMgr
- recvFinishPatchesOnPe()
: ComputeMgr
- recvFinishPatchOnPe()
: ComputeMgr
- recvFinishReductions()
: ComputeMgr
- recvForce()
: ComputeExtMgr
, ComputeFmmSerialMgr
, ComputeGBISserMgr
, ComputeMsmSerialMgr
, ComputeQMMgr
- recvForcesFromNeighbor()
: ComputePmeCUDADevice
- recvFullQM()
: ComputeQMMgr
- recvGrid()
: ComputePmeMgr
- recvHydroBasedCounter()
: ParallelIOMgr
- recvImmediateProxyAll()
: ProxyMgr
, NodeProxyMgr
- recvImmediateProxyData()
: ProxyMgr
, NodeProxyMgr
- recvImmediateResults()
: ProxyMgr
, NodeProxyMgr
- recvLaunchWork()
: ComputeMgr
- recvMessageEnqueueWork()
: ComputeMgr
- recvMICPEData()
: ComputeMgr
- RecvMigrate()
: LdbCoordinator
- recvMigrateAtomsCombined()
: PatchMgr
- recvMolInfo()
: ParallelIOMgr
- recvMovePatches()
: PatchMgr
- recvMsmBlockProxy()
: ComputeMsmMgr
- recvMsmC1HermiteBlockProxy()
: ComputeMsmMgr
- recvMsmC1HermiteGridCutoffProxy()
: ComputeMsmMgr
- recvMsmGridCutoffProxy()
: ComputeMsmMgr
- recvNodeAck()
: PmeZPencil
, PmeYPencil
- recvNodeAwareSpanningTree()
: HomePatch
, ProxyMgr
- recvNodeAwareSpanningTreeOnHomePatch()
: ProxyMgr
- recvNodeAwareSTParent()
: ProxyMgr
- recvNonbondedCUDASlaveReady()
: ComputeMgr
- recvNonbondedCUDASlaveSkip()
: ComputeMgr
- recvNonbondedMICSlaveReady()
: ComputeMgr
- recvNonbondedMICSlaveSkip()
: ComputeMgr
- recvOpenBoxesOnPe()
: ComputeMgr
- recvPartQM()
: ComputeQMMgr
- recvPatchProxyInfo()
: ProxyMgr
- recvPencilMapProxies()
: NodePmeMgr
- recvPencils()
: ComputePmeCUDAMgr
- recvPntChrg()
: ComputeQMMgr
- recvProxies()
: ProxyMgr
- recvProxyAll()
: ProxyMgr
- recvProxyData()
: ProxyMgr
- recvRecipEvir()
: ComputePmeMgr
- recvRegisterProxy()
: ProxyMgr
- recvReplicaDcdData()
: Output
- recvReplicaDcdInit()
: Output
- recvResult()
: ProxyMgr
- recvResults()
: ComputeEwald
, ComputeGlobal
, ProxyMgr
- recvSharedTrans()
: ComputePmeMgr
- recvSharedUntrans()
: ComputePmeMgr
- recvSkipPatchesOnPe()
: ComputeMgr
- recvSpanningTree()
: HomePatch
, ProxyMgr
- recvSpanningTreeOnHomePatch()
: ProxyMgr
- recvTrans()
: ComputePmeMgr
, NodePmeMgr
- recvUngrid()
: ComputePmeMgr
, NodePmeMgr
- recvUnregisterBoxesOnPe()
: ComputeMgr
- recvUnregisterProxy()
: ProxyMgr
- recvUntrans()
: ComputePmeMgr
, NodePmeMgr
- recvXTrans()
: NodePmeMgr
- recvYieldDevice()
: ComputeNonbondedCUDA
, ComputeMgr
, ComputeNonbondedMIC
- recvYTrans()
: NodePmeMgr
- recvYUntrans()
: NodePmeMgr
- recvZGrid()
: NodePmeMgr
- recvZUntrans()
: NodePmeMgr
- reduceVirialEnergy()
: CudaComputeNonbondedKernel
- ReductionMgr()
: ReductionMgr
- ReductionSet()
: ReductionSet
- ReductionSetData()
: ReductionSetData
- refine()
: Rebalancer
- refine_togrid()
: Rebalancer
- RefineOnly()
: RefineOnly
- RefineTorusLB()
: RefineTorusLB
- refSelStr()
: refSelStr
- registerArray()
: MsmBlockMap
, MsmGridCutoffMap
, PmePencilMap
, PmePencilXYZMap
, PmePencilXMap
, PmePencilXYMap
- registerAvgPositionPickup()
: Patch
- registerBornRadPickup()
: Patch
- registerCompute()
: ComputeMap
- registerComputePair()
: CudaComputeNonbonded
- registerComputeSelf()
: CudaComputeNonbonded
- registerDEdaSumDeposit()
: Patch
- registerDHdrPrefixPickup()
: Patch
- registerForceDeposit()
: Patch
- registerIDsCompAtomExt()
: AtomMapper
- registerIDsFullAtom()
: AtomMapper
- registerIntRadPickup()
: Patch
- registerLcpoTypePickup()
: Patch
- registerLocalPatchMap()
: NodeProxyMgr
- registerLocalProxyMgr()
: NodeProxyMgr
- registerNeighbor()
: ComputePmeCUDADevice
- registerPatch()
: PatchMap
, NodeProxyMgr
- registerPatches()
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- registerPatchMgr()
: PatchMap
- registerPositionPickup()
: Patch
- registerProxy()
: HomePatch
, ProxyMgr
- registerPsiSumDeposit()
: Patch
- registerRecvAtomsFromNeighbor()
: ComputePmeCUDADevice
- registerVelocityPickup()
: Patch
- registerXPencil()
: NodePmeMgr
- registerYPencil()
: NodePmeMgr
- registerZPencil()
: NodePmeMgr
- rehash()
: UniqueSetRaw< Elem >
, UniqueSet< Elem >
- reinitAtoms()
: WorkDistrib
- reinitialize()
: GridforceFullMainGrid
, GridforceGrid
, GridforceLiteGrid
- reinitVelocities()
: Sequencer
- reloadCharges()
: Node
, Molecule
, Sequencer
, Node
- reloadGridforceGrid()
: Node
- reloadStructure()
: Node
- remoteRegister()
: ReductionMgr
- remoteSubmit()
: ReductionMgr
- remoteUnregister()
: ReductionMgr
- remove()
: IRSet
, msm::PriorityQueue< T >
- removeData()
: ReductionSet
- removeEmptyOffset()
: ExclusionSignature
- removeEmptyTupleSigs()
: AtomSignature
- removeProxies()
: ProxyMgr
- removeProxy()
: ProxyMgr
- removeReady()
: CollectionMaster::CollectVectorSequence
- removeSelf()
: Entry< Elem >
- removeUnusedProxies()
: ProxyMgr
- reorder()
: Random
- replaceForces()
: HomePatch
- replica_comm_barrier()
: colvarproxy_namd
- replica_comm_recv()
: colvarproxy_namd
- replica_comm_send()
: colvarproxy_namd
- replica_enabled()
: colvarproxy_namd
- replica_index()
: colvarproxy_namd
- replicaDcdInit()
: Output
- replicaDcdOff()
: Output
- request_total_force()
: colvarproxy_namd
- requestAtom()
: GlobalMasterFreeEnergy
, GlobalMasterEasy
- requestedAtoms()
: GlobalMaster
- requestedGridObjs()
: GlobalMaster
- requestedGroups()
: GlobalMaster
- requestedTotalForces()
: GlobalMaster
- requestTotalForce()
: GlobalMaster
- require()
: ParseOptions
, RequireReduction
, ParseOptions
- requireB()
: ParseOptions
- requiredProxies()
: LdbCoordinator
- requirePatch()
: ComputeNonbondedMIC
, ComputeNonbondedCUDA
- rescale()
: Lattice
- rescaleaccelMD()
: Sequencer
, Controller
- rescaleSoluteCharges()
: Sequencer
- rescaleVelocities()
: Controller
, Sequencer
- rescaleVelocitiesByFactor()
: Sequencer
- resendMolecule()
: Node
- resendMolecule2()
: Node
- reset()
: CollectionMaster::CollectVectorInstance
, CollectionMgr::CollectVectorInstance
, msm::Grid< T >
, Rebalancer::pcpair
, msm::PatchDiagram
, msm::GridFixed< T, N >
, msm::PatchSend
, msm::Array< T >
, msm::BlockSend
, colvarproxy_namd
, msm::BlockDiagram
, Pairlists
, LCPONeighborList
, CollectProxyVectorInstance
- ResidueLookupElem()
: ResidueLookupElem
- residuename()
: PDBAtom
- residueseq()
: PDBAtom
- resize()
: ResizeArray< T >
, msm::Grid< T >
, msm::Array< T >
- ResizeArray()
: ResizeArray< T >
- ResizeArrayIter()
: ResizeArrayIter< Type >
- ResizeArrayPrimIter()
: ResizeArrayPrimIter< T >
- reSortTileLists()
: CudaTileListKernel
- restriction()
: MsmBlock
, MsmC1HermiteBlock
- restrictionKernel()
: MsmBlockKernel< Vtype, Mtype >
- resume()
: LdbCoordinator
- resume2()
: LdbCoordinator
- resumeAfterPapiMeasureBarrier()
: Node
- resumeAfterTraceBarrier()
: Node
, Controller
- ResumeFromSync()
: LdbCoordinator
- resumeReady()
: LdbCoordinator
- reverse_transform()
: Lattice
- revert()
: HomePatch
- rigid_bond_length()
: Molecule
- rlength()
: Vector
- rot()
: Matrix4
- rotate_axis()
: Matrix4
- run()
: Node
, Controller
, ScriptTcl
, Sequencer
- run_colvar_callback()
: colvarproxy_namd
- run_colvar_gradient_callback()
: colvarproxy_namd
- run_force_callback()
: colvarproxy_namd
- runComputeObjects()
: Sequencer
- runController()
: NamdState
- runSequencer()
: HomePatch