Here is a list of all class members with links to the classes they belong to:
- p -
- P
: Rebalancer
- p
: AngleElem
, BondElem
, GromacsPairElem
, ComputePatch
, ComputePatchPair
, PatchElem
, TholeElem
, Patch
, CrosstermElem
, TuplePatchElem
, Rebalancer::pcpair
, ImproperElem
, AnisoElem
, DihedralElem
, ComputeNonbondedCUDA::patch_record
, ExclElem
, ComputeGlobalDataMsg
, ComputeNonbondedMIC::patch_record
, nonbonded
- p_0_sortValues
: ComputeNonbondedWorkArrays
- p_avg
: Patch
- p_sum
: GridforceFullBaseGrid
- pack()
: GridforceFullBaseGrid
, GridforceFullMainGrid
, GridforceFullSubGrid
, GridforceLiteGrid
, MigrateAtomsMsg
, MigrateAtomsCombinedMsg
, PatchMap
, MovePatchesMsg
, ProxyResultMsg
, ProxySpanningTreeMsg
, TupleSignature
, AtomSignature
, ExclusionSignature
, DataStreamMsg
, ComputeConsForceMsg
, ComputeDPMEDataMsg
, ComputeDPMEResultsMsg
, ComputeGlobalDataMsg
, ComputeGlobalResultsMsg
, ComputeMap
, GridforceGrid
- pack_data()
: MGridforceParamsList
- pack_grid()
: GridforceGrid
- packSize()
: PatchMap
- pad
: AlignVector
- pad_n
: GridforceFullBaseGrid
- pad_p
: GridforceFullBaseGrid
- padding
: ComputeMsmMgr
, ProxyResultVarsizeMsg
- Padding
: AmberParm7Reader::FortranFormatSpecifier
- pairC12
: Molecule
, GromacsPairValue
, gromacsPair
- pairC6
: Molecule
, GromacsPairValue
, gromacsPair
- pairInteractionGroup1
: SimParameters
- pairInteractionGroup2
: SimParameters
- pairInteractionOn
: ComputeNonbondedUtil
, SimParameters
- pairInteractionSelf
: ComputeNonbondedUtil
, SimParameters
- pairlist
: ComputeNonbondedWorkArrays
- pairlist2
: ComputeNonbondedWorkArrays
- pairlistDist
: SimParameters
- pairlistGrow
: SimParameters
- pairlisti
: ComputeNonbondedWorkArrays
- pairlistm
: ComputeNonbondedWorkArrays
- pairlistmA1
: ComputeNonbondedWorkArrays
- pairlistmA2
: ComputeNonbondedWorkArrays
- pairlistmA3
: ComputeNonbondedWorkArrays
- pairlistmA4
: ComputeNonbondedWorkArrays
- pairlistMinProcs
: SimParameters
- pairlistnA0
: ComputeNonbondedWorkArrays
- pairlistnA1
: ComputeNonbondedWorkArrays
- pairlistnA2
: ComputeNonbondedWorkArrays
- pairlistnA3
: ComputeNonbondedWorkArrays
- pairlistnA4
: ComputeNonbondedWorkArrays
- pairlistnAlch
: ComputeNonbondedWorkArrays
- Pairlists()
: Pairlists
- pairlists
: ComputeNonbondedPair
, ComputeNonbondedSelf
, nonbonded
- pairlistsAge
: Sequencer
- pairlistsAreValid
: Sequencer
- pairlistShrink
: SimParameters
- pairlistsPerCycle
: SimParameters
- pairlistsValid
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
, ComputeNonbondedPair
, ComputeNonbondedSelf
- pairlistTolerance
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
, ComputeNonbondedPair
, ComputeNonbondedSelf
, Flags
- pairlistTrigger
: SimParameters
- pairlistWarningIndex
: ComputeNonbondedUtil
- pairlistWarnings
: Controller
- pairlistx
: ComputeNonbondedWorkArrays
- pairlistxA1
: ComputeNonbondedWorkArrays
- pairlistxA2
: ComputeNonbondedWorkArrays
- pairlistxA3
: ComputeNonbondedWorkArrays
- pairlistxA4
: ComputeNonbondedWorkArrays
- pairOn
: ComputePmeUtil
- papiMeasureBarrier()
: Node
- ParallelIOMgr()
: ParallelIOMgr
- param
: ScriptParamMsg
- Parameters()
: Parameters
- parameters
: nonbonded
, Node
- params
: ComputeNonbondedPair
, ComputeNonbondedSelf
- paraTypeCharmmOn
: SimParameters
- paraTypeXplorOn
: SimParameters
- parent
: DataExchanger
, GridforceFullSubGrid
, ParseOptions::DataElement
- parent_ptr
: ParseOptions::DataElement
- parm()
: parm
- parse()
: PDBAtom
- ParseOptions()
: ParseOptions
- part
: ComputeNonbondedMIC::compute_record
- particles
: ComputeDPMEDataMsg
- partition
: ComputeMap::ComputeData
, CompAtom
, ComputeMap
, RecBisection
- partner
: atom_constants
, AtomCstInfo
- Patch()
: Patch
- patch
: ComputeHomePatch
, ComputeLCPO
, ComputePatch
, ComputePatchPair
, CudaComputeNonbonded::PatchRecord
, HomePatchElem
, ProxyGBISP1ResultMsg
, ProxyGBISP2DataMsg
, ProxyGBISP2ResultMsg
, ProxyGBISP3DataMsg
, RegisterProxyMsg
, UnregisterProxyMsg
, ProxyDataMsg
, ProxyResultMsg
, ProxyResultVarsizeMsg
, ProxyNodeAwareSpanningTreeMsg
, ProxyCombinedResultRawMsg
, ProxyCombinedResultMsg
, ProxySpanningTreeMsg
, ProxyUsageKey
, Sequencer
, PatchMap
- patch1
: computeInfo
- patch2
: computeInfo
- patch_record()
: ComputeNonbondedCUDA::patch_record
, ComputeNonbondedMIC::patch_record
- patch_sortop_curve_a()
: patch_sortop_curve_a
- patch_sortop_curve_b()
: patch_sortop_curve_b
- patch_sortop_curve_c()
: patch_sortop_curve_c
- patchArray
: LdbCoordinator
- patchCnt
: MovePatchAtomsMsg
- patchcount
: ComputeGlobalDataMsg
- PatchData()
: msm::PatchData
- patchDataStrc()
: patchDataStrc
- patchDimension
: SimParameters
- PatchElem()
: PatchElem
- patches
: Rebalancer
- patchHandles
: LdbCoordinator
- patchID
: PatchElem
, TuplePatchElem
, ComputeLCPO
, msm::PatchData
, ComputeNonbondedCUDA::patch_record
, ComputeNonbondedMIC::patch_record
, GBISParamStruct
, ComputePatch
, ComputePatchPair
, CudaComputeNonbonded::PatchRecord
, msm::PatchSend
, Patch
, ProxyElem
, ProxyListInfo
- patchIDs
: PatchProxyListMsg
- patchInd
: CudaComputeNonbonded::ComputeRecord
, TileList
, CudaComputeRecord
- PatchInfo()
: PatchInfo
- patchList
: ComputeHomePatches
, msm::Map
- patchLoad()
: LdbCoordinator
- PatchMap
: PatchMgr
, PatchMap
- patchMap
: ComputeHomePatches
, ComputeHomeTuples< T, S, P >
, ComputeNonbondedCUDA
, ComputeNonbondedMIC
, LdbCoordinator
, Node
- patchMapData
: PatchMapMsg
- patchMapInit()
: WorkDistrib
- PatchMgr
: HomePatch
, PatchMgr
- patchMgr
: BOCgroup
- patchNAtoms
: LdbCoordinator
- patchNumList
: TileList
- patchPairsReordered
: ComputeNonbondedCUDA
- PatchProxyListMsg()
: PatchProxyListMsg
- patchPtr
: ComputeMsmMgr
- patchPtrArray()
: ComputeMsmMgr
- patchReady()
: Compute
, CudaComputeNonbonded
- PatchReady()
: Sync
- patchReadyQueueCount
: TileListStat
- PatchRec()
: ComputeMap::PatchRec
- PatchRecord()
: CudaComputeNonbonded::PatchRecord
- patchRecords
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- patchSet
: processorInfo
- pauseWork()
: LdbCoordinator
- pcgrid
: Rebalancer
- pcIndxs
: QMCoordMsg
- pcpair()
: Rebalancer::pcpair
- pcScheme
: QMGrpCalcMsg
- pcSelMode
: QMCoordMsg
- pd
: msm::PatchData
- pdb
: Node
- PDB()
: PDB
- PDBAtom()
: PDBAtom
- PDBAtomRecord()
: PDBAtomRecord
- PDBData()
: PDBData
- PDBFormatStyle
: PDBData
- PDBHetatm()
: PDBHetatm
- PDBNames
: PDBData
- PDBPossibleAtoms
: PDBAtom
- PDBType
: PDBData
- PDBUnknown()
: PDBUnknown
- pe
: PmeLaunchMsg
, CudaComputeNonbonded::PatchRecord
, CheckpointAtomsReqMsg
, CheckpointAtomsMsg
- PE
: StreamMessage
- pe
: PmeAtomMsg
, PmeForceMsg
- pe_sortop_bit_reversed()
: pe_sortop_bit_reversed
- pe_sortop_coord_x()
: pe_sortop_coord_x
- pe_sortop_coord_y()
: pe_sortop_coord_y
- pe_sortop_topo()
: TopoManagerWrapper::pe_sortop_topo
- pe_start
: NodePmeInfo
- peCompactOrdering
: WorkDistrib
- peCompactOrderingIndex
: WorkDistrib
- peDiffuseOrdering
: WorkDistrib
- peDiffuseOrderingIndex
: WorkDistrib
- peIDs
: proxyTreeNode
- peIter
: QMGrpCalcMsg
- peOrderingInit
: WorkDistrib
- peOrderingReady()
: WorkDistrib
- periodic_a()
: PatchMap
- periodic_b()
: PatchMap
- periodic_c()
: PatchMap
- permutation
: PmeKSpaceCompute
, PmeTranspose
- pes
: Rebalancer
- pExt
: nonbonded
, ComputePatch
, ComputePatchPair
, Patch
- pgc
: MsmGridCutoffKernel< Vtype, Mtype >
- pgvc
: MsmGridCutoffKernel< Vtype, Mtype >
- Phase
: parm
, AmberParm7Reader::Ambertoppar
- PhiStencil
: ComputeMsmMgr
- pi_ewaldcof
: ComputeNonbondedUtil
- pid
: ComputeMap::PatchRec
, ComputeNonbondedCUDA::compute_record
, ComputeNonbondedMIC::compute_record
, CudaComputeNonbonded::ComputeRecord
, HomePatchElem
, LocalID
, MovePatchesMsg
, CheckpointAtomsReqMsg
, CheckpointAtomsMsg
, ExchangeAtomsReqMsg
, ExchangeAtomsMsg
, MovePatch
, ComputeMap
, PatchMap
- pid_compare_priority()
: cr_sortop_reverse_priority
- pidList
: AtomsCntPerPatchMsg
, MovePatchAtomsMsg
- pids
: ComputeMap::ComputeData
- Pk
: parm
, AmberParm7Reader::Ambertoppar
- plcutoff
: nonbonded
- plcutoff2
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- plExtLen
: ProxyDataMsg
- plLen
: ProxyDataMsg
- PluginIOMgr()
: PluginIOMgr
- pmap
: patch_sortop_curve_a
, patch_sortop_curve_b
, patch_sortop_curve_c
- pmax
: GridforceFullSubGrid
- pme_kspace()
: PmeXPencil
- pme_select()
: SimParameters
- PmeAtomFiler()
: PmeAtomFiler
- PmeAtomStorage()
: PmeAtomStorage
- PMEBarrier
: SimParameters
- pmeComputes
: ComputePmeMgr
- PmeDoneMsg()
: PmeDoneMsg
- PMEEwaldCoefficient
: QMGrpCalcMsg
, SimParameters
- pmeGrid
: CudaPmeXYZInitMsg
, CudaPmeXYInitMsg
, CudaPmeXInitMsg
, PmePencilXYZ
, PmePencilXY
, PmePencilX
, PmePencilY
, PmePencilZ
, PmeKSpaceCompute
, PmeRealSpaceCompute
, PmeTranspose
- PMEGridSizeX
: SimParameters
- PMEGridSizeY
: SimParameters
- PMEGridSizeZ
: SimParameters
- PMEGridSpacing
: SimParameters
- PMEInterpOrder
: SimParameters
- PmeKSpace()
: PmeKSpace
- PmeKSpaceCompute()
: PmeKSpaceCompute
- pmeKSpaceCompute
: PmePencilXYZ
, PmePencilZ
- pmemgr_lock
: ComputePmeMgr
- PMEMinPoints
: SimParameters
- PMEMinSlices
: SimParameters
- pmeNodeProxy
: PmePencilInitMsgData
- PMEOffload
: SimParameters
- PMEOn
: QMForceMsg
, QMGrpCalcMsg
, SimParameters
- PmePencil()
: PmePencil< T >
- PmePencilInitMsg()
: PmePencilInitMsg
- PmePencilMap()
: PmePencilMap
- PMEPencils
: SimParameters
- PMEPencilsX
: SimParameters
- PMEPencilsXLayout
: SimParameters
- PMEPencilsY
: SimParameters
- PMEPencilsYLayout
: SimParameters
- PMEPencilsZ
: SimParameters
- PmePencilX()
: PmePencilX
- pmePencilX
: CudaPmeXInitMsg
- PmePencilXMap()
: PmePencilXMap
- pmePencilXY
: CudaPmeXYInitMsg
- PmePencilXY()
: PmePencilXY
- PmePencilXYMap()
: PmePencilXYMap
- PmePencilXYZ()
: PmePencilXYZ
- PmePencilXYZMap()
: PmePencilXYZMap
- PmePencilY()
: PmePencilY
- pmePencilY
: CudaPmeXInitMsg
- PmePencilY()
: PmePencilY
- pmePencilZ
: CudaPmeXYInitMsg
- PmePencilZ()
: PmePencilZ
- pmePencilZ
: CudaPmeXInitMsg
- PMEProcessors
: SimParameters
- pmeProxy
: PmePencilInitMsgData
- PmeRealSpace()
: PmeRealSpace
- PmeRealSpaceCompute()
: PmeRealSpaceCompute
- PMESendOrder
: SimParameters
- PMETolerance
: SimParameters
- PmeTranspose()
: PmeTranspose
- pmeTranspose
: PmePencilXY
, PmePencilX
, PmePencilY
, PmePencilZ
- PmeXPencil()
: PmeXPencil
- PmeYPencil()
: PmeYPencil
- PmeZPencil()
: PmeZPencil
- pmin
: GridforceFullSubGrid
- Pn
: parm
, AmberParm7Reader::Ambertoppar
- pntChrgDist()
: pntChrgDist
- Pointer()
: Pointer
- pointerToGaussBeg
: Molecule
- pointerToGaussEnd
: Molecule
- pointerToGoBeg
: Molecule
- pointerToGoEnd
: Molecule
- pointerToLJBeg
: Molecule
- pointerToLJEnd
: Molecule
- Polarizability
: AmberParm7Reader::Ambertoppar
- pollChargeGridReady()
: ComputePmeMgr
- pollForcesReady()
: ComputePmeMgr
- PolyDegree
: ComputeMsmMgr
- popn
: parm
- populateInitial()
: PmePencilXYMap
, PmePencilMap
, PmePencilXYZMap
, PmePencilXMap
- pos
: ComputeLCPO
, dummyData
, PmeTranspose
- posBoxP
: patchDataStrc
- posExt
: ComputeLCPO
- position
: ComputeGBISAtom
, ComputeExtAtom
, ComputeFmmSerialAtom
, ComputeMsmSerialAtom
, ComputeQMAtom
, ComputeQMPntChrg
, QMAtomData
, msm::AtomCoord
, CompAtom
- position_distance()
: colvarproxy_namd
- positionBox
: ComputeNonbondedMIC::patch_record
, PatchElem
, TuplePatchElem
, ComputeLCPO
, ComputeNonbondedCUDA::patch_record
, ComputePatch
, ComputePatchPair
, CudaComputeNonbonded::PatchRecord
, Patch
- positionBoxClosed()
: Patch
- positionComputeList
: Patch
- positionExtList
: ProxyDataMsg
- positionList
: ProxyDataMsg
- positionRescaleFactor
: ControllerBroadcasts
, Controller
- positionRescaleFactor2
: ControllerBroadcasts
- positionsReady()
: Patch
, HomePatch
- posNew
: HomePatch
- poten_fp
: GridforceFullBaseGrid
- ppbonded
: Controller
- ppint
: Controller
- ppnonbonded
: Controller
- pr
: cr_sortop_reverse_priority
- preadln()
: parm
- Precision
: AmberParm7Reader::FortranFormatSpecifier
- precisions
: CollectionMgr::CollectVectorInstance
- prepare_qm()
: Molecule
- prepareTileList()
: CudaTileListKernel
- prepProc
: QMGrpCalcMsg
- prepProcOn
: QMGrpCalcMsg
- pressure
: Controller
- pressure_amd
: Controller
- pressure_avg
: Controller
- pressure_nbond
: Controller
- pressure_normal
: Controller
- pressure_slow
: Controller
- pressure_tavg
: Controller
- pressureProfileAtomTypes
: GromacsPairElem
, ExclElem
, DihedralElem
, ComputeNonbondedUtil
, AnisoElem
, BondElem
, CrosstermElem
, ImproperElem
, SimParameters
, AngleElem
, TholeElem
- pressureProfileAverage
: Controller
- pressureProfileCount
: Controller
- pressureProfileData
: ComputeHomeTuples< T, S, P >
, ComputeNonbondedSelf
, ComputeNonbondedPair
- pressureProfileEwaldOn
: SimParameters
- pressureProfileEwaldX
: SimParameters
- pressureProfileEwaldY
: SimParameters
- pressureProfileEwaldZ
: SimParameters
- pressureProfileFreq
: SimParameters
- pressureProfileMin
: CrosstermElem
, DihedralElem
, ComputeNonbondedUtil
, AngleElem
, ImproperElem
, BondElem
, AnisoElem
, GromacsPairElem
, ExclElem
, TholeElem
- pressureProfileOn
: SimParameters
, ComputeNonbondedUtil
- pressureProfileReduction
: ComputeNonbondedPair
, ComputeNonbondedSelf
, nonbonded
- PressureProfileReduction()
: PressureProfileReduction
- pressureProfileReduction
: ComputeHomeTuples< T, S, P >
, Sequencer
- pressureProfileSlabs
: CrosstermElem
, GromacsPairElem
, ImproperElem
, Controller
, SimParameters
, BondElem
, ComputeHomeTuples< T, S, P >
, ComputeNonbondedUtil
, TholeElem
, ExclElem
, DihedralElem
, AnisoElem
, AngleElem
- pressureProfileThickness
: AngleElem
, BondElem
, ImproperElem
, ComputeNonbondedUtil
, AnisoElem
, ExclElem
, TholeElem
, CrosstermElem
, DihedralElem
, GromacsPairElem
- previous_NAMD_step
: colvarproxy_namd
- print()
: IRSet
, MoaData
, MsmTimer
, MsmProfiler
- print_angle_params()
: Parameters
- print_atoms()
: Molecule
- print_bond_params()
: Parameters
- print_bonds()
: Molecule
- print_crossterm_params()
: Parameters
- print_dihedral_params()
: Parameters
- Print_dU_dLambda_Info()
: ARestraintManager
- Print_dU_dLambda_Summary()
: ALambdaManager
- print_exclusions()
: Molecule
- print_go_params()
: Molecule
- print_go_sigmas()
: Molecule
- print_improper_params()
: Parameters
- Print_MCTI_Integration()
: ALambdaManager
- print_nbthole_pair_params()
: Parameters
- print_param_summary()
: Parameters
- print_vdw_pair_params()
: Parameters
- print_vdw_params()
: Parameters
- printBadContacts
: SimParameters
- printComputeMap()
: ComputeMap
- printDynamicsEnergies()
: Controller
- printEnergies()
: Controller
- PrintEnergyInfo()
: ARestraintManager
- printExclusions
: SimParameters
- printFepMessage()
: Controller
- PrintHeader()
: ALambdaManager
, ALambdaControl
- PrintInfo()
: ARestraint
, ADiheRestraint
, APosRestraint
, AnAngleRestraint
, ADistRestraint
- PrintLambdaHeader()
: ALambdaControl
, ALambdaManager
- printLoads()
: Rebalancer
- printLocalLdbReport()
: LdbCoordinator
- printMinimizeEnergies()
: Controller
- printOut()
: ProxyNodeAwareSpanningTreeMsg
- printPatchMap()
: PatchMap
- PrintPreInfo()
: ARestraintManager
- printRequiredProxies()
: LdbCoordinator
- PrintRestraintInfo()
: ARestraintManager
- printResults()
: Rebalancer
- PrintSomeSpaces()
: ALambdaManager
- printSummary()
: Rebalancer
- printTiMessage()
: Controller
- printTiming()
: Controller
- priority()
: Compute
, MsmGridCutoffKernel< Vtype, Mtype >
- PriorityQueue()
: msm::PriorityQueue< T >
- processData()
: GlobalMaster
- processFullQM()
: ComputeQM
- processor
: computeInfo
, ProxyUsageKey
, patchInfo
- processorArray
: LdbCoordinator
- processorInfo()
: processorInfo
- processors
: Rebalancer
- procID
: ProxyNodeAwareSpanningTreeMsg
- procNum()
: PmePencilXMap
, MsmBlockMap
, PmePencilMap
, MsmGridCutoffMap
, PmePencilXYMap
, PmePencilXYZMap
- procQMRes()
: ComputeQMMgr
- procTrans()
: ComputePmeMgr
- procUntrans()
: ComputePmeMgr
- projLineVec
: nonbonded
- PROLONGATE
: MsmTimer
- prolongation()
: MsmBlock
, MsmC1HermiteBlock
- prolongationKernel()
: MsmBlockKernel< Vtype, Mtype >
- proStencil
: MsmBlockKernel< Vtype, Mtype >
- proxies
: processorInfo
- proxiesOn
: patchInfo
- ProxyElem()
: ProxyElem
- proxylist
: ProxyTree
- proxyList
: ProxyListInfo
- proxyListLen
: PatchProxyListMsg
- ProxyMgr()
: ProxyMgr
- proxyMgr
: BOCgroup
- proxyMsgCount
: ProxyTree
- proxyPatch
: ProxyElem
- ProxyPatch()
: ProxyPatch
- proxyPEs
: PatchProxyListMsg
- proxyRecvSpanningTree
: SimParameters
- proxySendSpanningTree
: SimParameters
- ProxyTree()
: ProxyTree
- proxyTreeBranchFactor
: SimParameters
- proxyTreeNode()
: proxyTreeNode
- ProxyUsage()
: ProxyUsage
- proxyUsage
: Rebalancer
- ProxyUsageKey()
: ProxyUsageKey
- psiFin
: Patch
- psiSum
: Patch
, ComputeNonbondedCUDA::patch_record
, CudaComputeNonbonded::PatchRecord
, GBISParamStruct
, GBISResults< 1 >
, ComputeNonbondedMIC::patch_record
, ProxyGBISP1ResultMsg
- psiSumBox
: Patch
, ComputeNonbondedMIC::patch_record
, ComputeNonbondedSelf
, CudaComputeNonbonded::PatchRecord
, ComputeNonbondedCUDA::patch_record
, ComputeNonbondedPair
- psiSumBoxClosed()
: Patch
- psiSumComputeList
: Patch
- psiSumH
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- psiSumH_size
: ComputeNonbondedCUDA
- psiSumLen
: ProxyGBISP1ResultMsg
- publish()
: SimpleBroadcastObject< T >
- pup()
: Int3
, ConstPointer
, HashPoolAdaptorT< T >
, Pointer
, LocalLBInfoMsg
, MoaData
, Int2
- push_back()
: HashPool< T >
- put()
: MsmGridCutoffSetupMsg
, MOStream
, MsmC1HermiteGridCutoffProxyMsg
, MOStream
, GridMsg
, MOStream
, MsmBlockProxyMsg
, MOStream
, MsmGridCutoffProxyMsg
, MOStream
, MsmC1HermiteGridCutoffSetupMsg
, MOStream
, MsmC1HermiteBlockProxyMsg
, MOStream
- put_stir_startTheta()
: Molecule