- p -
- pack()
: DataStreamMsg
, ComputeConsForceMsg
, ComputeDPMEResultsMsg
, GridforceGrid
, MovePatchesMsg
, ProxyResultMsg
, GridforceFullBaseGrid
, ProxySpanningTreeMsg
, TupleSignature
, ComputeGlobalDataMsg
, GridforceFullMainGrid
, AtomSignature
, ExclusionSignature
, GridforceFullSubGrid
, ComputeDPMEDataMsg
, ComputeGlobalResultsMsg
, GridforceLiteGrid
, MigrateAtomsMsg
, ComputeMap
, MigrateAtomsCombinedMsg
, PatchMap
- pack_data()
: MGridforceParamsList
- pack_grid()
: GridforceGrid
- packSize()
: PatchMap
- Pairlists()
: Pairlists
- papiMeasureBarrier()
: Node
- ParallelIOMgr()
: ParallelIOMgr
- Parameters()
: Parameters
- parm()
: parm
- parse()
: PDBAtom
- ParseOptions()
: ParseOptions
- partition()
: ComputeMap
, RecBisection
- Patch()
: Patch
- patch()
: PatchMap
- 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
- PatchData()
: msm::PatchData
- patchDataStrc()
: patchDataStrc
- PatchElem()
: PatchElem
- PatchInfo()
: PatchInfo
- patchLoad()
: LdbCoordinator
- PatchMap()
: PatchMap
- patchMapInit()
: WorkDistrib
- PatchMgr()
: PatchMgr
- PatchProxyListMsg()
: PatchProxyListMsg
- patchPtrArray()
: ComputeMsmMgr
- patchReady()
: Compute
, CudaComputeNonbonded
- PatchReady()
: Sync
- PatchRec()
: ComputeMap::PatchRec
- PatchRecord()
: CudaComputeNonbonded::PatchRecord
- pauseWork()
: LdbCoordinator
- pcpair()
: Rebalancer::pcpair
- PDB()
: PDB
- PDBAtom()
: PDBAtom
- PDBAtomRecord()
: PDBAtomRecord
- PDBData()
: PDBData
- PDBHetatm()
: PDBHetatm
- PDBUnknown()
: PDBUnknown
- 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
- peOrderingReady()
: WorkDistrib
- periodic_a()
: PatchMap
- periodic_b()
: PatchMap
- periodic_c()
: PatchMap
- pid()
: ComputeMap
, PatchMap
- pid_compare_priority()
: cr_sortop_reverse_priority
- PluginIOMgr()
: PluginIOMgr
- pme_kspace()
: PmeXPencil
- pme_select()
: SimParameters
- PmeAtomFiler()
: PmeAtomFiler
- PmeAtomStorage()
: PmeAtomStorage
- PmeDoneMsg()
: PmeDoneMsg
- PmeKSpace()
: PmeKSpace
- PmeKSpaceCompute()
: PmeKSpaceCompute
- PmePencil()
: PmePencil< T >
- PmePencilInitMsg()
: PmePencilInitMsg
- PmePencilMap()
: PmePencilMap
- PmePencilX()
: PmePencilX
- PmePencilXMap()
: PmePencilXMap
- PmePencilXY()
: PmePencilXY
- PmePencilXYMap()
: PmePencilXYMap
- PmePencilXYZ()
: PmePencilXYZ
- PmePencilXYZMap()
: PmePencilXYZMap
- PmePencilY()
: PmePencilY
- PmePencilZ()
: PmePencilZ
- PmeRealSpace()
: PmeRealSpace
- PmeRealSpaceCompute()
: PmeRealSpaceCompute
- PmeTranspose()
: PmeTranspose
- PmeXPencil()
: PmeXPencil
- PmeYPencil()
: PmeYPencil
- PmeZPencil()
: PmeZPencil
- pntChrgDist()
: pntChrgDist
- Pointer()
: Pointer
- pollChargeGridReady()
: ComputePmeMgr
- pollForcesReady()
: ComputePmeMgr
- populateInitial()
: PmePencilMap
, PmePencilXYZMap
, PmePencilXMap
, PmePencilXYMap
- position_distance()
: colvarproxy_namd
- positionBoxClosed()
: Patch
- positionsReady()
: HomePatch
, Patch
- preadln()
: parm
- prepare_qm()
: Molecule
- prepareTileList()
: CudaTileListKernel
- PressureProfileReduction()
: PressureProfileReduction
- print()
: MoaData
, MsmTimer
, MsmProfiler
, IRSet
- 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
- printComputeMap()
: ComputeMap
- printDynamicsEnergies()
: Controller
- printEnergies()
: Controller
- PrintEnergyInfo()
: ARestraintManager
- printFepMessage()
: Controller
- PrintHeader()
: ALambdaControl
, ALambdaManager
- PrintInfo()
: ARestraint
, APosRestraint
, ADistRestraint
, ADiheRestraint
, AnAngleRestraint
- 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
- PriorityQueue()
: msm::PriorityQueue< T >
- processData()
: GlobalMaster
- processFullQM()
: ComputeQM
- processorInfo()
: processorInfo
- procNum()
: PmePencilMap
, PmePencilXYMap
, MsmBlockMap
, MsmGridCutoffMap
, PmePencilXYZMap
, PmePencilXMap
- procQMRes()
: ComputeQMMgr
- procTrans()
: ComputePmeMgr
- procUntrans()
: ComputePmeMgr
- prolongation()
: MsmBlock
, MsmC1HermiteBlock
- prolongationKernel()
: MsmBlockKernel< Vtype, Mtype >
- ProxyElem()
: ProxyElem
- ProxyMgr()
: ProxyMgr
- ProxyPatch()
: ProxyPatch
- ProxyTree()
: ProxyTree
- proxyTreeNode()
: proxyTreeNode
- ProxyUsage()
: ProxyUsage
- ProxyUsageKey()
: ProxyUsageKey
- psiSumBoxClosed()
: Patch
- publish()
: SimpleBroadcastObject< T >
- pup()
: HashPoolAdaptorT< T >
, Pointer
, Int2
, Int3
, ConstPointer
, LocalLBInfoMsg
, MoaData
- push_back()
: HashPool< T >
- put()
: GridMsg
, MOStream
, MsmC1HermiteGridCutoffProxyMsg
, MOStream
, MsmGridCutoffSetupMsg
, MOStream
, MsmBlockProxyMsg
, MOStream
, MsmC1HermiteBlockProxyMsg
, MOStream
, MsmC1HermiteGridCutoffSetupMsg
, MOStream
, MsmGridCutoffProxyMsg
- put_stir_startTheta()
: Molecule