- c -
- c()
: Lattice
- C1Matrix()
: C1Matrix
- C1Vector()
: C1Vector
- c_p()
: Lattice
- c_r()
: Lattice
- calc_accelMDG_E_k()
: Controller
- calc_accelMDG_force_factor()
: Controller
- calc_accelMDG_mean_std()
: Controller
- calc_error()
: ComputeNonbondedUtil
- calc_pair()
: ComputeNonbondedUtil
- calc_pair_energy()
: ComputeNonbondedUtil
- calc_pair_energy_fep()
: ComputeNonbondedUtil
- calc_pair_energy_fullelect()
: ComputeNonbondedUtil
- calc_pair_energy_fullelect_fep()
: ComputeNonbondedUtil
- calc_pair_energy_fullelect_go()
: ComputeNonbondedUtil
- calc_pair_energy_fullelect_int()
: ComputeNonbondedUtil
- calc_pair_energy_fullelect_les()
: ComputeNonbondedUtil
- calc_pair_energy_fullelect_pprof()
: ComputeNonbondedUtil
- calc_pair_energy_fullelect_tabener()
: ComputeNonbondedUtil
- calc_pair_energy_fullelect_ti()
: ComputeNonbondedUtil
- calc_pair_energy_go()
: ComputeNonbondedUtil
- calc_pair_energy_int()
: ComputeNonbondedUtil
- calc_pair_energy_les()
: ComputeNonbondedUtil
- calc_pair_energy_merge_fullelect()
: ComputeNonbondedUtil
- calc_pair_energy_merge_fullelect_fep()
: ComputeNonbondedUtil
- calc_pair_energy_merge_fullelect_go()
: ComputeNonbondedUtil
- calc_pair_energy_merge_fullelect_int()
: ComputeNonbondedUtil
- calc_pair_energy_merge_fullelect_les()
: ComputeNonbondedUtil
- calc_pair_energy_merge_fullelect_pprof()
: ComputeNonbondedUtil
- calc_pair_energy_merge_fullelect_tabener()
: ComputeNonbondedUtil
- calc_pair_energy_merge_fullelect_ti()
: ComputeNonbondedUtil
- calc_pair_energy_pprof()
: ComputeNonbondedUtil
- calc_pair_energy_slow_fullelect()
: ComputeNonbondedUtil
- calc_pair_energy_slow_fullelect_fep()
: ComputeNonbondedUtil
- calc_pair_energy_slow_fullelect_go()
: ComputeNonbondedUtil
- calc_pair_energy_slow_fullelect_les()
: ComputeNonbondedUtil
- calc_pair_energy_slow_fullelect_pprof()
: ComputeNonbondedUtil
- calc_pair_energy_slow_fullelect_tabener()
: ComputeNonbondedUtil
- calc_pair_energy_slow_fullelect_ti()
: ComputeNonbondedUtil
- calc_pair_energy_tabener()
: ComputeNonbondedUtil
- calc_pair_energy_ti()
: ComputeNonbondedUtil
- calc_pair_fullelect()
: ComputeNonbondedUtil
- calc_pair_fullelect_go()
: ComputeNonbondedUtil
- calc_pair_fullelect_les()
: ComputeNonbondedUtil
- calc_pair_fullelect_pprof()
: ComputeNonbondedUtil
- calc_pair_fullelect_tabener()
: ComputeNonbondedUtil
- calc_pair_fullelect_ti()
: ComputeNonbondedUtil
- calc_pair_go()
: ComputeNonbondedUtil
- calc_pair_les()
: ComputeNonbondedUtil
- calc_pair_merge_fullelect()
: ComputeNonbondedUtil
- calc_pair_merge_fullelect_go()
: ComputeNonbondedUtil
- calc_pair_merge_fullelect_les()
: ComputeNonbondedUtil
- calc_pair_merge_fullelect_pprof()
: ComputeNonbondedUtil
- calc_pair_merge_fullelect_tabener()
: ComputeNonbondedUtil
- calc_pair_merge_fullelect_ti()
: ComputeNonbondedUtil
- calc_pair_pprof()
: ComputeNonbondedUtil
- calc_pair_slow_fullelect()
: ComputeNonbondedUtil
- calc_pair_slow_fullelect_go()
: ComputeNonbondedUtil
- calc_pair_slow_fullelect_les()
: ComputeNonbondedUtil
- calc_pair_slow_fullelect_pprof()
: ComputeNonbondedUtil
- calc_pair_slow_fullelect_tabener()
: ComputeNonbondedUtil
- calc_pair_slow_fullelect_ti()
: ComputeNonbondedUtil
- calc_pair_tabener()
: ComputeNonbondedUtil
- calc_pair_ti()
: ComputeNonbondedUtil
- calc_self()
: ComputeNonbondedUtil
- calc_self_energy()
: ComputeNonbondedUtil
- calc_self_energy_fep()
: ComputeNonbondedUtil
- calc_self_energy_fullelect()
: ComputeNonbondedUtil
- calc_self_energy_fullelect_fep()
: ComputeNonbondedUtil
- calc_self_energy_fullelect_go()
: ComputeNonbondedUtil
- calc_self_energy_fullelect_int()
: ComputeNonbondedUtil
- calc_self_energy_fullelect_les()
: ComputeNonbondedUtil
- calc_self_energy_fullelect_pprof()
: ComputeNonbondedUtil
- calc_self_energy_fullelect_tabener()
: ComputeNonbondedUtil
- calc_self_energy_fullelect_ti()
: ComputeNonbondedUtil
- calc_self_energy_go()
: ComputeNonbondedUtil
- calc_self_energy_int()
: ComputeNonbondedUtil
- calc_self_energy_les()
: ComputeNonbondedUtil
- calc_self_energy_merge_fullelect()
: ComputeNonbondedUtil
- calc_self_energy_merge_fullelect_fep()
: ComputeNonbondedUtil
- calc_self_energy_merge_fullelect_go()
: ComputeNonbondedUtil
- calc_self_energy_merge_fullelect_int()
: ComputeNonbondedUtil
- calc_self_energy_merge_fullelect_les()
: ComputeNonbondedUtil
- calc_self_energy_merge_fullelect_pprof()
: ComputeNonbondedUtil
- calc_self_energy_merge_fullelect_tabener()
: ComputeNonbondedUtil
- calc_self_energy_merge_fullelect_ti()
: ComputeNonbondedUtil
- calc_self_energy_pprof()
: ComputeNonbondedUtil
- calc_self_energy_slow_fullelect()
: ComputeNonbondedUtil
- calc_self_energy_slow_fullelect_fep()
: ComputeNonbondedUtil
- calc_self_energy_slow_fullelect_go()
: ComputeNonbondedUtil
- calc_self_energy_slow_fullelect_les()
: ComputeNonbondedUtil
- calc_self_energy_slow_fullelect_pprof()
: ComputeNonbondedUtil
- calc_self_energy_slow_fullelect_tabener()
: ComputeNonbondedUtil
- calc_self_energy_slow_fullelect_ti()
: ComputeNonbondedUtil
- calc_self_energy_tabener()
: ComputeNonbondedUtil
- calc_self_energy_ti()
: ComputeNonbondedUtil
- calc_self_fullelect()
: ComputeNonbondedUtil
- calc_self_fullelect_go()
: ComputeNonbondedUtil
- calc_self_fullelect_les()
: ComputeNonbondedUtil
- calc_self_fullelect_pprof()
: ComputeNonbondedUtil
- calc_self_fullelect_tabener()
: ComputeNonbondedUtil
- calc_self_fullelect_ti()
: ComputeNonbondedUtil
- calc_self_go()
: ComputeNonbondedUtil
- calc_self_les()
: ComputeNonbondedUtil
- calc_self_merge_fullelect()
: ComputeNonbondedUtil
- calc_self_merge_fullelect_go()
: ComputeNonbondedUtil
- calc_self_merge_fullelect_les()
: ComputeNonbondedUtil
- calc_self_merge_fullelect_pprof()
: ComputeNonbondedUtil
- calc_self_merge_fullelect_tabener()
: ComputeNonbondedUtil
- calc_self_merge_fullelect_ti()
: ComputeNonbondedUtil
- calc_self_pprof()
: ComputeNonbondedUtil
- calc_self_slow_fullelect()
: ComputeNonbondedUtil
- calc_self_slow_fullelect_go()
: ComputeNonbondedUtil
- calc_self_slow_fullelect_les()
: ComputeNonbondedUtil
- calc_self_slow_fullelect_pprof()
: ComputeNonbondedUtil
- calc_self_slow_fullelect_tabener()
: ComputeNonbondedUtil
- calc_self_slow_fullelect_ti()
: ComputeNonbondedUtil
- calc_self_tabener()
: ComputeNonbondedUtil
- calc_self_ti()
: ComputeNonbondedUtil
- calcAtomsInEachPatch()
: ParallelIOMgr
- calcBlockWork()
: ComputeMsmMgr
- calcFixVirial()
: Sequencer
- calcGBIS()
: ComputeNonbondedUtil
- calcGcutWork()
: ComputeMsmMgr
- calcGridCoord()
: PmeRealSpaceCompute
- calcKineticEnergy()
: Sequencer
- calcMOPAC()
: ComputeQMMgr
- calcORCA()
: ComputeQMMgr
- calcPressure()
: Controller
- calculate()
: colvarproxy_namd
, GlobalMaster
, GlobalMasterIMD
, GlobalMasterTcl
, GlobalMasterTest
- calcUSR()
: ComputeQMMgr
- calpmf()
: eABF
, eABF1D
- center()
: PatchMap
- chain()
: PDBAtom
- changedAtoms()
: GlobalMaster
- changedForces()
: GlobalMaster
- changedGridObjs()
: GlobalMaster
- changedGroups()
: GlobalMaster
- chargeGridReady()
: ComputePmeMgr
- chargeGridSubmitted()
: ComputePmeMgr
- check()
: GlobalMaster
- check_atom_id()
: colvarproxy_namd
- check_consistency()
: ParseOptions
- checkexcl()
: Molecule
- checkIn()
: OwnerBox< Owner, Data >
- checkMap()
: AtomMap
, ComputeMap
, PatchMap
- checkOut()
: OwnerBox< Owner, Data >
- checkpoint()
: HomePatch
- cid()
: PatchMap
- clear()
: HashPool< T >
, PmeAtomStorage
, ofstream_namd
, MGridforceParamsList
, msm::PriorityQueue< T >
, ResizeArray< T >
, UniqueSet< Elem >
, Entry< Elem >
, EntryGlob< Elem >
, UniqueSetRaw< Elem >
- Clear()
: AGroup
, ALambdaManager
- clear_atom()
: colvarproxy_namd
- clear_atom_group()
: colvarproxy_namd
- clear_volmap()
: colvarproxy_namd
- clearChain()
: Entry< Elem >
, EntryGlob< Elem >
- clearChanged()
: GlobalMaster
- clearTileListStat()
: CudaTileListKernel
- clientAdd()
: OwnerBox< Owner, Data >
- clientClose()
: OwnerBox< Owner, Data >
- clientOpen()
: OwnerBox< Owner, Data >
- clientRemove()
: OwnerBox< Owner, Data >
- clipBlockToIndexRange()
: msm::Map
- clipBlockToIndexRangeFold()
: msm::Map
- clipIndexToLevel()
: msm::Map
- cloneCompute()
: ComputeMap
- close()
: Box< Owner, Data >
, ofstream_namd
, OwnerBox< Owner, Data >
- close_dcdfile()
: SimParameters
- close_output_stream()
: colvarproxy_namd
- close_veldcdfile()
: SimParameters
- ClusterCoorElem()
: ClusterCoorElem
- ClusterElem()
: ClusterElem
- CollectionMaster()
: CollectionMaster
- CollectionMgr()
: CollectionMgr
- collectLoads()
: LdbCoordinator
- CollectProxyVectorInstance()
: CollectProxyVectorInstance
- CollectProxyVectorSequence()
: CollectProxyVectorSequence
- CollectVectorInstance()
: CollectionMaster::CollectVectorInstance
, CollectionMgr::CollectVectorInstance
- CollectVectorSequence()
: CollectionMaster::CollectVectorSequence
- colvarproxy_namd()
: colvarproxy_namd
- Communicate()
: Communicate
- compare()
: HashPoolAdaptorT< T >
, ProxyUsageKey
- compareChecksums()
: Controller
- compute()
: ComputeMap
- Compute()
: Compute
- compute()
: ComputeMsmMgr
, MsmGridCutoffKernel< Vtype, Mtype >
- compute_a()
: GridforceFullBaseGrid
- compute_b()
: GridforceFullBaseGrid
, GridforceFullMainGrid
, GridforceFullSubGrid
- compute_d2V()
: GridforceFullBaseGrid
- compute_d3V()
: GridforceFullBaseGrid
- compute_derivative_grids()
: GridforceLiteGrid
- compute_dV()
: GridforceFullBaseGrid
- compute_energy()
: PmeKSpace
- compute_energy_orthogonal_helper()
: PmeKSpace
- compute_energy_orthogonal_subset()
: PmeKSpace
- compute_forces()
: PmeRealSpace
- compute_forces_order4_partial()
: PmeRealSpace
- compute_LJcorrection()
: Molecule
- compute_V()
: GridforceFullBaseGrid
- compute_VdV()
: GridforceFullMainGrid
, GridforceGrid
, GridforceFullBaseGrid
, GridforceLiteGrid
- compute_wts()
: GridforceLiteGrid
- computeAlchWork()
: Controller
- ComputeAngles()
: ComputeAngles
- ComputeAniso()
: ComputeAniso
- computeAverage()
: Rebalancer
- ComputeBondedCUDAKernel()
: ComputeBondedCUDAKernel
- ComputeBonds()
: ComputeBonds
- ComputeConsForce()
: ComputeConsForce
- ComputeConsForceMsg()
: ComputeConsForceMsg
- ComputeConsTorque()
: ComputeConsTorque
- ComputeCrossterms()
: ComputeCrossterms
- ComputeCUDAMgr()
: ComputeCUDAMgr
- ComputeCylindricalBC()
: ComputeCylindricalBC
- ComputeData()
: ComputeMap::ComputeData
- ComputeDihedrals()
: ComputeDihedrals
- ComputeDPMEDataMsg()
: ComputeDPMEDataMsg
- ComputeDPMEResultsMsg()
: ComputeDPMEResultsMsg
- ComputeEField()
: ComputeEField
- ComputeEwald()
: ComputeEwald
- ComputeExcls()
: ComputeExcls
- ComputeExt()
: ComputeExt
- ComputeExtMgr()
: ComputeExtMgr
- ComputeFmmSerial()
: ComputeFmmSerial
- ComputeFmmSerialMgr()
: ComputeFmmSerialMgr
- computeForce()
: AngleElem
, BondElem
, CrosstermElem
, DihedralElem
, ImproperElem
, ExclElem
, TholeElem
, GromacsPairElem
, AnisoElem
- ComputeFullDirect()
: ComputeFullDirect
- ComputeGBISser()
: ComputeGBISser
- ComputeGBISserMgr()
: ComputeGBISserMgr
- ComputeGlobal()
: ComputeGlobal
- ComputeGlobalDataMsg()
: ComputeGlobalDataMsg
- ComputeGlobalResultsMsg()
: ComputeGlobalResultsMsg
- ComputeGridForce()
: ComputeGridForce
- ComputeGromacsPair()
: ComputeGromacsPair
- ComputeHomePatch()
: ComputeHomePatch
- ComputeHomePatches()
: ComputeHomePatches
- ComputeHomeTuples()
: ComputeHomeTuples< T, S, P >
- ComputeImpropers()
: ComputeImpropers
- ComputeLCPO()
: ComputeLCPO
- ComputeMap()
: ComputeMap
- computeMax()
: Rebalancer
- ComputeMgr()
: ComputeMgr
- ComputeMoa()
: ComputeMoa
- ComputeMsm()
: ComputeMsm
- ComputeMsmMgr()
: ComputeMsmMgr
- ComputeMsmSerial()
: ComputeMsmSerial
- ComputeMsmSerialMgr()
: ComputeMsmSerialMgr
- ComputeNonbondedCUDA()
: ComputeNonbondedCUDA
- ComputeNonbondedMIC()
: ComputeNonbondedMIC
- ComputeNonbondedPair()
: ComputeNonbondedPair
- ComputeNonbondedSelf()
: ComputeNonbondedSelf
- ComputeNonbondedUtil()
: ComputeNonbondedUtil
- ComputePatch()
: ComputePatch
- ComputePatchPair()
: ComputePatchPair
- ComputePme()
: ComputePme
- ComputePmeCUDA()
: ComputePmeCUDA
- ComputePmeCUDADevice()
: ComputePmeCUDADevice
- ComputePmeCUDAMgr()
: ComputePmeCUDAMgr
- ComputePmeMgr()
: ComputePmeMgr
- ComputePmeUtil()
: ComputePmeUtil
- ComputeQM()
: ComputeQM
- ComputeQMAtom()
: ComputeQMAtom
- ComputeQMMgr()
: ComputeQMMgr
- ComputeQMPntChrg()
: ComputeQMPntChrg
- ComputeRestraints()
: ComputeRestraints
- ComputeSelfAngles()
: ComputeSelfAngles
- ComputeSelfAniso()
: ComputeSelfAniso
- ComputeSelfBonds()
: ComputeSelfBonds
- ComputeSelfCrossterms()
: ComputeSelfCrossterms
- ComputeSelfDihedrals()
: ComputeSelfDihedrals
- ComputeSelfExcls()
: ComputeSelfExcls
- ComputeSelfGromacsPair()
: ComputeSelfGromacsPair
- ComputeSelfImpropers()
: ComputeSelfImpropers
- ComputeSelfThole()
: ComputeSelfThole
- ComputeSelfTuples()
: ComputeSelfTuples< T, S, P >
- ComputeSphericalBC()
: ComputeSphericalBC
- ComputeStir()
: ComputeStir
- ComputeTclBC()
: ComputeTclBC
- ComputeThole()
: ComputeThole
- configFileInit()
: NamdState
- ConfigList()
: ConfigList
- configListInit()
: NamdState
- ConfigListNode()
: ConfigList::ConfigListNode
- const_begin()
: Array< Elem, Size >
, ResizeArray< T >
- const_end()
: ResizeArray< T >
, Array< Elem, Size >
- constant()
: Matrix4
- ConstPointer()
: ConstPointer
- contributeHostDeviceLDB()
: WorkDistrib
- contributeToParent()
: NodeProxyMgr
- Controller()
: Controller
- ControllerBroadcasts()
: ControllerBroadcasts
- convertscale()
: eABF1D
- coord()
: TopoManagerWrapper
- coordArray()
: msm::PatchData
- coordinate()
: Output
- coordinateNeeded()
: Output
- coordinates()
: PDBAtom
- coords()
: TopoManagerWrapper
- copy()
: ResizeArray< T >
, msm::Array< T >
- copyAtoms()
: PmeRealSpaceCompute
, CudaPmeRealSpaceCompute
- copyDataDeviceToDevice()
: CudaPmeTranspose
- copyDataDeviceToHost()
: CudaPmeTranspose
- copyDataHostToDevice()
: CudaPmeTranspose
- copyDataToPeerDeviceYZX()
: CudaPmeTranspose
- copyDataToPeerDeviceZXY()
: CudaPmeTranspose
- copyPencils()
: ComputePmeMgr
- copyResults()
: ComputePmeMgr
- correctMomentum()
: Controller
, Sequencer
- CpuPmeAtomStorage()
: CpuPmeAtomStorage
- cr_sortop_distance()
: cr_sortop_distance
- cr_sortop_reverse_priority()
: cr_sortop_reverse_priority
- createAtomLists()
: WorkDistrib
- createCommands()
: Measure
- createComputes()
: ComputeMgr
- createCudaComputeNonbonded()
: ComputeCUDAMgr
- createDevicesAndAtomFiler()
: ComputePmeCUDAMgr
- createHomePatch()
: PatchMgr
- createHomePatches()
: ParallelIOMgr
, WorkDistrib
- createLoadBalancer()
: LdbCoordinator
- createPatchProxyListMsg()
: PatchProxyListMsg
- createProxies()
: ProxyMgr
- createProxy()
: ProxyMgr
- createProxyInfo()
: NodeProxyMgr
- createSpanningTree()
: Rebalancer
- createSTForHomePatches()
: NodeProxyMgr
- cross()
: AVector
, Vector
- crossterm_params()
: crossterm_params
- CrosstermElem()
: CrosstermElem
- cuda_submit_charges()
: ComputePmeMgr
- CudaComputeGBISKernel()
: CudaComputeGBISKernel
- CudaComputeNonbonded()
: CudaComputeNonbonded
- CudaComputeNonbondedKernel()
: CudaComputeNonbondedKernel
- CudaFFTCompute()
: CudaFFTCompute
- CudaNonbondedTables()
: CudaNonbondedTables
- CudaPmeAtomStorage()
: CudaPmeAtomStorage
- CudaPmeKSpaceCompute()
: CudaPmeKSpaceCompute
- CudaPmePencilX()
: CudaPmePencilX
- CudaPmePencilXY()
: CudaPmePencilXY
- CudaPmePencilXYZ()
: CudaPmePencilXYZ
- CudaPmePencilY()
: CudaPmePencilY
- CudaPmePencilZ()
: CudaPmePencilZ
- CudaPmeRealSpaceCompute()
: CudaPmeRealSpaceCompute
- CudaPmeTranspose()
: CudaPmeTranspose
- CudaPmeXInitMsg()
: CudaPmeXInitMsg
- CudaPmeXYInitMsg()
: CudaPmeXYInitMsg
- CudaPmeXYZInitMsg()
: CudaPmeXYZInitMsg
- CudaTileListKernel()
: CudaTileListKernel
- cycleBarrier()
: Sequencer
, Controller