Here is a list of all class members with links to the classes they belong to:
- a -
- A
: LJTable::TableEntry
, go_pair
, indexed_vdw_pair
- a()
: Lattice
, ComputeMsmMgr
- A
: vdw_pair_params
- a
: NL_Msm_t
, sortop_base
- A12_f
: ComputeNonbondedUtil
- A14
: vdw_pair_params
, indexed_vdw_pair
- A6_f
: ComputeNonbondedUtil
- a_cut
: GBISParamStruct
, GBISParam< 1 >
, GBISParam< 3 >
- a_data_dev
: ComputePmeMgr
- a_data_host
: ComputePmeMgr
- a_dim
: TopoManagerWrapper
- a_f
: NL_Msm_t
- a_mod
: TopoManagerWrapper
- a_p()
: Lattice
- a_r()
: Lattice
- a_rot
: TopoManagerWrapper
- a_total
: nodesort
- aa
: thole
- aaAngleExp
: SimParameters
- abuffer
: msm::Array< T >
- accelMDalpha
: SimParameters
- accelMDDebugOn
: SimParameters
- accelMDdihe
: SimParameters
- accelMDdoDihe
: ComputeHomeTuples< T, S, P >
- accelMDdual
: SimParameters
- accelMDdV
: Controller
- accelMDdVAverage
: Controller
- accelMDE
: SimParameters
- accelMDFirstStep
: SimParameters
- accelMDG
: SimParameters
- accelMDGcMDPrepSteps
: SimParameters
- accelMDGcMDSteps
: SimParameters
- accelMDGEquiPrepSteps
: SimParameters
- accelMDGEquiSteps
: SimParameters
- accelMDGiE
: SimParameters
- accelMDGresetVaftercmd
: SimParameters
- accelMDGRestart
: SimParameters
- accelMDGRestartFile
: SimParameters
- accelMDGSigma0D
: SimParameters
- accelMDGSigma0P
: SimParameters
- accelMDGStatWindow
: SimParameters
- accelMDLastStep
: SimParameters
- accelMDOn
: ComputeNonbondedUtil
, SimParameters
- accelMDOutFreq
: SimParameters
- accelMDRescaleFactor
: ControllerBroadcasts
- accelMDTalpha
: SimParameters
- accelMDTE
: SimParameters
- access_iout_obj()
: infostream
- Accumulate()
: ALambdaControl
, ALambdaManager
- ackAtomsToHomePatchProcs()
: ParallelIOMgr
- activate_pencils()
: ComputePmeMgr
, ComputePmeCUDADevice
, ComputePmeCUDAMgr
- active
: msm::FoldFactor
- activePatches
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- adaptTempAutoDt
: Controller
, SimParameters
- adaptTempBetaMax
: Controller
- adaptTempBetaMin
: Controller
- adaptTempBetaN
: Controller
- adaptTempBin
: Controller
- adaptTempBins
: Controller
, SimParameters
- adaptTempCg
: Controller
- adaptTempCgamma
: SimParameters
- adaptTempDBeta
: Controller
- adaptTempDebug
: SimParameters
- adaptTempDt
: Controller
, SimParameters
- adaptTempDTave
: Controller
- adaptTempDTavenum
: Controller
- adaptTempDtMax
: Controller
- adaptTempDtMin
: Controller
- adaptTemperature
: ControllerBroadcasts
- adaptTempFirstStep
: SimParameters
- adaptTempFreq
: SimParameters
- adaptTempInFile
: SimParameters
- adaptTempInit()
: Controller
- adaptTempLangevin
: SimParameters
- adaptTempLastStep
: SimParameters
- adaptTempOn
: SimParameters
- adaptTempOutFreq
: SimParameters
- adaptTempPotEnergyAve
: Controller
- adaptTempPotEnergyAveDen
: Controller
- adaptTempPotEnergyAveNum
: Controller
- adaptTempPotEnergySamples
: Controller
- adaptTempPotEnergyVar
: Controller
- adaptTempPotEnergyVarNum
: Controller
- adaptTempRandom
: SimParameters
- adaptTempRescale
: SimParameters
- adaptTempRestartFile
: Controller
, SimParameters
- adaptTempRestartFreq
: SimParameters
- adaptTempT
: Controller
, Sequencer
- adaptTempTmax
: SimParameters
- adaptTempTmin
: SimParameters
- adaptTempUpdate()
: Controller
, Sequencer
- adaptTempWriteRestart()
: Controller
- Add()
: AGroup
, ALambdaManager
, ARestraintManager
- add()
: MGridforceParamsList
, MigrateAtomsCombinedMsg
, SubmitReduction
, ResizeArray< T >
, SortedArray< Type >
, UniqueSet< Elem >
, UniqueSetRaw< Elem >
, UniqueSortedArray< Type >
- add14Type()
: VDWTable
- add_element()
: ConfigList
- add_energy()
: colvarproxy_namd
- addAngle()
: GenericMol
- addAtom()
: GenericMol
- addAtoms()
: PmeAtomStorage
- addAtomsWithIndex()
: PmeAtomStorage
- addBond()
: GenericMol
- addCharge()
: MsmBlock
, MsmC1HermiteBlock
- addClient()
: GlobalMasterServer
- addDihedral()
: GenericMol
- addEnergy()
: GlobalMasterEasy
- addForce()
: GlobalMasterEasy
, GlobalMasterFreeEnergy
- AddForces()
: ARestraintManager
- addForceToMomentum()
: HomePatch
, Sequencer
- addForceToMomentum3()
: HomePatch
, Sequencer
- addIndex()
: Pairlists
- addMovDragToPosition()
: Sequencer
- addPairGaussType2()
: PairTable
- addPairLJType2()
: PairTable
- addPotential()
: ComputeMsmMgr
, msm::PatchData
, MsmBlock
, MsmC1HermiteBlock
- addPotentialC1Hermite()
: msm::PatchData
- addRattleForce()
: HomePatch
- addRecipEvirClient()
: ComputePmeMgr
- addRotDragToPosition()
: Sequencer
- addToRemoteSequenceNumber
: ReductionSet
- addToSubgridsFlat()
: GridforceFullSubGrid
- addType()
: AtomTable
, BondTable
, AngleTable
, DihedralTable
, VDWTable
- addVelocityToPosition()
: HomePatch
, Sequencer
- addVirialContrib()
: ComputeMsmMgr
- ADiheRestraint()
: ADiheRestraint
- ADistRestraint()
: ADistRestraint
- adjustBackgroundLoadAndComputeAverage()
: Rebalancer
- af
: TuplePatchElem
- AGroup()
: AGroup
- aid
: CollectVectorMsg
, CollectVectorVarMsg
, CollectionMgr::CollectVectorInstance
, ComputeConsForceMsg
, ComputeGlobalDataMsg
, ComputeGlobalResultsMsg
, CollectProxyVectorInstance
- aid_size
: CollectVectorMsg
- ALambdaControl()
: ALambdaControl
- ALambdaManager()
: ALambdaManager
- alch_unpert_angles
: Molecule
- alch_unpert_bonds
: Molecule
- alch_unpert_dihedrals
: Molecule
- alchBondDecouple
: SimParameters
- alchBondLambdaEnd
: SimParameters
- alchDecouple
: ComputeNonbondedUtil
, ComputePmeUtil
, SimParameters
- alchDroppedAngles
: Molecule
- alchDroppedDihedrals
: Molecule
- alchDroppedImpropers
: Molecule
- alchElecLambdaStart
: ComputePmeUtil
, SimParameters
- alchEnsembleAvg
: SimParameters
- alchEquilSteps
: SimParameters
- alchFepOn
: ComputeNonbondedUtil
, ComputePmeUtil
, SimParameters
- alchFepOnAtStartup
: SimParameters
- alchIDWSFreq
: SimParameters
- alchLambda
: SimParameters
- alchLambda2
: SimParameters
- alchLambdaFreq
: SimParameters
- alchLambdaIDWS
: SimParameters
- alchMethod
: SimParameters
- alchOn
: ComputePmeUtil
, SimParameters
- alchOnAtStartup
: SimParameters
- alchOutFile
: SimParameters
- alchOutFreq
: SimParameters
- alchRepLambdaEnd
: SimParameters
- alchTemp
: SimParameters
- alchThermIntOn
: ComputeNonbondedUtil
, ComputePmeUtil
, SimParameters
- alchThermIntOnAtStartup
: SimParameters
- alchVdwLambdaEnd
: SimParameters
- alchVdwShiftCoeff
: ComputeNonbondedUtil
, SimParameters
- alchWCAOn
: ComputeNonbondedUtil
, SimParameters
- alchWork
: Controller
- alen
: msm::Array< T >
- Alg7()
: Alg7
- AlgNbor()
: AlgNbor
- algorithm()
: Controller
, Sequencer
- AlgRecBisection()
: AlgRecBisection
- AlignVector()
: AlignVector
- allAtoms
: MovePatchAtomsMsg
- allExclCnt
: ExclusionSignature
- allocateCids()
: ComputeMap
- allocateMap()
: AtomMap
- allPes
: ProxyNodeAwareSpanningTreeMsg
- allTuples
: ExclusionSignature
- alpha
: drude_constants
- alpha_cutoff
: SimParameters
- alpha_max
: GBISParamStruct
, SimParameters
- alphai
: nbthole_pair_params
, indexed_nbthole_pair
, nbthole_pair_value
- alphaj
: nbthole_pair_params
, indexed_nbthole_pair
, nbthole_pair_value
- alternatelocation()
: PDBAtom
- amax
: msm::Array< T >
- amberOn
: SimParameters
- amd_reduction
: Controller
- amdDiheVirialIndex_XX
: ComputeBondedCUDAKernel
- amdDiheVirialIndex_XY
: ComputeBondedCUDAKernel
- amdDiheVirialIndex_XZ
: ComputeBondedCUDAKernel
- amdDiheVirialIndex_YX
: ComputeBondedCUDAKernel
- amdDiheVirialIndex_YY
: ComputeBondedCUDAKernel
- amdDiheVirialIndex_YZ
: ComputeBondedCUDAKernel
- amdDiheVirialIndex_ZX
: ComputeBondedCUDAKernel
- amdDiheVirialIndex_ZY
: ComputeBondedCUDAKernel
- amdDiheVirialIndex_ZZ
: ComputeBondedCUDAKernel
- amdf
: Results
- AnAngleRestraint()
: AnAngleRestraint
- angle
: angle_params
, lphost
- angle_array
: Parameters
- angle_type
: angle
- AngleAt1
: parm
, AmberParm7Reader::Ambertoppar
- AngleAt2
: parm
, AmberParm7Reader::Ambertoppar
- AngleAt3
: parm
, AmberParm7Reader::Ambertoppar
- angleCnt
: AtomSignature
- AngleElem()
: AngleElem
, Molecule
, AngleElem
- angleEnergyIndex
: AngleElem
- angleEnergyIndex_f
: AngleElem
- angleEnergyIndex_ti_1
: AngleElem
- angleEnergyIndex_ti_2
: AngleElem
- AngleHAt1
: AmberParm7Reader::Ambertoppar
, parm
- AngleHAt2
: parm
, AmberParm7Reader::Ambertoppar
- AngleHAt3
: parm
, AmberParm7Reader::Ambertoppar
- AngleHNum
: parm
, AmberParm7Reader::Ambertoppar
- AngleNum
: parm
, AmberParm7Reader::Ambertoppar
- angleSigIndices
: AtomSigInfo
- angleSigs
: AtomSignature
- AnisoElem
: Molecule
, AnisoElem
- anisoEnergyIndex
: AnisoElem
- anisoEnergyIndex_f
: AnisoElem
- anisoEnergyIndex_ti_1
: AnisoElem
- anisoEnergyIndex_ti_2
: AnisoElem
- ANISOU
: PDBData
- ANTERP
: MsmTimer
- anterpolation()
: msm::PatchData
- anterpolationC1Hermite()
: msm::PatchData
- APosRestraint()
: APosRestraint
- append()
: CollectionMaster::CollectVectorInstance
, CollectionMgr::CollectVectorInstance
, ResidueLookupElem
, CollectProxyVectorInstance
, msm::Array< T >
- appForces
: GlobalMaster
- appForcesChanged
: GlobalMaster
- appliedForces()
: GlobalMaster
- apply_transform()
: Lattice
- Approx
: ComputeMsmMgr
- approx
: ComputeMsmMgr
, NL_Msm_t
- ARestraint()
: ARestraint
- ARestraintManager()
: ARestraintManager
- Array()
: Array< Elem, Size >
, msm::Array< T >
, Array< Elem, Size >
, msm::Array< T >
- assign()
: Rebalancer
- assign_angle_index()
: Parameters
- assign_bond_index()
: Parameters
- assign_crossterm_index()
: Parameters
- assign_dihedral_index()
: Parameters
- assign_improper_index()
: Parameters
- assign_vdw_index()
: Parameters
- assignBaseNode()
: PatchMap
- assignNode()
: PatchMap
- assignNodeToPatch()
: WorkDistrib
- assignPatches()
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
, CudaComputeNonbonded
- assignPatchesOnPe()
: CudaComputeNonbonded
- assignToPatch()
: PatchMap
- at_index()
: MGridforceParamsList
- atmIDs
: qmSolvData
- atoBool()
: MGridforceParamsList
- atom
: PmeAtomStorage
, NL_Msm_t
, MovePatchesMsg
, PDB
- ATOM
: PDBData
- atom1
: dihedral
, bond
, angle
, improper
, crossterm
, gromacsPair
, aniso
, thole
, Exclusion
, lphost
- atom1name
: nbthole_pair_params
, vdw_pair_params
, table_pair_params
, bond_params
, improper_params
, angle_params
, dihedral_params
, crossterm_params
- atom1wild
: dihedral_params
- atom2
: gromacsPair
, angle
, bond
, dihedral
, crossterm
, thole
, Exclusion
, improper
, lphost
, aniso
- atom2name
: vdw_pair_params
, nbthole_pair_params
, crossterm_params
, bond_params
, dihedral_params
, improper_params
, table_pair_params
, angle_params
- atom2wild
: dihedral_params
- atom3
: improper
, dihedral
, aniso
, thole
, angle
, crossterm
, lphost
- atom3name
: crossterm_params
, angle_params
, improper_params
, dihedral_params
- atom3wild
: dihedral_params
- atom4
: dihedral
, aniso
, crossterm
, improper
, lphost
, thole
- atom4name
: dihedral_params
, crossterm_params
, improper_params
- atom4wild
: dihedral_params
- atom5
: crossterm
- atom5name
: crossterm_params
- atom6
: crossterm
- atom6name
: crossterm_params
- atom7
: crossterm
- atom7name
: crossterm_params
- atom8
: crossterm
- atom8name
: crossterm_params
- atom_f
: NL_Msm_t
- atom_type_name()
: Parameters
- atomChainTypes
: Molecule
- atomcharge()
: Molecule
- atomFixed
: CompAtomExt
- AtomicInt
: PmePencil< T >
- atomID
: ImproperElem
, BondElem
, AngleElem
, AnisoElem
, DihedralElem
, TholeElem
, position_index
, HydrogenGroupID
, ExclElem
- atomid
: MoveAtomMsg
- atomID
: GromacsPairElem
, CrosstermElem
- atomIdBegin
: GlobalMaster
- atomIdEnd
: GlobalMaster
- atomIndex
: ResidueLookupElem
, PmeAtomStorage
- atomList
: MoveInputAtomsMsg
- atomMap
: ComputeNonbondedCUDA
, ComputeNonbondedMIC
- AtomMap()
: AtomMap
- atomMap
: ComputeHomeTuples< T, S, P >
, Node
- AtomMapper
: AtomMap
- atomMapper
: Patch
- AtomMapper()
: AtomMapper
- atommass()
: Molecule
- atomname
: vdw_params
, atom_name_info
- atomnameIdx
: AtomNameIdx
- atomNameIdx
: OutputAtomRecord::shortVals
, BasicAtomInfo
- AtomNames
: AmberParm7Reader::Ambertoppar
, parm
- AtomNumbers
: AmberParm7Reader::Ambertoppar
- atomPositionBegin
: GlobalMaster
- AtomRes
: parm
, AmberParm7Reader::Ambertoppar
- atoms
: PmeAtomPencilMsg
, HomePatch::checkpoint_t
, CheckpointAtomsMsg
, ComputeNonbondedCUDA
, PmeAtomMsg
, ExchangeAtomsMsg
, PDB
- atoms_1to4()
: Molecule
- atoms_map
: colvarproxy_namd
- atoms_size
: ComputeNonbondedCUDA
- atomsChanged
: ComputeNonbondedMIC
, ComputeNonbondedCUDA
- atomsCnt
: ClusterSizeMsg
, ClusterElem
- atomsCntList
: AtomsCntPerPatchMsg
- atomSigIdx
: BasicAtomInfo
, OutputAtomRecord::integerVals
- AtomSigInfo()
: AtomSigInfo
- AtomSignature()
: AtomSignature
- atomsInGroup
: HydrogenGroupID
, OutputAtomRecord::integerVals
- atomsInMigrationGroup
: OutputAtomRecord::integerVals
, HydrogenGroupID
- atomSort_0_sortValues__
: ComputeNonbondedWorkArrays
- atomSort_1_sortValues__
: ComputeNonbondedWorkArrays
- AtomsPerMolecule
: AmberParm7Reader::Ambertoppar
- atomStart
: CudaComputeNonbonded::PatchRecord
, CudaPatchRecord
- AtomSym
: parm
, AmberParm7Reader::Ambertoppar
- AtomTree
: parm
, AmberParm7Reader::Ambertoppar
- atomtype
: atom_name_info
- atomTypeIdx
: OutputAtomRecord::shortVals
, BasicAtomInfo
- atomtypeIdx
: AtomNameIdx
- atomUpdate()
: ComputePmeCUDA
, ComputePme
, ComputeNonbondedCUDA
, ComputeHomePatches
, ComputeHomeTuples< T, S, P >
, ComputeLCPO
, Compute
, CudaComputeNonbonded
, ComputeNonbondedMIC
, ComputePatchPair
, ComputeHomePatch
, ComputePatch
- atomvdwtype()
: Molecule
- AtSyncBarrierReached()
: LdbCoordinator
- AUTHOR
: PDBData
- auxFilename
: SimParameters
- available
: processorInfo
- AVector()
: AVector
- averageLoad
: SplitComputesMsg
, Rebalancer
- avg_count
: Controller
- avgCompute
: SplitComputesMsg
- avgPlLen
: ProxyDataMsg
- avgPositionBox
: PatchElem
, Patch
, ComputeNonbondedSelf
, TuplePatchElem
, ComputeNonbondedPair
- avgPositionBoxClosed()
: Patch
- avgPositionComputeList
: Patch
- avgPositionList
: ProxyDataMsg
- avgPositionPtrBegin
: Patch
- avgPositionPtrEnd
: Patch
- awaitBOCCheckIn()
: Node
- awaken()
: BroadcastClient
, BackEnd
, Controller
, Sequencer
- awakenSequencers()
: LdbCoordinator