- a -
- a()
: Lattice
- a_p()
: Lattice
- a_r()
: Lattice
- access_iout_obj()
: infostream
- Accumulate()
: ALambdaControl
, ALambdaManager
- ackAtomsToHomePatchProcs()
: ParallelIOMgr
- activate_pencils()
: ComputePmeMgr
, ComputePmeCUDADevice
, ComputePmeCUDAMgr
- adaptTempInit()
: Controller
- adaptTempUpdate()
: Controller
, Sequencer
- adaptTempWriteRestart()
: Controller
- Add()
: ALambdaManager
, ARestraintManager
- add()
: MGridforceParamsList
, MigrateAtomsCombinedMsg
, SubmitReduction
, ResizeArray< T >
, SortedArray< Type >
, UniqueSet< Elem >
, UniqueSetRaw< Elem >
, UniqueSortedArray< Type >
- Add()
: AGroup
- 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
- addToSubgridsFlat()
: GridforceFullSubGrid
- addType()
: DihedralTable
, VDWTable
, AtomTable
, BondTable
, AngleTable
- addVelocityToPosition()
: HomePatch
, Sequencer
- addVirialContrib()
: ComputeMsmMgr
- ADiheRestraint()
: ADiheRestraint
- ADistRestraint()
: ADistRestraint
- adjustBackgroundLoadAndComputeAverage()
: Rebalancer
- AGroup()
: AGroup
- ALambdaControl()
: ALambdaControl
- ALambdaManager()
: ALambdaManager
- Alg7()
: Alg7
- AlgNbor()
: AlgNbor
- algorithm()
: Controller
, Sequencer
- AlgRecBisection()
: AlgRecBisection
- AlignVector()
: AlignVector
- allocateCids()
: ComputeMap
- allocateMap()
: AtomMap
- alternatelocation()
: PDBAtom
- AnAngleRestraint()
: AnAngleRestraint
- AngleElem()
: AngleElem
- AnisoElem()
: AnisoElem
- anterpolation()
: msm::PatchData
- anterpolationC1Hermite()
: msm::PatchData
- APosRestraint()
: APosRestraint
- append()
: ResidueLookupElem
, CollectionMaster::CollectVectorInstance
, CollectionMgr::CollectVectorInstance
, msm::Array< T >
, CollectProxyVectorInstance
- appliedForces()
: GlobalMaster
- apply_transform()
: Lattice
- 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
- atoBool()
: MGridforceParamsList
- atom()
: PDB
- atom_type_name()
: Parameters
- atomcharge()
: Molecule
- AtomMap()
: AtomMap
- AtomMapper()
: AtomMapper
- atommass()
: Molecule
- atoms()
: PDB
- atoms_1to4()
: Molecule
- AtomSigInfo()
: AtomSigInfo
- AtomSignature()
: AtomSignature
- atomUpdate()
: ComputePme
, ComputeNonbondedMIC
, ComputePatch
, Compute
, ComputeHomePatch
, ComputeLCPO
, ComputeNonbondedCUDA
, ComputePatchPair
, ComputePmeCUDA
, CudaComputeNonbonded
, ComputeHomeTuples< T, S, P >
, ComputeHomePatches
- atomvdwtype()
: Molecule
- AtSyncBarrierReached()
: LdbCoordinator
- AVector()
: AVector
- avgPositionBoxClosed()
: Patch
- awaitBOCCheckIn()
: Node
- awaken()
: Sequencer
, BroadcastClient
, Controller
, BackEnd
- awakenSequencers()
: LdbCoordinator