- a -

• AngleElem : Molecule
• AnisoElem : Molecule
• AtomMapper : AtomMap

- b -

• BondElem : Molecule
• Box< Owner, Data > : OwnerBox< Owner, Data >
• BroadcastMgr : BroadcastMsg

- c -

• CheckpointMsg : Controller
• colvarproxy_namd : ScriptTcl
• ComputeGlobal : HomePatch
• ComputeMgr : ComputeMap
• ComputePme : ComputePmeMgr , NodePmeMgr
• ComputePmeMgr : ComputePme , NodePmeMgr
• Controller : NamdState , ScriptTcl
• cross : Vector
• CrosstermElem : Molecule

- d -

• DataExchanger : ScriptTcl
• diagonal : Tensor
• DihedralElem : Molecule

- e -

• EntryGlob< Elem > : Entry< Elem >
• ExclElem : Molecule

- g -

• GlobalMasterTcl : ScriptTcl
• Grid< T > : msm::GridFixed< T, N >
• GridforceFullBaseGrid : GridforceFullMainGrid , GridforceFullSubGrid
• GridforceFullMainGrid : GridforceFullBaseGrid , GridforceFullSubGrid
• GridforceFullSubGrid : GridforceFullBaseGrid , GridforceFullMainGrid
• GromacsPairElem : Molecule

- h -

• HomePatch : Sequencer

- i -

• IMDOutput : GlobalMasterIMD
• ImproperElem : Molecule

- m -

• memusage : memusageinit
• Molecule : Parameters
• msm::PatchData : ComputeMsmMgr
• MsmBlock : ComputeMsmMgr
• MsmBlockMap : ComputeMsmMgr
• MsmGridCutoffMap : ComputeMsmMgr

- n -

• Namd : NamdState
• Node : Controller , NamdState
• NodePmeMgr : ComputePmeMgr

- o -

• off_diagonal : Tensor
• OneFourNbTholeElem : Molecule
• operator!= : Tensor , Vector
• operator* : C1Matrix , C1Vector , MathArray< Elem, Size > , Tensor , Vector
• operator+ : C1Vector , cudaTensor , MathArray< Elem, Size > , Tensor , Vector
• operator- : MathArray< Elem, Size > , Tensor , Vector
• operator/ : MathArray< Elem, Size > , Tensor , Vector
• operator== : Tensor , Vector
• outer : Tensor
• OwnerBox< Owner, Data > : Box< Owner, Data >

- p -

• PatchMap : PatchMgr
• PatchMgr : HomePatch

- r -

• ReductionMgr : RequireReductionCharm , SubmitReductionCharm
• RequireReduction : ReductionMgr
• RequireReductionCharm : ReductionMgr
• RequireReductionShared : ReductionMgr
• ResizeArray< Elem > : ResizeArrayRaw< Elem >
• ResizeArrayIter< Elem > : ResizeArray< Elem > , ResizeArrayRaw< Elem >

- s -

• ScriptTcl : Controller , NamdState
• Sequencer : HomePatch
• SequencerCUDA : HomePatch , Sequencer
• SetEqual : AVector
• SimParameters : Output
• SortableResizeArray< Elem > : ResizeArrayRaw< Elem >
• SortedArray< Elem > : ResizeArrayRaw< Elem >
• SubmitReduction : ReductionMgr
• SubmitReductionCharm : ReductionMgr
• SubmitReductionShared : ReductionMgr
• swap : msm::Array< T >
• symmetric : Tensor

- t -

• TholeElem : Molecule
• trace : Tensor
• transpose : Tensor
• triangular : Tensor

- u -

• UniqueSet< Elem > : UniqueSetRaw< Elem >
• UniqueSetIter< Elem > : EntryGlob< Elem > , UniqueSet< Elem > , UniqueSetRaw< Elem >
• UniqueSetRaw< Elem > : Entry< Elem > , EntryGlob< Elem >
• UniqueSortedArray< Elem > : ResizeArrayRaw< Elem >

- w -

• WorkDistrib : ComputeMap , Molecule , PatchMap