- a -

• AngleElem : AngleElem, Molecule
• atom : PDB, colvarmodule::atom, MovePatchesMsg, colvarmodule
• atom_group : colvarmodule::atom_group, colvarmodule

- b -

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

- c -

• colvarbias_meta : colvarbias_meta, colvarbias_meta::hill
• colvarproxy : colvarmodule
• ComputeGlobal : ComputeGlobal, HomePatch
• ComputeMgr : ComputeMgr, ComputeMap
• ComputePme : ComputePme, ComputePmeMgr
• Controller : Controller, ScriptTcl, NamdState
• cross : Vector, AVector
• CrosstermElem : CrosstermElem, Molecule
• cvm::atom : colvarproxy_namd

- d -

• diagonal : Tensor
• DihedralElem : DihedralElem, Molecule

- e -

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

- g -

• GlobalMasterTcl : GlobalMasterTcl, ScriptTcl

- h -

• HomePatch : Sequencer

- i -

• ImproperElem : ImproperElem, Molecule

- m -

• memusage : memusageinit

- n -

• Namd : NamdState
• Node : Node, NamdState

- o -

• off_diagonal : Tensor
• operator * : Vector, UniqueSetIter< T >, Tensor, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, MathArray< Elem, Size >, AVector, colvarmodule::quaternion, colvarmodule::rmatrix, colvarmodule::vector1d< T, length >, colvarmodule::rvector
• operator!= : Vector, UniqueSetIter< T >, Tensor, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, colvarmodule::rvector
• operator+ : Vector, Tensor, MathArray< Elem, Size >, AVector, colvarmodule::quaternion, colvarmodule::rvector
• operator- : Vector, Tensor, MathArray< Elem, Size >, AVector, colvarmodule::quaternion, colvarmodule::rvector
• operator/ : Vector, Tensor, MathArray< Elem, Size >, AVector, colvarmodule::quaternion, colvarmodule::rvector
• operator< : nodesort, Exclusion, MovePatch, HydrogenGroupID, HomePatchElem, vmdforce, ExclElem, ImproperElem, TuplePatchElem, PatchElem, DihedralElem, CrosstermElem, BondElem, AngleElem, colvarbias_meta::hill
• operator<< : infostream, datastream, colvarmodule::quaternion, colvarmodule::matrix2d< T, outer_length, inner_length >, colvarmodule::vector1d< T, length >, colvarbias_meta::hill
• operator<= : colvarbias_meta::hill
• operator== : nodesort, Vector, UniqueSetIter< T >, Tensor, ExclusionSignature, AtomSignature, TupleSignature, Exclusion, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ProxyElem, MovePatch, HydrogenGroupID, HomePatchElem, vmdforce, ExclElem, ImproperElem, TuplePatchElem, PatchElem, DihedralElem, CrosstermElem, BondElem, AngleElem, colvarmodule::rvector, colvarbias_meta::hill, BOID, TaggedMsg, BroadcastClientElem
• operator> : colvarbias_meta::hill
• operator>= : colvarbias_meta::hill
• operator>> : colvarmodule::quaternion, colvarparse::read_block
• OptPmeCompute : OptPmeCompute, OptPmeMgr
• outer : Tensor, colvarmodule::rvector
• OwnerBox<Owner,Data> : Box< Owner, Data >

- p -

• PatchMap : PatchMap, PatchMgr
• PatchMgr : PatchMgr, HomePatch
• PositionBox<Owner> : PositionOwnerBox< Owner >
• PositionOwnerBox<Owner> : PositionBox< Owner >

- r -

• ReductionMgr : ReductionMgr, RequireReduction, SubmitReduction
• RequireReduction : ReductionMgr
• ResizeArray<Elem> : ResizeArrayRaw< Elem >
• ResizeArrayIter<Elem> : ResizeArrayRaw< Elem >, ResizeArray< Elem >

- s -

• ScriptTcl : ScriptTcl, NamdState, Controller
• Sequencer : Sequencer, HomePatch
• SetEqual : AVector
• SortableResizeArray<Elem> : ResizeArrayRaw< Elem >
• SubmitReduction : ReductionMgr
• symmetric : Tensor

- t -

• trace : Tensor
• transpose : Tensor, Matrix4, Matrix4TMD, colvarmodule::rmatrix
• triangular : Tensor

- u -

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

- w -

• WorkDistrib : WorkDistrib, PatchMap, ComputeMap

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