- a -

• a() : Lattice
• a_p() : Lattice
• a_r() : Lattice
• Accumulate() : ALambdaManager, ALambdaControl
• activate_pencils() : ComputePmeMgr
• Add() : ARestraintManager, ALambdaManager, AGroup
• add() : UniqueSortedArray< Elem >, UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ResizeArray< Elem >, SubmitReduction, MigrateAtomsCombinedMsg
• add14Type() : VDWTable
• add_element() : ConfigList
• addAngle() : GenericMol
• addAtom() : GenericMol
• addBond() : GenericMol
• addClient() : GlobalMasterServer
• addDihedral() : GenericMol
• addEnergy() : GlobalMasterEasy
• addForce() : GlobalMasterFreeEnergy, GlobalMasterEasy
• AddForces() : ARestraintManager
• addForceToMomentum() : Sequencer, HomePatch
• addMovDragToPosition() : Sequencer
• addRotDragToPosition() : Sequencer
• addType() : VDWTable, DihedralTable, AngleTable, BondTable, AtomTable
• addVelocityToPosition() : Sequencer, HomePatch
• ADiheRestraint() : ADiheRestraint
• ADistRestraint() : ADistRestraint
• adjustBackgroundLoadAndComputeAverage() : Rebalancer
• AGroup() : AGroup
• ALambdaControl() : ALambdaControl
• ALambdaManager() : ALambdaManager
• Alg7() : Alg7
• AlgNbor() : AlgNbor
• algorithm() : Sequencer, Controller
• AlgRecBisection() : AlgRecBisection
• AlignVector() : AlignVector
• alloc() : ReductionSubmitMsg
• allocateCids() : ComputeMap
• allocateMap() : AtomMap
• alternatelocation() : PDBAtom
• AnAngleRestraint() : AnAngleRestraint
• AngleElem() : AngleElem, Molecule
• APosRestraint() : APosRestraint
• append() : ResidueLookupElem, CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
• appliedForces() : GlobalMaster
• apply_transform() : Lattice
• ARestraint() : ARestraint
• ARestraintManager() : ARestraintManager
• Array() : Array< Elem, Size >
• 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
• assignToPatch() : PatchMap
• atom() : PDB, MovePatchesMsg
• atom_type_name() : Parameters
• atomcharge() : Molecule
• AtomMap() : AtomMap
• atommass() : Molecule
• atoms() : PDB, AtomStaticInfoMsg
• AtomsDisInfo() : AtomsDisInfo
• AtomSigInfo() : AtomSigInfo
• AtomSignature() : AtomSignature
• atomUpdate() : ComputePatchPair, ComputePatch, ComputeHomeTuples< T, S, P >, ComputeHomePatches, ComputeHomePatch, Compute
• atomvdwtype() : Molecule
• AVector() : AVector
• avgPositionBoxClosed() : Patch
• awaitBOCCheckIn() : Node
• awaken() : Sequencer, Controller, BroadcastClient, BackEnd
• awakenSequencers() : LdbCoordinator

- b -

• b() : Lattice, netint, GridforceGrid::box
• b_p() : Lattice
• b_r() : Lattice
• backward_fft() : PmeXPencil, PmeYPencil, PmeZPencil
• barrier() : LdbCoordinator, BackEnd
• base_init() : PmePencil< T >
• basenode() : PatchMap
• basePatchIDList() : PatchMap
• begin() : UniqueSetIter< T >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ResizeArray< Elem >, Array< Elem, Size >
• berendsenPressure() : Sequencer, Controller
• binaryRefine() : RefineTorusLB
• BOCCheckIn() : Node
• BOID() : BOID
• BondElem() : BondElem, Molecule
• boxClosed() : ProxyPatch, Patch, HomePatch
• brickDim() : Rebalancer
• BroadcastClient() : BroadcastClient
• BroadcastClientElem() : BroadcastClientElem
• BroadcastMgr() : BroadcastMgr, BroadcastMsg
• BroadcastMsg() : BroadcastMsg
• bsearch() : SortedArray< Elem >, SortableResizeArray< Elem >
• build_constant_forces() : Molecule
• build_constorque_params() : Molecule
• build_constraint_params() : Molecule
• build_exPressure_atoms() : Molecule
• build_extra_bonds() : Molecule
• build_fep_flags() : Molecule
• build_fixed_atoms() : Molecule
• build_gridforce_params() : Molecule
• build_langevin_params() : Molecule
• build_movdrag_params() : Molecule
• build_rotdrag_params() : Molecule
• build_stirred_atoms() : Molecule
• buildProxySpanningTree() : ProxyMgr
• buildProxySpanningTree2() : ProxyMgr
• buildSpanningTree() : HomePatch
• buildSpanningTree0() : ProxyMgr

- c -

• c() : Lattice, Rebalancer::pcpair, CrosstermValue
• c_p() : Lattice
• c_r() : Lattice
• caclNumAtomsInEachPatch() : WorkDistrib
• 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_int() : ComputeNonbondedUtil
• calc_pair_energy_fullelect_les() : ComputeNonbondedUtil
• calc_pair_energy_fullelect_pprof() : ComputeNonbondedUtil
• calc_pair_energy_fullelect_ti() : 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_int() : ComputeNonbondedUtil
• calc_pair_energy_merge_fullelect_les() : ComputeNonbondedUtil
• calc_pair_energy_merge_fullelect_pprof() : 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_les() : ComputeNonbondedUtil
• calc_pair_energy_slow_fullelect_pprof() : ComputeNonbondedUtil
• calc_pair_energy_slow_fullelect_ti() : ComputeNonbondedUtil
• calc_pair_energy_ti() : ComputeNonbondedUtil
• calc_pair_fullelect() : ComputeNonbondedUtil
• calc_pair_fullelect_les() : ComputeNonbondedUtil
• calc_pair_fullelect_pprof() : ComputeNonbondedUtil
• calc_pair_fullelect_ti() : ComputeNonbondedUtil
• calc_pair_les() : ComputeNonbondedUtil
• calc_pair_merge_fullelect() : ComputeNonbondedUtil
• calc_pair_merge_fullelect_les() : ComputeNonbondedUtil
• calc_pair_merge_fullelect_pprof() : ComputeNonbondedUtil
• calc_pair_merge_fullelect_ti() : ComputeNonbondedUtil
• calc_pair_pprof() : ComputeNonbondedUtil
• calc_pair_slow_fullelect() : ComputeNonbondedUtil
• calc_pair_slow_fullelect_les() : ComputeNonbondedUtil
• calc_pair_slow_fullelect_pprof() : ComputeNonbondedUtil
• calc_pair_slow_fullelect_ti() : 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_int() : ComputeNonbondedUtil
• calc_self_energy_fullelect_les() : ComputeNonbondedUtil
• calc_self_energy_fullelect_pprof() : ComputeNonbondedUtil
• calc_self_energy_fullelect_ti() : 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_int() : ComputeNonbondedUtil
• calc_self_energy_merge_fullelect_les() : ComputeNonbondedUtil
• calc_self_energy_merge_fullelect_pprof() : 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_les() : ComputeNonbondedUtil
• calc_self_energy_slow_fullelect_pprof() : ComputeNonbondedUtil
• calc_self_energy_slow_fullelect_ti() : ComputeNonbondedUtil
• calc_self_energy_ti() : ComputeNonbondedUtil
• calc_self_fullelect() : ComputeNonbondedUtil
• calc_self_fullelect_les() : ComputeNonbondedUtil
• calc_self_fullelect_pprof() : ComputeNonbondedUtil
• calc_self_fullelect_ti() : ComputeNonbondedUtil
• calc_self_les() : ComputeNonbondedUtil
• calc_self_merge_fullelect() : ComputeNonbondedUtil
• calc_self_merge_fullelect_les() : ComputeNonbondedUtil
• calc_self_merge_fullelect_pprof() : ComputeNonbondedUtil
• calc_self_merge_fullelect_ti() : ComputeNonbondedUtil
• calc_self_pprof() : ComputeNonbondedUtil
• calc_self_slow_fullelect() : ComputeNonbondedUtil
• calc_self_slow_fullelect_les() : ComputeNonbondedUtil
• calc_self_slow_fullelect_pprof() : ComputeNonbondedUtil
• calc_self_slow_fullelect_ti() : ComputeNonbondedUtil
• calc_self_ti() : ComputeNonbondedUtil
• calculate() : GlobalMasterTest, GlobalMasterTcl, GlobalMasterIMD, GlobalMaster
• chain() : PDBAtom
• changedAtoms() : GlobalMaster
• changedForces() : GlobalMaster
• changedGroups() : GlobalMaster
• check() : GlobalMaster
• check_consistancy() : ParseOptions
• checkexcl() : Molecule
• checkIn() : PositionOwnerBox< Owner >, OwnerBox< Owner, Data >
• checkMap() : PatchMap, ComputeMap, AtomMap
• checkOut() : PositionOwnerBox< Owner >, OwnerBox< Owner, Data >
• checkpoint() : HomePatch
• cid() : PatchMap, Compute
• Clear() : ALambdaManager, AGroup
• clear() : UniqueSetRaw< Elem >, EntryGlob< Elem >, Entry< Elem >, UniqueSet< Elem >
• clearChain() : EntryGlob< Elem >, Entry< Elem >
• clearChanged() : GlobalMaster
• clearMap() : AtomMap
• close() : PositionOwnerBox< Owner >, PositionBox< Owner >, OwnerBox< Owner, Data >, Box< Owner, Data >
• CollectionMaster() : CollectionMaster
• CollectionMasterHandler() : CollectionMasterHandler
• CollectionMgr() : CollectionMgr
• CollectVectorInstance() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
• Communicate() : Communicate
• compare() : ProxyUsageKey
• compareChecksums() : Controller
• CompAtom() : CompAtom
• CompAtomExt() : CompAtomExt
• Compute() : Compute
• compute() : ComputeMap, LocalWorkMsg, ComputeMap::ComputeData
• compute_energy() : PmeKSpace
• compute_forces() : PmeRealSpace
• ComputeAngles() : ComputeAngles
• computeAverage() : Rebalancer
• ComputeBonds() : ComputeBonds
• ComputeConsForce() : ComputeConsForce
• ComputeConsForceMsg() : ComputeConsForceMsg
• ComputeConsTorque() : ComputeConsTorque
• ComputeCrossterms() : ComputeCrossterms
• ComputeCylindricalBC() : ComputeCylindricalBC
• ComputeData() : ComputeMap::ComputeData
• ComputeDihedrals() : ComputeDihedrals
• ComputeDPMEDataMsg() : ComputeDPMEDataMsg
• ComputeDPMEResultsMsg() : ComputeDPMEResultsMsg
• ComputeEField() : ComputeEField
• ComputeEwald() : ComputeEwald
• ComputeExt() : ComputeExt
• ComputeExtMgr() : ComputeExtMgr
• computeForce() : ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
• ComputeFullDirect() : ComputeFullDirect
• ComputeGlobal() : ComputeGlobal, HomePatch
• ComputeGlobalConfigMsg() : ComputeGlobalConfigMsg
• ComputeGlobalDataMsg() : ComputeGlobalDataMsg
• ComputeGlobalResultsMsg() : ComputeGlobalResultsMsg
• ComputeGridForce() : ComputeGridForce
• ComputeHomePatch() : ComputeHomePatch
• ComputeHomePatches() : ComputeHomePatches
• ComputeHomeTuples() : ComputeHomeTuples< T, S, P >
• ComputeImpropers() : ComputeImpropers
• ComputeMap() : ComputeMap
• computeMax() : Rebalancer
• ComputeMgr() : ComputeMgr, ComputeMap
• ComputeNonbondedPair() : ComputeNonbondedPair
• ComputeNonbondedSelf() : ComputeNonbondedSelf
• ComputeNonbondedUtil() : ComputeNonbondedUtil
• ComputePatch() : ComputePatch
• ComputePatchPair() : ComputePatchPair
• ComputePme() : ComputePme, ComputePmeMgr
• ComputePmeMgr() : ComputePmeMgr
• ComputeRestraints() : ComputeRestraints
• ComputeSelfAngles() : ComputeSelfAngles
• ComputeSelfBonds() : ComputeSelfBonds
• ComputeSelfCrossterms() : ComputeSelfCrossterms
• ComputeSelfDihedrals() : ComputeSelfDihedrals
• ComputeSelfImpropers() : ComputeSelfImpropers
• ComputeSelfTuples() : ComputeSelfTuples< T, S, P >
• ComputeSphericalBC() : ComputeSphericalBC
• ComputeStir() : ComputeStir
• ComputeTclBC() : ComputeTclBC
• configFileInit() : NamdState
• ConfigList() : ConfigList
• configListInit() : NamdState
• ConfigListNode() : ConfigList::ConfigListNode
• const_begin() : ResizeArray< Elem >, Array< Elem, Size >
• const_end() : ResizeArray< Elem >, Array< Elem, Size >
• Controller() : Controller, NamdState
• ControllerBroadcasts() : ControllerBroadcasts
• coordinate() : Output
• coordinateNeeded() : Output
• coordinates() : PDBAtom
• copyPencils() : ComputePme
• copyResults() : ComputePme
• correctMomentum() : Sequencer, Controller
• createAtomLists() : WorkDistrib
• createComputes() : ComputeMgr
• createHomePatch() : PatchMgr
• createHomePatches() : WorkDistrib
• createLoadBalancer() : LdbCoordinator
• createProxies() : ProxyMgr
• createProxy() : ProxyMgr
• createSpanningTree() : Rebalancer
• cross() : Vector, AVector
• crossterm_params() : crossterm_params
• CrosstermElem() : CrosstermElem, Molecule
• cycleBarrier() : Sequencer, Controller

- d -

• DataElement() : ParseOptions::DataElement
• datastream() : datastream
• deAssign() : Rebalancer
• decrement() : ProxyUsage
• decrSTLoad() : Rebalancer
• defined() : ParseOptions
• del() : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ResizeArrayRaw< Elem >, ResizeArray< Elem >
• delData() : ReductionSet
• deleteMax() : maxHeap
• deleteMin() : minHeap
• delta() : Lattice, four_body_consts
• delTmpPatchAtomsList() : PatchMap
• depositCombinedResultMsg() : ProxyPatch
• depositMigration() : HomePatch
• diagonal() : Tensor
• dihedral_params() : dihedral_params
• DihedralElem() : DihedralElem, Molecule
• disposePositions() : CollectionMaster
• disposeVelocities() : CollectionMaster
• Dist() : AVector
• distribute() : MigrateAtomsCombinedMsg
• DistributeForce() : ARestraint
• distributeHomePatches() : WorkDistrib
• DistSqr() : AVector
• doAtomMigration() : HomePatch
• doForce() : ComputeStir, ComputeSphericalBC, ComputeRestraints, ComputePatchPair, ComputePatch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomePatch, ComputeGridForce, ComputeEField, ComputeCylindricalBC, ComputeConsTorque, ComputeConsForce
• doGroupSizeCheck() : HomePatch
• doMarginCheck() : HomePatch
• done_reading_files() : Parameters
• done_reading_structure() : Parameters
• doneDCD() : FileIOMgr, FileIO
• doneSaveComputeMap() : WorkDistrib
• doneUpdateLocalComputes() : ComputeMgr
• doPairlistCheck() : HomePatch
• dot() : Vector, AVector
• downstream() : PatchMap
• downstream2() : PatchMap
• downstreamNeighbors() : PatchMap
• doWork() : ComputeTclBC, ComputeSelfTuples< T, S, P >, ComputePme, ComputePatchPair, ComputePatch, ComputeHomeTuples< T, S, P >, ComputeHomePatch, ComputeGlobal, ComputeFullDirect, ComputeExt, ComputeEwald, Compute

- e -

• EarlyExit() : ARestraint
• earlyExit() : Node
• easy_calc() : GlobalMasterMisc, GlobalMasterEasy
• easy_init() : GlobalMasterMisc, GlobalMasterEasy
• element() : PDBAtom
• enableEarlyExit() : Node
• enableExitScheduler() : Node
• enableScriptBarrier() : Node
• end() : UniqueSetIter< T >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ResizeArray< Elem >, MOStream, Array< Elem, Size >
• endd() : datastream
• endi() : infostream
• endWork() : LdbCoordinator
• energy() : Output, ExtForceMsg
• enqueue() : CollectionMaster::CollectVectorSequence
• enqueueAngles() : WorkDistrib
• enqueueBonds() : WorkDistrib
• enqueueCollections() : Controller
• enqueueCrossterms() : WorkDistrib
• enqueueDihedrals() : WorkDistrib
• enqueueImpropers() : WorkDistrib
• enqueuePme() : WorkDistrib
• enqueuePositions() : CollectionMasterHandler, CollectionMaster
• enqueuePositionsFromHandler() : CollectionMaster
• enqueueSelfA() : WorkDistrib
• enqueueSelfB() : WorkDistrib
• enqueueVelocities() : CollectionMasterHandler, CollectionMaster
• enqueueVelocitiesFromHandler() : CollectionMaster
• enqueueWork() : WorkDistrib, Compute
• enqueueWorkA() : WorkDistrib
• enqueueWorkB() : WorkDistrib
• enqueueWorkC() : WorkDistrib
• ExclSigInfo() : ExclSigInfo
• Exclusion() : Exclusion
• ExclusionCheck() : ExclusionCheck
• ExclusionSignature() : ExclusionSignature
• ExecuteMigrations() : LdbCoordinator
• exists() : ParseOptions
• exit() : BackEnd
• ExitSchedOn() : BackEnd
• exitScheduler() : Node
• ExpectMigrate() : LdbCoordinator
• ExtForce() : ExtForce

- f -

• fft_init() : PmeXPencil, PmeYPencil, PmeZPencil
• field() : PDBData
• FileIO() : FileIOMgr, FileIO
• fill_charges() : PmeRealSpace
• fillHomePatchAtomList() : PatchMgr
• fillOnePatchAtoms() : WorkDistrib
• find() : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, Set, ResizeArrayRaw< Elem >, ResizeArray< Elem >, ConfigList
• find_extremes() : PDB
• findOffset() : ExclusionSignature
• firstwat() : parm
• floatcomplex() : floatcomplex
• FloatVector() : FloatVector
• footnote() : PDBAtom
• forceBoxClosed() : Patch
• forcedAtoms() : GlobalMaster
• forward_fft() : PmeXPencil, PmeYPencil, PmeZPencil
• free() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance

- g -

• gather_coordinates() : IMDOutput
• gather_energies() : IMDOutput
• gaussian() : Random
• gaussian_vector() : Random
• genclose() : parm
• GenericAngle() : GenericAngle
• GenericAtom() : GenericAtom
• GenericBond() : GenericBond
• GenericDihedral() : GenericDihedral
• GenericMol() : GenericMol
• genopen() : parm
• get() : ParseOptions, parm, MIStream, SimpleBroadcastObject< T >
• get_acceptor() : Molecule
• get_all_positions() : PDB
• get_angle() : Molecule
• get_angle_params() : Parameters
• get_angles_for_atom() : Molecule
• get_atom_from_index_in_residue() : Molecule
• get_atom_from_name() : Molecule
• get_atomtype() : Molecule
• get_bond() : Molecule
• get_bond_params() : Parameters
• get_bonds_for_atom() : Molecule
• get_box() : GridforceGrid
• get_center() : GridforceGrid
• get_cluster() : Molecule
• get_clusterSize() : Molecule
• get_cons_params() : Molecule
• get_constorque_params() : Molecule
• get_crossterm() : Molecule
• get_crossterms_for_atom() : Molecule
• get_dihedral() : Molecule
• get_dihedral_multiplicity() : Parameters
• get_dihedral_params() : Parameters
• get_dihedrals_for_atom() : Molecule
• get_donor() : Molecule
• Get_dU_dLambda() : AForcingDiheRestraint, AForcingAngleRestraint, AForcingDistRestraint, AForcingPosRestraint, ARestraint
• get_excl_check_for_atom() : Molecule
• get_exclusion() : Molecule
• get_exclusions_for_atom() : Molecule
• get_fep_type() : Molecule
• get_full_exclusions_for_atom() : Molecule
• get_gridfrc_grid() : Molecule
• get_gridfrc_params() : Molecule
• get_groupSize() : Molecule
• get_improper() : Molecule
• get_improper_multiplicity() : Parameters
• get_improper_params() : Parameters
• get_impropers_for_atom() : Molecule
• get_inv() : GridforceGrid
• get_mod_exclusions_for_atom() : Molecule
• get_mother_atom() : Molecule
• get_movdrag_params() : Molecule
• get_num_vdw_params() : Parameters
• get_position_for_atom() : PDB
• get_residue_size() : Molecule
• get_rotdrag_params() : Molecule
• get_stir_refPos() : Molecule
• get_stir_startTheta() : Molecule
• get_table() : LJTable
• get_table_dim() : LJTable
• get_vdw_pair_params() : Parameters
• get_vdw_params() : Parameters
• get_vmd_forces() : GlobalMasterIMD
• GetAccumulation() : ALambdaManager, ALambdaControl
• getANewMsg() : ProxyNodeAwareSpanningTreeMsg, ProxyResultVarsizeMsg
• GetAngle() : ARestraint
• getAngle() : GromacsTopFile, GenericMol
• getAngleParams() : GromacsTopFile
• GetAngleTarget() : AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AnAngleRestraint
• getAtom() : GromacsTopFile, GenericMol
• getAtomArrayIndex() : AtomsDisInfo
• getAtomi() : GenericDihedral, GenericAngle, GenericBond
• getAtomID() : GlobalMasterFreeEnergy, GlobalMasterEasy
• getAtomIdBegin() : GlobalMaster
• getAtomIdEnd() : GlobalMaster
• getAtomj() : GenericDihedral, GenericAngle, GenericBond
• getAtomk() : GenericDihedral, GenericAngle
• getAtoml() : GenericDihedral
• getAtomList() : HomePatch
• getAtomName() : GenericAtom
• getAtomParams() : GromacsTopFile
• getAtomPositionBegin() : GlobalMaster
• getAtoms() : Molecule
• getBond() : GromacsTopFile, GenericMol
• getBondParams() : GromacsTopFile
• GetBound() : ABoundAngleRestraint, ABoundDistRestraint, ABoundPosRestraint
• getbuf() : BroadcastMgr
• getCharge() : GenericAtom
• getData() : ReductionSet, PressureProfileReduction
• GetDihe() : ARestraint
• getDihedral() : GromacsTopFile, GenericMol
• getDihedralParams() : GromacsTopFile
• GetDiheTarget1() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, ADiheRestraint
• GetDiheTarget2() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, ADiheRestraint
• GetDistance() : AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, APosRestraint
• GetDistTarget() : AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, ADistRestraint
• GetE() : ADiheRestraint, AnAngleRestraint, ADistRestraint, APosRestraint
• GetEnergy() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, ARestraint
• getFlags() : ComputeHomePatches
• getForceIdBegin() : GlobalMaster
• getForceIdEnd() : GlobalMaster
• GetGrad() : ADiheRestraint, AnAngleRestraint, ADistRestraint, APosRestraint
• GetGradient() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, ARestraint
• getGroupMassBegin() : GlobalMaster
• getGroupMassEnd() : GlobalMaster
• getGroupPositionBegin() : GlobalMaster
• getGroupPositionEnd() : GlobalMaster
• getIndex() : DihedralTable, AngleTable, BondTable
• GetIntegration() : ALambdaManager, ALambdaControl
• GetIntervalAngle() : ABoundDiheRestraint
• GetKf() : ARestraint
• GetLambdaKf() : ARestraint, ALambdaControl
• GetLambdaRef() : ARestraint, ALambdaControl
• GetLambdas() : ALambdaManager
• getLastAtomsForcedBegin() : GlobalMaster
• getLastAtomsForcedEnd() : GlobalMaster
• getLastForcesBegin() : GlobalMaster
• GetLowerAngle() : ABoundDiheRestraint
• getMass() : GenericAtom, GlobalMasterFreeEnergy, GlobalMasterEasy
• getMasterNode() : ComputeEwald
• getMessage() : Communicate
• getMol() : MolInst
• getMoleculePointers() : ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
• getName() : GenericMol
• getNewArray() : ObjectArena< Type >
• getNum() : MolInst
• GetNum_dU_dLambda() : ALambdaManager, ALambdaControl
• GetNumAccumStepsSoFar() : ALambdaManager, ALambdaControl
• getNumAngleParams() : GromacsTopFile
• getNumAngles() : GromacsTopFile, MolInst, GenericMol
• getNumAtomParams() : GromacsTopFile
• getNumAtoms() : Patch, GromacsTopFile, MolInst, GenericMol, GlobalMasterFreeEnergy, GlobalMasterEasy
• getNumBondParams() : GromacsTopFile
• getNumBonds() : GromacsTopFile, MolInst, GenericMol
• getNumComputes() : Patch
• getNumDihedralParams() : GromacsTopFile
• getNumDihedrals() : GromacsTopFile, MolInst, GenericMol
• getNumFixedAtoms() : Patch
• GetNumGroups() : ARestraint
• GetNumInGroup() : AGroup
• GetNumObjects() : ALambdaManager
• getNumPatches() : Compute
• getNumRes() : MolInst, GenericMol
• GetNumRestraints() : ARestraintManager
• GetNumSteps() : ALambdaControl
• GetNumStepsSoFar() : ALambdaManager, ALambdaControl
• getNumStepsToRun() : LdbCoordinator
• getOwner() : PositionOwnerBox< Owner >, PositionBox< Owner >
• GetPaddedTaskStr() : ALambdaControl
• getParameterPointers() : ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
• getParams() : VDWTable, DihedralTable, AngleTable, BondTable, AtomTable
• getPatchID() : Patch
• getPosition() : GlobalMasterFreeEnergy, GlobalMasterEasy
• GetPosTarget() : AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, APosRestraint
• getPtree() : ProxyMgr
• getRecvSpanning() : ProxyMgr
• GetRefAngle() : AFixedDiheRestraint, ABoundAngleRestraint, AFixedAngleRestraint
• GetRefDist() : ABoundDistRestraint, AFixedDistRestraint, ABoundPosRestraint
• GetRefPos() : ABoundPosRestraint, AFixedPosRestraint
• getResNum() : GenericAtom
• getResType() : GenericAtom
• getScript() : Node
• getSendSpanning() : ProxyMgr
• getSpanningTreeChild() : ProxyPatch
• getSpanningTreeNChild() : ProxyPatch
• getSpanningTreeParent() : ProxyPatch
• GetStartAngle() : AForcingDiheRestraint, AForcingAngleRestraint
• GetStartDist() : AForcingDistRestraint
• GetStartPos() : AForcingPosRestraint
• GetStopAngle() : AForcingDiheRestraint, AForcingAngleRestraint
• GetStopDist() : AForcingDistRestraint
• GetStopPos() : AForcingPosRestraint
• GetStr() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, ARestraint
• getSystemName() : GromacsTopFile
• GetTask() : ALambdaControl
• GetTaskStr() : ALambdaControl
• getTmpPatchAtomsList() : PatchMap
• getTotalForce() : GlobalMaster
• GetTotalNumSteps() : ALambdaManager
• getTupleInfo() : ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
• getType() : AtomTable, GenericAtom, GenericDihedral, GenericAngle, GenericBond
• getTypeNum() : GenericAtom
• GetUpperAngle() : ABoundDiheRestraint
• getVal() : ProxyUsage
• getVDWParams() : GromacsTopFile
• GlobalMaster() : GlobalMaster
• GlobalMasterEasy() : GlobalMasterEasy
• GlobalMasterFreeEnergy() : GlobalMasterFreeEnergy
• GlobalMasterIMD() : GlobalMasterIMD
• GlobalMasterMisc() : GlobalMasterMisc
• GlobalMasterServer() : GlobalMasterServer
• GlobalMasterSMD() : GlobalMasterSMD
• GlobalMasterTcl() : GlobalMasterTcl
• GlobalMasterTMD() : GlobalMasterTMD
• gotoUsed() : UniqueSetIter< T >
• gradU() : ADiheRestraint
• gridCalc1() : ComputePmeMgr
• gridCalc2() : ComputePmeMgr
• gridCalc3() : ComputePmeMgr
• GridforceGrid() : GridforceGrid
• gridsize_a() : PatchMap
• gridsize_b() : PatchMap
• gridsize_c() : PatchMap
• GromacsTopFile() : GromacsTopFile
• groupForces() : GlobalMaster

- h -

• hash() : Exclusion, ProxyUsageKey, ProxyElem, ImproperElem, TuplePatchElem, DihedralElem, CrosstermElem, BondElem, AngleElem, BOID, TaggedMsg, BroadcastClientElem
• hasNewAtoms() : Patch
• head() : ConfigList
• holdComputes() : Sync
• homePatch() : PatchMgr, PatchMap, ComputeHomePatch
• HomePatchElem() : HomePatchElem
• homePatchIDList() : PatchMap
• homePatchList() : PatchMap
• HydrogenGroupID() : HydrogenGroupID

- i -

• identity() : Tensor, Matrix4
• IMDOutput() : IMDOutput
• ImproperElem() : ImproperElem, Molecule
• IncCurrStep() : ALambdaManager, ALambdaControl
• increment() : ProxyUsage
• incrSTLoad() : Rebalancer
• index() : SortedArray< Elem >, Lattice, ParseOptions::DataElement, vdw_params, crossterm_params, improper_params, dihedral_params, angle_params, bond_params, LocalID, StreamMessage, vmdforce
• index_a() : PatchMap
• index_b() : PatchMap
• index_c() : PatchMap
• infostream() : infostream
• Init() : ALambdaControl
• init() : SortableResizeArray< Elem >, Random, BackEnd
• initAndSendHomePatch() : WorkDistrib
• initialize() : LdbCoordinator, GridforceGrid, ComputeSelfTuples< T, S, P >, ComputePmeMgr, ComputePatchPair, ComputePatch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >, ComputeHomePatches, ComputeHomePatch, Compute
• initialize_config_data() : SimParameters
• initialize_pencils() : ComputePmeMgr
• InitProxyUsage() : Rebalancer
• initTmpPatchAtomsList() : PatchMap
• ins() : ResizeArrayRaw< Elem >
• insert() : UniqueSortedArray< Elem >, SortedArray< Elem >, Set, ResizeArray< Elem >, maxHeap, minHeap
• insertioncode() : PDBAtom
• Instance() : PatchMap, ComputeMap, AtomMap
• integer() : Random
• integrate() : Sequencer, Controller
• Integrate_MCTI() : ALambdaManager, ALambdaControl
• is_atom_constorqued() : Molecule
• is_atom_constrained() : Molecule
• is_atom_exPressure() : Molecule
• is_atom_fixed() : Molecule
• is_atom_gridforced() : Molecule
• is_atom_movdragged() : Molecule
• is_atom_rotdragged() : Molecule
• is_atom_stirred() : Molecule
• is_group_fixed() : Molecule
• is_hydrogen() : Molecule
• is_hydrogenGroupParent() : Molecule
• is_lp() : Molecule
• is_oxygen() : Molecule
• is_water() : Molecule
• IsActive() : ALambdaControl
• isAtomBased() : ComputeMap
• isAvailableOn() : Rebalancer
• isEmpty() : TupleSignature
• IsEndOf_MCTI() : ALambdaManager, ALambdaControl
• IsEndOf_MCTI_Step() : ALambdaManager, ALambdaControl
• IsFirstStep() : ALambdaManager, ALambdaControl
• IsForcing() : AForcingDiheRestraint, AForcingAngleRestraint, AForcingDistRestraint, AForcingPosRestraint, ARestraint
• isOpen() : PositionOwnerBox< Owner >, OwnerBox< Owner, Data >
• isPatchBased() : ComputeMap
• isPmeProcessor() : ComputePmeMgr
• IsTimeToClearAccumulator() : ALambdaManager, ALambdaControl
• IsTimeToPrint() : ALambdaManager, ALambdaControl
• IsTimeToPrint_dU_dLambda() : ALambdaManager, ALambdaControl
• isUsed() : Entry< Elem >
• item() : ResizeArray< Elem >, RequireReduction, SubmitReduction
• iterator() : Set, maxHeap, minHeap, ResizeArray< Elem >, Array< Elem, Size >

- l -

• langevin_param() : Molecule
• langevinPiston() : Sequencer
• langevinPiston1() : Controller
• langevinPiston2() : Controller
• langevinVelocities() : Sequencer
• langevinVelocitiesBBK1() : Sequencer
• langevinVelocitiesBBK2() : Sequencer
• Lattice() : Lattice
• LdbCoordinator() : LdbCoordinator
• length() : Vector, IMDheader
• length2() : Vector
• List() : AGroup
• listNode() : listNode
• LJTable() : LJTable
• load() : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ScriptTcl, InfoRecord
• loadTuples() : ComputeHomeTuples< T, S, P >
• loadTuplesForAtom() : ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
• localID() : AtomMap
• LOCALMOD() : infostream, datastream
• lookup() : ResidueLookupElem

- m -

• main() : main
• makeHeaps() : Rebalancer
• makePatches() : PatchMap
• makeTwoHeaps() : Rebalancer
• mapComputes() : WorkDistrib
• MathArray() : MathArray< Elem, Size >
• Matrix4() : Matrix4
• max_a() : PatchMap
• max_b() : PatchMap
• max_c() : PatchMap
• maxHeap() : maxHeap
• maximumMove() : Sequencer, SimParameters
• measure() : ScriptTcl
• memusageinit() : memusageinit
• messageBOCCheckIn() : Node
• messageEnqueueWork() : WorkDistrib
• messageRun() : Node
• messageStartUp() : Node
• Migrate() : LdbCoordinator
• MigrateAtomsCombinedMsg() : MigrateAtomsCombinedMsg
• MigrateAtomsMsg() : MigrateAtomsMsg
• min_a() : PatchMap
• min_b() : PatchMap
• min_c() : PatchMap
• minHeap() : minHeap
• minimizationQuenchVelocity() : Sequencer
• minimize() : Sequencer, Controller
• minpoint() : minpoint
• MIStream() : MIStream
• mod2() : floatcomplex
• modifyAppliedForces() : GlobalMaster
• modifyForcedAtoms() : GlobalMaster
• modifyGroupForces() : GlobalMaster
• modifyRequestedAtoms() : GlobalMaster
• modifyRequestedGroups() : GlobalMaster
• Molecule() : Molecule
• MolInst() : MolInst
• mollyAverage() : HomePatch
• mollyMollify() : HomePatch
• MOStream() : MOStream
• moveAllBy() : PatchMgr
• moveAtom() : PatchMgr
• MovePatch() : MovePatch
• movePatch() : PatchMgr
• MovePatchesMsg() : MovePatchesMsg
• moveto() : parm, MoveAtomMsg
• multirefine() : Rebalancer
• multmatrix() : Matrix4
• multpoint() : Matrix4
• myid() : Node
• myRemove() : Set

- n -

• NamdCentLB() : NamdCentLB
• NamdNborLB() : NamdNborLB
• NamdState() : NamdState
• name() : PDBAtom, ParseOptions::DataElement, ConfigList::ConfigListNode
• nearest() : Lattice
• newCid() : PatchMap
• newInputStream() : Communicate
• newlist() : Pairlists
• newMinimizeDirection() : Sequencer
• newMinimizePosition() : Sequencer
• newNode() : ComputeMap
• newOutputStream() : Communicate
• newPid() : ComputeMap
• newRefine() : RefineTorusLB
• newsize() : Pairlists
• next() : EntryGlob< Elem >, Entry< Elem >, Set, maxHeap, minHeap, Iterator, listNode, ReductionSetData, PAL, vdw_pair_params, crossterm_params, improper_params, dihedral_params, StreamMessage, ResidueLookupElem, heapIterator, ConfigList::ConfigListNode, StringList, FileStack
• nextlist() : Pairlists
• node() : PatchMap, ComputeMap, nodesort, ProxySpanningTreeMsg, ProxyResultVarsizeMsg, ProxyResultMsg, UnregisterProxyMsg, RegisterProxyMsg, ProxyListElem, ComputeMap::ComputeData, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, BOCgroup
• Node() : Node, NamdState
• nodeDone() : LdbCoordinator
• nodesort() : nodesort
• notfree() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
• noWork() : ComputeNonbondedPair, Compute
• num() : ParseOptions
• num_atoms() : PDB
• numAtomBased() : ComputeMap
• numAvailable() : Rebalancer
• numaway_a() : PatchMap
• numaway_b() : PatchMap
• numaway_c() : PatchMap
• numCids() : PatchMap
• numComputes() : ComputeMap, Rebalancer, LdbCoordinator
• numElements() : Set, maxHeap, minHeap
• numHomePatches() : PatchMap
• numNodes() : Node
• numNodesWithPatches() : PatchMap
• numPartitions() : ComputeMap, ComputeMap::ComputeData
• numPatchBased() : ComputeMap
• numPatches() : PatchMap, Rebalancer
• numPatchesOnNode() : PatchMap
• numPids() : ComputeMap, ComputeMap::ComputeData
• numProxies() : ProxyMgr, Rebalancer

- o -

• Object() : Sync, ReductionMgr, ProxyMgr, PatchMgr, PatchMap, Node, LdbCoordinator, ComputeMap, CollectionMgr, CollectionMasterHandler, CollectionMaster, BroadcastMgr, AtomMap
• ObjectArena() : ObjectArena< Type >
• occupancy() : PDBAtom
• offset() : Lattice, TupleSignature, MoveAllByMsg, nonbonded
• okay() : ConfigList
• oneAwayNeighbors() : PatchMap
• oneOrTwoAwayNeighbors() : PatchMap
• open() : PositionOwnerBox< Owner >, PositionBox< Owner >, OwnerBox< Owner, Data >, Box< Owner, Data >
• openSync() : Sync
• operator *() : Vector, UniqueSetIter< T >, Tensor, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, MathArray< Elem, Size >, AVector
• operator *=() : Vector, Tensor, MathArray< Elem, Size >, AVector, floatcomplex
• operator!=() : Vector, UniqueSetIter< T >, Tensor, ResizeArrayPrimIter< T >, ResizeArrayIter< T >
• operator+() : Vector, Tensor, MathArray< Elem, Size >, AVector
• operator++() : UniqueSetIter< T >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >
• operator+=() : Vector, Tensor, MathArray< Elem, Size >, AVector, floatcomplex
• operator-() : Vector, Tensor, MathArray< Elem, Size >, AVector
• operator-=() : Vector, Tensor, MathArray< Elem, Size >
• operator->() : UniqueSetIter< T >, ResizeArrayIter< T >
• operator/() : Vector, Tensor, MathArray< Elem, Size >, AVector
• operator/=() : Vector, Tensor, MathArray< Elem, Size >, AVector
• operator<() : nodesort, Exclusion, MovePatch, HydrogenGroupID, HomePatchElem, vmdforce, ImproperElem, TuplePatchElem, PatchElem, DihedralElem, CrosstermElem, BondElem, AngleElem
• operator<<() : infostream, datastream
• operator=() : Vector, UniqueSortedArray< Elem >, UniqueSetRaw< Elem >, Entry< Elem >, UniqueSetIter< T >, UniqueSet< Elem >, Tensor, ExclusionSignature, AtomSignature, TupleSignature, SortedArray< Elem >, SortableResizeArray< Elem >, ResizeArrayRaw< Elem >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ResizeArray< Elem >, Flags, proxyTreeNode, CompAtomExt, CompAtom, ExclusionCheck, MathArray< Elem, Size >, HomePatchElem, vmdforce, AVector, ALambdaControl, AGroup, floatcomplex, Array< Elem, Size >
• operator==() : nodesort, Vector, UniqueSetIter< T >, Tensor, ExclusionSignature, AtomSignature, TupleSignature, Exclusion, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ProxyElem, MovePatch, HydrogenGroupID, HomePatchElem, vmdforce, ImproperElem, TuplePatchElem, PatchElem, DihedralElem, CrosstermElem, BondElem, AngleElem, BOID, TaggedMsg, BroadcastClientElem
• operator[]() : Vector, ResizeArrayRaw< Elem >, ResizeArray< Elem >, AVector, ARestraintManager, ALambdaManager, AGroup, Array< Elem, Size >
• optional() : ParseOptions
• optionalB() : ParseOptions
• order_init() : PmePencil< T >
• origin() : PatchMap, Lattice
• orthogonal() : Lattice
• Out() : AVector
• outerAdd() : Tensor
• output() : TupleSignature, Node
• Output() : Output, AVector
• outputExtendedSystem() : Controller
• outputFepEnergy() : Controller
• outputTiEnergy() : Controller
• OwnerBox() : OwnerBox< Owner, Data >

- p -

• pack() : ExclusionSignature, AtomSignature, TupleSignature, ReductionSubmitMsg, ProxySpanningTreeMsg, ProxyCombinedResultMsg, ProxyResultMsg, ProxyAtomsMsg, MovePatchesMsg, PatchMap, MigrateAtomsCombinedMsg, MigrateAtomsMsg, GridforceGrid, ComputeMap, ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeGlobalConfigMsg, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, ComputeConsForceMsg, EnqueueDataMsg, DataStreamMsg, CollectVectorMsg
• packSize() : PatchMap, ComputeMap
• Pairlists() : Pairlists
• Parameters() : Parameters
• parm() : parm
• parse() : PDBAtom
• ParseOptions() : ParseOptions
• partition() : RecBisection, ComputeMap, CompAtom, ComputeMap::ComputeData
• Patch() : Patch
• patch() : PatchMap, Sequencer, ProxyUsageKey, ProxySpanningTreeMsg, ProxyCombinedResultMsg, ProxyNodeAwareSpanningTreeMsg, ProxyResultVarsizeMsg, ProxyResultMsg, ProxyDataMsg, ProxyAtomsMsg, UnregisterProxyMsg, RegisterProxyMsg, HomePatchElem, ComputePatchPair, ComputePatch, ComputeHomePatch
• PatchElem() : PatchElem
• patchLoad() : LdbCoordinator
• PatchMap() : PatchMap, PatchMgr
• patchMapInit() : WorkDistrib
• PatchMgr() : PatchMgr, HomePatch
• patchReady() : Compute
• PatchReady() : Sync
• PatchRec() : ComputeMap::PatchRec
• pcpair() : Rebalancer::pcpair
• PDB() : PDB
• PDBAtom() : PDBAtom
• PDBAtomRecord() : PDBAtomRecord
• PDBData() : PDBData
• PDBHetatm() : PDBHetatm
• PDBUnknown() : PDBUnknown
• periodic_a() : PatchMap
• periodic_b() : PatchMap
• periodic_c() : PatchMap
• pid() : PatchMap, ComputeMap, MovePatch, MovePatchesMsg, LocalID, HomePatchElem, ComputeMap::PatchRec
• pme_kspace() : PmeXPencil
• PmeKSpace() : PmeKSpace
• PmePencil() : PmePencil< T >
• PmePencilInitMsg() : PmePencilInitMsg
• PmeRealSpace() : PmeRealSpace
• PmeXPencil() : PmeXPencil
• PmeYPencil() : PmeYPencil
• PmeZPencil() : PmeZPencil
• positionBoxClosed() : Patch
• PositionOwnerBox() : PositionOwnerBox< Owner >
• positionsReady() : Patch, HomePatch
• preadln() : parm
• preCreateHomePatch() : PatchMgr
• preCreateHomePatches() : WorkDistrib
• PressureProfileReduction() : PressureProfileReduction
• print() : Set, AtomMap
• print_angle_params() : Parameters
• print_atoms() : Molecule
• print_bond_params() : Parameters
• print_bonds() : Molecule
• print_crossterm_params() : Parameters
• print_dihedral_params() : Parameters
• Print_dU_dLambda_Info() : ARestraintManager
• Print_dU_dLambda_Summary() : ALambdaManager
• print_exclusions() : Molecule
• print_improper_params() : Parameters
• Print_MCTI_Integration() : ALambdaManager
• print_param_summary() : Parameters
• print_vdw_pair_params() : Parameters
• print_vdw_params() : Parameters
• printComputeMap() : ComputeMap
• printDynamicsEnergies() : Controller
• printEnergies() : Controller
• PrintEnergyInfo() : ARestraintManager
• printFepMessage() : Controller
• PrintHeader() : ALambdaManager, ALambdaControl
• PrintInfo() : ADiheRestraint, AnAngleRestraint, ADistRestraint, APosRestraint, ARestraint
• PrintLambdaHeader() : ALambdaManager, ALambdaControl
• printLoads() : Rebalancer
• printLocalLdbReport() : LdbCoordinator
• printMinimizeEnergies() : Controller
• printOut() : ProxyNodeAwareSpanningTreeMsg
• printPatchMap() : PatchMap
• PrintPreInfo() : ARestraintManager
• printRequiredProxies() : LdbCoordinator
• PrintRestraintInfo() : ARestraintManager
• printResults() : Rebalancer
• PrintSomeSpaces() : ALambdaManager
• printSummary() : Rebalancer
• printTiMessage() : Controller
• printTiming() : Controller
• priority() : Compute
• processData() : GlobalMaster
• ProcessMigrate() : LdbCoordinator
• processorInfo() : processorInfo
• ProxyElem() : ProxyElem
• ProxyListElem() : ProxyListElem
• ProxyMgr() : ProxyMgr
• ProxyPatch() : ProxyPatch
• ProxyTree() : ProxyTree
• proxyTreeNode() : proxyTreeNode
• ProxyUsage() : ProxyUsage
• ProxyUsageKey() : ProxyUsageKey
• publish() : SimpleBroadcastObject< T >
• put() : MOStream
• put_stir_startTheta() : Molecule

- q -

• quenchVelocities() : Sequencer

- r -

• Random() : Random, AVector
• range() : ParseOptions, ParseOptions::DataElement
• rattle1() : Sequencer, HomePatch
• rattle2() : Sequencer, HomePatch
• read_charmm_parameter_file() : Parameters
• read_fortran_12I6() : parm
• read_parameter_file() : Parameters
• read_parm() : Parameters, Molecule
• read_psf_file() : Molecule
• readparm() : parm
• ready() : CollectionMaster::CollectVectorInstance
• reassignVelocities() : Sequencer, Controller
• rebalance() : LdbCoordinator
• rebalanceLoad() : Sequencer, Controller
• Rebalancer() : Rebalancer
• RecBisection() : RecBisection
• receive_Molecule() : Molecule
• receive_Parameters() : Parameters
• receive_SimParameters() : SimParameters
• receiveAll() : ProxyPatch
• receiveAtoms() : ProxyPatch
• ReceiveAtSync() : LdbCoordinator
• receiveData() : ProxyPatch
• receiveDataStream() : CollectionMaster
• receivePositions() : CollectionMaster
• receivePressure() : Controller
• receiveResults() : HomePatch
• receiveVelocities() : CollectionMaster
• recv_grid() : PmeZPencil
• recv_trans() : PmeXPencil, PmeYPencil
• recv_untrans() : PmeYPencil, PmeZPencil
• recvArrays() : ComputePmeMgr
• recvAtoms() : PatchMgr
• recvAtomsCoor() : AtomsDisInfo
• recvAtomsForces() : AtomsDisInfo
• recvBroadcast() : BroadcastMgr
• recvComputeConsForceMsg() : ComputeMgr
• recvComputeDPMEData() : ComputeMgr
• recvComputeDPMEResults() : ComputeMgr
• recvComputeEwaldData() : ComputeMgr
• recvComputeEwaldResults() : ComputeMgr
• recvComputeGlobalConfig() : ComputeMgr
• recvComputeGlobalData() : ComputeMgr
• recvComputeGlobalResults() : ComputeMgr
• recvComputeMapChanges() : WorkDistrib
• recvConfig() : ComputeGlobal
• recvCoord() : ComputeExtMgr
• recvCoordinates() : FileIOMgr, FileIO
• recvData() : GlobalMasterServer, ComputeEwald
• recvEnableEarlyExit() : Node
• recvEnableExitScheduler() : Node
• recvForce() : ComputeExtMgr
• recvGrid() : ComputePmeMgr
• recvImmediateProxyAll() : ProxyMgr
• recvImmediateProxyData() : ProxyMgr
• recvImmediateResults() : ProxyMgr
• RecvMigrate() : LdbCoordinator
• recvMigrateAtoms() : PatchMgr
• recvMigrateAtomsCombined() : PatchMgr
• recvMovePatches() : PatchMgr
• recvNodeAwareSpanningTree() : ProxyMgr, HomePatch
• recvNodeAwareSpanningTreeOnHomePatch() : ProxyMgr
• recvNodeAwareSTParent() : ProxyMgr
• recvProxies() : ProxyMgr
• recvProxyAll() : ProxyMgr
• recvProxyData() : ProxyMgr
• recvRegisterProxy() : ProxyMgr
• recvResults() : ProxyMgr, ComputeGlobal, ComputeEwald
• recvSpanningTree() : ProxyMgr, HomePatch
• recvSpanningTreeOnHomePatch() : ProxyMgr
• recvStaticInfo() : AtomsDisInfo
• recvTrans() : ComputePmeMgr
• recvUngrid() : ComputePmeMgr
• recvUnregisterProxy() : ProxyMgr
• recvUntrans() : ComputePmeMgr
• reduce() : ResizeArray< Elem >
• ReductionMgr() : ReductionMgr, RequireReduction, SubmitReduction
• ReductionSet() : ReductionSet
• ReductionSetData() : ReductionSetData
• refine() : Rebalancer
• refine_togrid() : Rebalancer
• RefineOnly() : RefineOnly
• RefineTorusLB() : RefineTorusLB
• registerAvgPositionPickup() : Patch
• registerCompute() : ComputeMap
• registerForceDeposit() : Patch
• registerIDs() : AtomMap
• registerPatch() :