- A
: indexed_vdw_pair, vdw_pair_params, LJTable::TableEntry
- A14
: indexed_vdw_pair, vdw_pair_params
- a_total
: nodesort
- aaAngleExp
: SimParameters
- actualNumAtoms
: AtomStaticInfoMsg
- addToRemoteSequenceNumber
: ReductionSet
- aid
: ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeGlobalConfigMsg, ComputeConsForceMsg, CollectionMgr::CollectVectorInstance, CollectVectorMsg
- allPes
: ProxyNodeAwareSpanningTreeMsg
- amberOn
: SimParameters
- angle
: angle_params
- angle_array
: Parameters
- angle_type
: angle
- AngleAt1
: parm
- AngleAt2
: parm
- AngleAt3
: parm
- angleCnt
: AtomSignature
- AngleHAt1
: parm
- AngleHAt2
: parm
- AngleHAt3
: parm
- AngleHNum
: parm
- AngleNum
: parm
- angleSigIndices
: AtomSigInfo
- angleSigs
: AtomSignature
- atom
: PDB, MovePatchesMsg
- atom1
: Exclusion, crossterm, improper, dihedral, angle, bond
- atom1name
: vdw_pair_params, crossterm_params, improper_params, dihedral_params, angle_params, bond_params
- atom1wild
: dihedral_params
- atom2
: Exclusion, crossterm, improper, dihedral, angle, bond
- atom2name
: vdw_pair_params, crossterm_params, improper_params, dihedral_params, angle_params, bond_params
- atom2wild
: dihedral_params
- atom3
: crossterm, improper, dihedral, angle
- atom3name
: crossterm_params, improper_params, dihedral_params, angle_params
- atom3wild
: dihedral_params
- atom4
: crossterm, improper, dihedral
- atom4name
: crossterm_params, improper_params, dihedral_params
- atom4wild
: dihedral_params
- atom5
: crossterm
- atom5name
: crossterm_params
- atom6
: crossterm
- atom6name
: crossterm_params
- atom7
: crossterm
- atom7name
: crossterm_params
- atom8
: crossterm
- atom8name
: crossterm_params
- atomFixed
: CompAtom
- atomid
: MoveAtomMsg
- atomID
: HydrogenGroupID, ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
- atomIDList
: ProxyAtomsMsg
- atomIndex
: ResidueLookupElem
- atomMap
: Node, ComputeHomeTuples< T, S, P >
- atomname
: atom_name_info, vdw_params
- atomNameIdx
: BasicAtomInfo
- atomnameIdx
: AtomNameIdx
- AtomNames
: parm
- AtomRes
: parm
- atoms
: PDB, AtomStaticInfoMsg
- atomsCnt
: AtomsDisInfo
- atomSigIdx
: BasicAtomInfo
- atomsInGroup
: HydrogenGroupID
- AtomSym
: parm
- AtomTree
: parm
- atomtype
: atom_name_info
- atomTypeIdx
: BasicAtomInfo
- atomtypeIdx
: AtomNameIdx
- auxFilename
: SimParameters
- available
: processorInfo
- averageLoad
: Rebalancer
- avg_count
: Controller
- avgPlLen
: ProxyDataMsg
- avgPositionBox
: Patch, ComputeNonbondedSelf, ComputeNonbondedPair, TuplePatchElem, PatchElem
- avgPositionComputeList
: Patch
- avgPositionList
: ProxyDataMsg
- avgPositionPtrBegin
: Patch
- avgPositionPtrEnd
: Patch
- c
: Lattice, Rebalancer::pcpair, CrosstermValue
- c0
: ComputeNonbondedUtil
- c1
: ComputeNonbondedUtil
- c3
: ComputeNonbondedUtil
- c5
: ComputeNonbondedUtil
- c6
: ComputeNonbondedUtil
- c7
: ComputeNonbondedUtil
- c8
: ComputeNonbondedUtil
- c_total
: nodesort
- calcFullPair
: ComputeNonbondedUtil
- calcFullPairEnergy
: ComputeNonbondedUtil
- calcFullSelf
: ComputeNonbondedUtil
- calcFullSelfEnergy
: ComputeNonbondedUtil
- calcMergePair
: ComputeNonbondedUtil
- calcMergePairEnergy
: ComputeNonbondedUtil
- calcMergeSelf
: ComputeNonbondedUtil
- calcMergeSelfEnergy
: ComputeNonbondedUtil
- calcPair
: ComputeNonbondedUtil
- calcPairEnergy
: ComputeNonbondedUtil
- calcSelf
: ComputeNonbondedUtil
- calcSelfEnergy
: ComputeNonbondedUtil
- calcSlowPair
: ComputeNonbondedUtil
- calcSlowPairEnergy
: ComputeNonbondedUtil
- calcSlowSelf
: ComputeNonbondedUtil
- calcSlowSelfEnergy
: ComputeNonbondedUtil
- cellBasisVector1
: SimParameters
- cellBasisVector2
: SimParameters
- cellBasisVector3
: SimParameters
- cellOrigin
: SimParameters
- cg
: PmeParticle, EwaldParticle
- charge
: atom_constants, CompAtom
- chargeIdx
: BasicAtomInfo
- Charges
: parm
- checkpoint_berendsenPressure_avg
: Controller
- checkpoint_berendsenPressure_count
: Sequencer, Controller
- checkpoint_langevinPiston_strainRate
: Controller
- checkpoint_lattice
: Controller
- checkpoint_stored
: Controller
- checksum
: StreamMessage
- cid
: PatchMap, Compute
- clients
: GlobalMasterIMD
- Cn1
: parm
- Cn2
: parm
- Cno
: parm
- COLDOn
: SimParameters
- COLDRate
: SimParameters
- COLDTemp
: SimParameters
- collection
: Sequencer, Controller
- collectionMgr
: BOCgroup
- commOnly
: SimParameters, ComputeNonbondedUtil
- comMove
: SimParameters
- compute
: ComputeMap, LocalWorkMsg, ComputeMap::ComputeData
- computeArray
: LdbCoordinator
- computeBgPairHeap
: Rebalancer
- computeBgSelfHeap
: Rebalancer
- computeChecksum
: Controller
- computeExtMgr
: BOCgroup
- computeGlobalObject
: ComputeMgr
- computeLoad
: processorInfo
- computeMap
: Node, LdbCoordinator
- computeMapData
: MapDistribMsg
- computeMgr
: Node, BOCgroup
- computePairHeap
: Rebalancer
- computePmeMgr
: BOCgroup
- computes
: Rebalancer
- computeSelfHeap
: Rebalancer
- computeSet
: processorInfo
- config
: GlobalMasterEasy
- configList
: Node
- consForce
: Molecule
- consForceFile
: SimParameters
- consForceIndexes
: Molecule
- consForceOn
: SimParameters
- consForceScaling
: SimParameters
- consTorqueAxisFile
: SimParameters
- consTorqueFile
: SimParameters
- consTorqueGlobVal
: SimParameters
- consTorqueIndexes
: Molecule
- consTorqueOn
: SimParameters
- consTorqueParams
: Molecule
- consTorquePivotFile
: SimParameters
- consTorqueValFile
: SimParameters
- constraintExp
: SimParameters
- constraintScaling
: SimParameters
- constraintsOn
: SimParameters
- constrXOn
: SimParameters
- constrYOn
: SimParameters
- constrZOn
: SimParameters
- controllerExpected
: LdbCoordinator
- controllerReported
: LdbCoordinator
- controllerThread
: LdbCoordinator
- controlNumDegFreedom
: Controller
- controlPressure
: Controller
- controlPressure_nbond
: Controller
- controlPressure_normal
: Controller
- controlPressure_slow
: Controller
- coord
: MoveAtomMsg, ExtCoordMsg
- coords
: Node
- coordtmp
: GlobalMasterIMD
- coordtmpsize
: GlobalMasterIMD
- corr_table
: ComputeNonbondedUtil
- counter
: TaggedMsg
- crossterm_array
: Parameters
- crossterm_type
: crossterm
- crosstermCnt
: AtomSignature
- crosstermSigIndices
: AtomSigInfo
- crosstermSigs
: AtomSignature
- Cutcap
: parm
- cutoff
: SimParameters, ComputeNonbondedUtil
- cutoff2
: ComputeNonbondedUtil
- cylindricalBCAxis
: SimParameters
- cylindricalBCexp1
: SimParameters
- cylindricalBCexp2
: SimParameters
- cylindricalBCk1
: SimParameters
- cylindricalBCk2
: SimParameters
- cylindricalBCl1
: SimParameters
- cylindricalBCl2
: SimParameters
- cylindricalBCOn
: SimParameters
- cylindricalBCr1
: SimParameters
- cylindricalBCr2
: SimParameters
- cylindricalCenter
: SimParameters
- d00
: CrosstermData
- d01
: CrosstermData
- d10
: CrosstermData
- d11
: CrosstermData
- daCutoffDist
: SimParameters
- daOffDist
: SimParameters
- daOnDist
: SimParameters
- data
: ReductionSetData, ReductionSubmitMsg, PAL, StreamMessage, ConfigList::ConfigListNode, StringList, PmePencil< T >, PmePencilInitMsg, CollectionMgr::CollectVectorSequence, CollectionMgr::CollectVectorInstance, DataStreamMsg, CollectVectorMsg, CollectionMaster::CollectVectorSequence, CollectionMaster::CollectVectorInstance, Array< Elem, Size >
- data_read
: parm
- dataQueue
: ReductionSet
- dataSize
: ReductionSetData, ReductionSubmitMsg
- dcdFilename
: SimParameters
- dcdFrequency
: SimParameters
- dcdUnitCell
: SimParameters
- decouple
: SimParameters, ComputeNonbondedUtil
- default_coor
: PDBAtom
- default_occupancy
: PDBAtom
- default_residueseq
: PDBAtom
- default_serial
: PDBAtom
- default_temperaturefactor
: PDBAtom
- deleted
: heapRecord
- delta
: Lattice, four_body_consts
- destNodeID
: MigrationInfo
- destPatchID
: MigrationInfo, MigrateAtomsCombinedMsg, MigrateAtomsMsg
- dG
: Controller
- dhaCutoffAngle
: SimParameters
- dhaOffAngle
: SimParameters
- dhaOnAngle
: SimParameters
- dielectric
: SimParameters
- dielectric_1
: ComputeNonbondedUtil
- DihAt1
: parm
- DihAt2
: parm
- DihAt3
: parm
- DihAt4
: parm
- dihedral_array
: Parameters
- dihedral_type
: dihedral
- dihedralCnt
: AtomSignature
- dihedralOn
: SimParameters
- dihedralSigIndices
: AtomSigInfo
- dihedralSigs
: AtomSignature
- DihHAt1
: parm
- DihHAt2
: parm
- DihHAt3
: parm
- DihHAt4
: parm
- DihHNum
: parm
- DihNum
: parm
- dim2
: PmeGrid
- dim3
: PmeGrid
- dimension
: crossterm_params
- disAtoms
: AtomsDisInfo
- distance
: bond_params
- distAttExp
: SimParameters
- distRepExp
: SimParameters
- doEnergy
: Flags
- doFullElectrostatics
: Flags
- doLoadTuples
: ComputeHomeTuples< T, S, P >
- doMolly
: Flags
- doNonbonded
: Flags
- dt
: SimParameters
- dudx
: minpoint
- dummy
: SimParameters
- f
: Results, Patch, TuplePatchElem, PatchElem, ComputeGlobalResultsMsg, ComputeConsForceMsg
- f_0
: ComputeNonbondedWorkArrays
- fast_table
: ComputeNonbondedUtil
- fdata
: ParseOptions::DataElement, CollectionMgr::CollectVectorInstance, CollectVectorMsg, CollectionMaster::CollectVectorInstance
- fdef
: ParseOptions::DataElement
- fepElecLambdaStart
: SimParameters, ComputeNonbondedUtil
- fepEquilSteps
: SimParameters
- fepFile
: Controller
- FepNo
: Controller
- fepOn
: SimParameters, ComputeNonbondedUtil
- fepOutFile
: SimParameters
- fepOutFreq
: SimParameters
- fepSum
: Controller
- fepTemp
: SimParameters
- fepVdwLambdaEnd
: SimParameters, ComputeNonbondedUtil
- fepVdwShiftCoeff
: SimParameters, ComputeNonbondedUtil
- ff
: nonbonded
- fflush_count
: Controller
- FFTWEstimate
: SimParameters
- FFTWUseWisdom
: SimParameters
- FFTWWisdomFile
: SimParameters
- FFTWWisdomString
: SimParameters
- fgrid
: PmeGridMsg
- fid
: ComputeGlobalDataMsg
- file
: FileStack
- filename
: FileStack
- firstAssignInRefine
: Rebalancer
- firstLdbStep
: SimParameters, LdbCoordinator
- firstResid
: ResidueLookupElem
- firstTime
: GlobalMasterMisc
- firstTimestep
: SimParameters
- fixedAtomsForces
: SimParameters
- fixedAtomsOn
: SimParameters, ComputeNonbondedUtil
- fixedPosition
: FullAtom
- fixglist
: ComputeNonbondedWorkArrays
- flags
: ProxyDataMsg, Patch, ExclusionCheck
- flLen
: ProxyResultVarsizeMsg
- FMAFFTBlock
: SimParameters
- FMAFFTOn
: SimParameters
- FMALevels
: SimParameters
- FMAMp
: SimParameters
- FMAOn
: SimParameters
- fmaTheta
: SimParameters
- force
: ExtForce, vmdforce, ExtForceMsg
- forceArr
: ProxyResultVarsizeMsg
- forceBox
: Patch, ProxyListElem, ComputePatchPair, TuplePatchElem, PatchElem
- forceComputeList
: Patch
- forceconstant
: angle_params, bond_params
- forceList
: ProxyCombinedResultMsg, ProxyResultMsg
- forces
: ComputeDPMEResultsMsg
- found
: SortedArray< Elem >
- fptr
: ParseOptions::DataElement
- freeEnergyOn
: SimParameters
- from
: LdbMigrateMsg
- fromNodeID
: MovePatchesMsg, MigrateAtomsCombinedMsg, MigrateAtomsMsg
- full_table
: ComputeNonbondedUtil
- fullDirectOn
: SimParameters
- fullElectFrequency
: SimParameters
- fullExclCnt
: ExclusionSignature
- fullExclOffset
: ExclSigInfo
- fullf
: nonbonded
- fullf_0
: ComputeNonbondedWorkArrays
- fullOffset
: ExclusionSignature
- i
: doublecomplex, Transform, netint, floatcomplex
- Iac
: parm
- Iblo
: parm
- id
: Iterator, CompAtom, BOID, BroadcastClient
- Id
: InfoRecord
- idata
: ParseOptions::DataElement
- idef
: ParseOptions::DataElement
- idleTime
: processorInfo
- IfBox
: parm
- IfCap
: parm
- imd
: Node
- IMDfreq
: SimParameters
- IMDignore
: SimParameters, GlobalMasterIMD
- IMDon
: SimParameters
- IMDport
: SimParameters
- IMDwait
: SimParameters, GlobalMasterIMD
- improper_array
: Parameters
- improper_type
: improper
- improperCnt
: AtomSignature
- improperSigIndices
: AtomSigInfo
- improperSigs
: AtomSignature
- imsg
: PmePencil< T >
- ind1
: indexed_vdw_pair
- ind2
: indexed_vdw_pair
- index
: SortedArray< Elem >, Lattice, ParseOptions::DataElement, vdw_params, crossterm_params, improper_params, dihedral_params, angle_params, bond_params, LocalID, StreamMessage, vmdforce
- info
: listNode, heapRecord
- initdata
: PmePencil< T >
- initialTemp
: SimParameters
- inMigration
: HomePatch
- Ipatm
: parm
- Ipres
: parm
- iptr
: ParseOptions::DataElement
- Iptres
: parm
- is_defined
: ParseOptions::DataElement
- is_optional
: ParseOptions::DataElement
- isBasePatch
: ComputeHomeTuples< T, S, P >
- isGP
: HydrogenGroupID
- isReal
: TupleSignature
- isSorted
: SortedArray< Elem >
- isZero
: ProxyResultVarsizeMsg
- ititl
: parm
- l
: EnqueueDataMsg
- lambda
: SimParameters, ComputeNonbondedUtil
- lambda2
: SimParameters, ComputeNonbondedUtil
- lambda_table
: ComputeNonbondedUtil
- langevinDamping
: SimParameters
- langevinHydrogen
: SimParameters
- langevinOn
: SimParameters
- langevinPiston_strainRate
: Controller
- langevinPistonDecay
: SimParameters
- langevinPistonOn
: SimParameters
- langevinPistonPeriod
: SimParameters
- langevinPistonTarget
: SimParameters
- langevinPistonTemp
: SimParameters
- langevinTemp
: SimParameters
- lastLdbStep
: SimParameters
- lastResid
: ResidueLookupElem
- latqueue
: CollectionMaster::CollectVectorSequence
- lattice
: SimParameters, Flags, SetLatticeMsg, Patch, PmePencil< T >, PmeTransMsg, PmeGridMsg, ExtCoordMsg, CollectionMaster::CollectVectorInstance
- ldBarrierHandle
: LdbCoordinator
- ldbBackgroundScaling
: SimParameters
- ldbCoordinator
: Node, BOCgroup
- ldbCycleNum
: LdbCoordinator
- ldbHomeBackgroundScaling
: SimParameters
- ldbPeriod
: SimParameters
- ldbPMEBackgroundScaling
: SimParameters
- ldbStatsFP
: LdbCoordinator
- ldbSteps
: Sequencer, Controller
- ldbStrategy
: SimParameters
- ldbUnloadOne
: SimParameters
- ldbUnloadPME
: SimParameters
- ldbUnloadRank
: SimParameters
- ldbUnloadRankZero
: SimParameters
- ldbUnloadSMP
: SimParameters
- ldbUnloadZero
: SimParameters
- left
: indexed_vdw_pair, vdw_params, angle_params, bond_params
- len
: StreamMessage, PmeGridMsg
- length
: Vector, IMDheader
- lesFactor
: SimParameters, ComputeNonbondedUtil
- lesOn
: SimParameters, ComputeNonbondedUtil
- lesReduceMass
: SimParameters
- lesReduceTemp
: SimParameters
- lesScaling
: ComputeNonbondedUtil
- limitDist
: SimParameters
- linenumber
: FileStack
- ljEnergy
: Controller
- ljEnergy_f
: Controller
- ljEnergy_ti_1
: Controller
- ljEnergy_ti_2
: Controller
- ljTable
: ComputeNonbondedUtil
- load
: UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ScriptTcl, InfoRecord
- loc
: GridforceGrid::box
- localIndex
: ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
- localWorkMsg
: Compute
- longSplitting
: SimParameters
- low
: netint
- lowest
: netint
- m_Kf
: ARestraint
- m_LambdaKf
: ARestraint
- m_LambdaRef
: ARestraint
- m_NumGroups
: ARestraint
- m_pCOMs
: ARestraint
- m_pGroups
: ARestraint
- m_x
: AVector
- m_y
: AVector
- m_z
: AVector
- many_allowed
: ParseOptions::DataElement
- margin
: SimParameters
- marginViolations
: HomePatch, Controller
- mass
: atom_constants, FullAtom
- Masses
: parm
- massIdx
: BasicAtomInfo
- master
: SlaveInitMsg, MasterHandlerInitMsg
- max
: ExclusionCheck
- maxAtomMovement
: Flags
- maxExclusionFlags
: SimParameters
- maxForceMerged
: Flags
- maxForceUsed
: Flags
- maxGroupRadius
: Flags
- maximumMove
: Sequencer, SimParameters
- maxPairPart
: SimParameters
- maxPart
: nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair
- maxSelfPart
: SimParameters
- maxTime
: computeInfo
- Mbona
: parm
- mergeCrossterms
: SimParameters
- migrationList
: MigrateAtomsCombinedMsg, MigrateAtomsMsg
- min
: ExclusionCheck
- min_energy
: Controller
- min_f_dot_f
: Controller
- min_f_dot_v
: Controller
- min_huge_count
: Controller
- min_v_dot_v
: Controller
- minAtomsPerPatch
: SimParameters
- minBabyStep
: SimParameters
- minimizeCGOn
: SimParameters
- minimizeCoefficient
: ControllerBroadcasts
- minimizeOn
: SimParameters
- minLineGoal
: SimParameters
- minPart
: nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair
- minTime
: computeInfo
- minTinyStep
: SimParameters
- miscForcesOn
: SimParameters
- mList
: MigrationInfo
- modExclCnt
: ExclusionSignature
- modExclOffset
: ExclSigInfo
- modified
: Exclusion
- modOffset
: ExclusionSignature
- mol
: ComputeNonbondedUtil
- molecule
: Node
- mollyIter
: SimParameters
- mollyOn
: SimParameters
- mollyTol
: SimParameters
- momentumCorrection
: ControllerBroadcasts
- movDragFile
: SimParameters
- movDragGlobVel
: SimParameters
- movDragOn
: SimParameters
- movDragVelFile
: SimParameters
- moveto
: parm, MoveAtomMsg
- moveToNode
: ComputeMap::ComputeData
- movingConstraintsOn
: SimParameters
- movingConsVel
: SimParameters
- Mphia
: parm
- msg
: TaggedMsg
- msgbuf
: HomePatch
- msgSize
: TaggedMsg
- Mtheta
: parm
- MTSAlgorithm
: SimParameters
- multiplicity
: ImproperValue, DihedralValue, improper_params, dihedral_params
- myHandle
: LdbCoordinator
- myKSpace
: PmeXPencil
- myOMid
: LdbCoordinator
- mySegid
: ResidueLookupElem
- n
: four_body_consts
- N
: SimParameters
- name
: PDBAtom, ParseOptions::DataElement, ConfigList::ConfigListNode
- Nat3
: parm
- Natcap
: parm
- Natom
: parm
- Natyp
: parm
- Nbona
: parm
- nbondFreq
: Controller
- Nbonh
: parm
- nComputesExpected
: LdbCoordinator
- nComputesReported
: LdbCoordinator
- needs_reply
: PmePencil< T >
- net_dE
: Controller
- net_dEdl_elec_1
: Controller
- net_dEdl_elec_2
: Controller
- net_dEdl_lj_1
: Controller
- net_dEdl_lj_2
: Controller
- net_dEdl_PME
: Controller
- newaid
: ComputeGlobalResultsMsg
- newgdef
: ComputeGlobalResultsMsg
- newNodes
: ComputeMapChangeMsg
- 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
- nextSequenceNumber
: ReductionSet
- Nhparm
: parm
- nLocalComputes
: LdbCoordinator
- nLocalPatches
: LdbCoordinator
- Nmxrs
: parm
- Nnb
: parm
- no_footnote
: PDBAtom
- node
: PatchMap, ComputeMap, nodesort, ProxySpanningTreeMsg, ProxyResultVarsizeMsg, ProxyResultMsg, UnregisterProxyMsg, RegisterProxyMsg, ProxyListElem, ComputeMap::ComputeData, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, BOCgroup
- nodecount
: ProxyMgr
- nodeID
: MovePatch, proxyTreeNode
- nodes
: ProxyCombinedResultMsg
- nodesDone
: LdbCoordinator
- nonbondedFrequency
: SimParameters
- nonbondedGroupIsAtom
: CompAtom
- nonbondedScaling
: SimParameters
- noPatchesOnOne
: SimParameters
- noPatchesOnZero
: SimParameters
- Nparm
: parm
- nPatches
: LdbCoordinator
- npatches
: nodesort
- nPatchesExpected
: LdbCoordinator
- nPatchesReported
: LdbCoordinator
- Nphb
: parm
- Nphia
: parm
- Nphih
: parm
- Nptra
: parm
- nRegisteredObjs
: LdbCoordinator
- Nres
: parm
- Nspm
: parm
- Nspsol
: parm
- nStatsMessagesExpected
: LdbCoordinator
- nStatsMessagesReceived
: LdbCoordinator
- Ntheta
: parm
- Ntheth
: parm
- Nttyp
: parm
- Ntype2d
: parm
- Ntypes
: parm
- numAcceptors
: Molecule
- Numang
: parm
- NumAngleParams
: Parameters
- numAngles
: Molecule
- numAtoms
: Patch, Molecule, MigrateAtomsCombinedMsg, patchInfo, ComputePatchPair, ComputePatch, nonbonded, ComputeHomePatch, ExtCoordMsg
- numAtomsPair
: SimParameters
- numAtomsPair2
: SimParameters
- numAtomsSelf
: SimParameters
- numAtomsSelf2
: SimParameters
- Numbnd
: parm
- NumBondParams
: Parameters
- numBonds
: Molecule
- numCalcAngles
: Molecule
- numCalcBonds
: Molecule
- numCalcCrossterms
: Molecule
- numCalcDihedrals
: Molecule
- numCalcExclusions
: Molecule
- numCalcImpropers
: Molecule
- numComputes
: ComputeMap, Rebalancer, LdbCoordinator
- numConsForce
: Molecule
- numConsTorque
: Molecule
- numConstraints
: Molecule
- NumCrosstermParams
: Parameters
- numCrossterms
: Molecule
- numDegFreedom
: Controller
- NumDihedralParams
: Parameters
- numDihedrals
: Molecule
- numDonors
: Molecule
- numExclusions
: Molecule
- numExPressureAtoms
: Molecule
- numFepFinal
: Molecule
- numFepInitial
: Molecule
- numFixedAtoms
: Patch, Molecule
- numFixedGroups
: Molecule
- numFixedRigidBonds
: Molecule
- numGridforces
: Molecule
- numHydrogenGroups
: Molecule
- NumImproperParams
: Parameters
- numImpropers
: Molecule
- numLP
: Molecule
- numMlBuf
: HomePatch
- numMovDrag
: Molecule
- numMultipleDihedrals
: Molecule
- numMultipleImpropers
: Molecule
- numNewNodes
: ComputeMapChangeMsg
- numNodesWithProxies
: ProxyNodeAwareSpanningTreeMsg
- numOffset
: TupleSignature
- numParticles
: ComputeDPMEResultsMsg, ComputeDPMEDataMsg
- numPartitions
: ComputeMap, ComputeMap::ComputeData
- numParts
: nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair
- numPatches
: PatchMap, Rebalancer
- numPes
: proxyTreeNode
- numPesAvailable
: Rebalancer
- numPesOfNode
: ProxyNodeAwareSpanningTreeMsg
- numPids
: ComputeMap, ComputeMap::ComputeData
- numPidsAllocated
: ComputeMap::ComputeData
- numProxies
: ProxyMgr, Rebalancer
- numRealBonds
: Molecule
- numRigidBonds
: Molecule
- numRotDrag
: Molecule
- numStepsToRun
: LdbCoordinator
- numStirredAtoms
: Molecule
- numTotalExclusions
: Molecule
- nx
: LocalPmeInfo, PmeTransMsg
- ny
: PmeXPencil, PmeUntransMsg
- ny_after_transpose
: LocalPmeInfo
- nz
: PmeXPencil
- p
: Rebalancer::pcpair, Patch, nonbonded, ImproperElem, TuplePatchElem, PatchElem, ComputeGlobalDataMsg, DihedralElem, CrosstermElem, BondElem, AngleElem
- P
: Rebalancer
- p_avg
: Patch
- pad
: AlignVector
- padding
: ProxyResultVarsizeMsg
- pairInteractionGroup1
: SimParameters
- pairInteractionGroup2
: SimParameters
- pairInteractionOn
: SimParameters, ComputeNonbondedUtil
- pairInteractionSelf
: SimParameters, ComputeNonbondedUtil
- pairlist
: ComputeNonbondedWorkArrays
- pairlist2
: ComputeNonbondedWorkArrays
- pairlistDist
: SimParameters
- pairlistGrow
: SimParameters
- pairlisti
: ComputeNonbondedWorkArrays
- pairlistm
: ComputeNonbondedWorkArrays
- pairlistmA1
: ComputeNonbondedWorkArrays
- pairlistmA2
: ComputeNonbondedWorkArrays
- pairlistmA3
: ComputeNonbondedWorkArrays
- pairlistmA4
: ComputeNonbondedWorkArrays
- pairlistMinProcs
: SimParameters
- pairlistnA0
: ComputeNonbondedWorkArrays
- pairlistnA1
: ComputeNonbondedWorkArrays
- pairlistnA2
: ComputeNonbondedWorkArrays
- pairlistnA3
: ComputeNonbondedWorkArrays
- pairlistnA4
: ComputeNonbondedWorkArrays
- pairlistnAlch
: ComputeNonbondedWorkArrays
- pairlists
: nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair
- pairlistsAge
: Sequencer
- pairlistsAreValid
: Sequencer
- pairlistShrink
: SimParameters
- pairlistsPerCycle
: SimParameters
- pairlistsValid
: ComputeNonbondedSelf, ComputeNonbondedPair
- pairlistTolerance
: Flags, ComputeNonbondedSelf, ComputeNonbondedPair
- pairlistTrigger
: SimParameters
- pairlistWarnings
: Controller
- pairlistx
: ComputeNonbondedWorkArrays
- pairlistxA1
: ComputeNonbondedWorkArrays
- pairlistxA2
: ComputeNonbondedWorkArrays
- pairlistxA3
: ComputeNonbondedWorkArrays
- pairlistxA4
: ComputeNonbondedWorkArrays
- param
: ScriptParamMsg
- parameters
: Node
- paraTypeCharmmOn
: SimParameters
- paraTypeXplorOn
: SimParameters
- parent
: ParseOptions::DataElement
- parent_ptr
: ParseOptions::DataElement
- particles
: ComputeDPMEDataMsg
- partition
: RecBisection, ComputeMap, CompAtom, ComputeMap::ComputeData
- partner
: AtomCstInfo, atom_constants
- patch
: PatchMap, Sequencer, ProxyUsageKey, ProxySpanningTreeMsg, ProxyCombinedResultMsg, ProxyNodeAwareSpanningTreeMsg, ProxyResultVarsizeMsg, ProxyResultMsg, ProxyDataMsg, ProxyAtomsMsg, UnregisterProxyMsg, RegisterProxyMsg, HomePatchElem, ComputePatchPair, ComputePatch, ComputeHomePatch
- patch1
: computeInfo
- patch2
: computeInfo
- patchArray
: LdbCoordinator
- patchBased
: ComputeMap::ComputeData
- patchDimension
: SimParameters
- patches
: Rebalancer
- patchHandles
: LdbCoordinator
- patchID
: ProxyElem, Patch, ComputePatchPair, TuplePatchElem, PatchElem
- patchList
: ComputeHomePatches
- patchMap
: Node, LdbCoordinator, ComputeHomeTuples< T, S, P >, ComputeHomePatches
- patchMapData
: MapDistribMsg
- patchMgr
: BOCgroup
- patchNAtoms
: LdbCoordinator
- patchSet
: processorInfo
- pdb
: Node
- PDBNames
: PDBData
- PE
: StreamMessage
- peIDs
: proxyTreeNode
- pes
: Rebalancer
- Phase
: parm
- pi_ewaldcof
: ComputeNonbondedUtil
- pid
: PatchMap, ComputeMap, MovePatch, MovePatchesMsg, LocalID, HomePatchElem, ComputeMap::PatchRec
- pids
: ComputeMap::ComputeData
- Pk
: parm
- plcutoff
: nonbonded
- plExtLen
: ProxyDataMsg
- plLen
: ProxyDataMsg
- PMEBarrier
: SimParameters
- PMEEwaldCoefficient
: SimParameters
- PMEGridSizeX
: SimParameters
- PMEGridSizeY
: SimParameters
- PMEGridSizeZ
: SimParameters
- PMEGridSpacing
: SimParameters
- PMEInterpOrder
: SimParameters
- PMEMinPoints
: SimParameters
- PMEMinSlices
: SimParameters
- PMEOn
: SimParameters
- PMEPencils
: SimParameters
- PMEProcessors
: SimParameters
- pmeProxy
: PmePencilInitMsgData
- PMETolerance
: SimParameters
- Pn
: parm
- popn
: parm
- position
: CompAtom
- positionBox
: Patch, ComputePatchPair, TuplePatchElem, PatchElem
- positionComputeList
: Patch
- positionExtList
: ProxyDataMsg
- positionList
: ProxyDataMsg
- positionRescaleFactor
: ControllerBroadcasts
- ppbonded
: Controller
- ppint
: Controller
- ppnonbonded
: Controller
- precisions
: CollectionMgr::CollectVectorInstance
- pressure
: Controller
- pressure_avg
: Controller
- pressure_nbond
: Controller
- pressure_normal
: Controller
- pressure_slow
: Controller
- pressure_tavg
: Controller
- pressureProfileAtomTypes
: SimParameters, ComputeNonbondedUtil, ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
- pressureProfileAverage
: Controller
- pressureProfileCount
: Controller
- pressureProfileData
: ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >
- pressureProfileEwaldOn
: SimParameters
- pressureProfileEwaldX
: SimParameters
- pressureProfileEwaldY
: SimParameters
- pressureProfileEwaldZ
: SimParameters
- pressureProfileFreq
: SimParameters
- pressureProfileMin
: ComputeNonbondedUtil, ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
- pressureProfileOn
: SimParameters, ComputeNonbondedUtil
- pressureProfileReduction
: Sequencer, nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >
- pressureProfileSlabs
: SimParameters, Controller, ComputeNonbondedUtil, ImproperElem, ComputeHomeTuples< T, S, P >, DihedralElem, CrosstermElem, BondElem, AngleElem
- pressureProfileThickness
: ComputeNonbondedUtil, ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
- processor
: ProxyUsageKey, patchInfo, computeInfo
- processorArray
: LdbCoordinator
- processors
: Rebalancer
- procID
: ProxyNodeAwareSpanningTreeMsg
- procsPerNode
: SimParameters
- proxies
: processorInfo
- proxiesOn
: patchInfo
- proxylist
: ProxyTree
- proxyMgr
: BOCgroup
- proxyMsgCount
: ProxyTree
- proxyPatch
: ProxyElem
- proxyUsage
: Rebalancer
- r
: doublecomplex, TuplePatchElem, PatchElem, floatcomplex
- r2_delta
: ComputeNonbondedUtil
- r2_delta_1
: ComputeNonbondedUtil
- r2_delta_exp
: ComputeNonbondedUtil
- r2_table
: ComputeNonbondedUtil
- r2list
: ComputeNonbondedWorkArrays
- r_ub
: AngleValue, angle_params
- random
: Sequencer, Controller
- randomSeed
: SimParameters
- range
: ParseOptions, ParseOptions::DataElement
- readExclusions
: SimParameters
- reassignFreq
: SimParameters
- reassignHold
: SimParameters
- reassignIncr
: SimParameters
- reassignTemp
: SimParameters
- recent_dEdl_elec_1
: Controller
- recent_dEdl_elec_2
: Controller
- recent_dEdl_lj_1
: Controller
- recent_dEdl_lj_2
: Controller
- recent_dEdl_PME
: Controller
- recent_TiNo
: Controller
- reconfig
: ComputeGlobalResultsMsg
- reduction
: Sequencer, Controller, ComputeStir, ComputeSphericalBC, ComputeRestraints, nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >, ComputeGridForce, ComputeEField, ComputeCylindricalBC
- reductionMgr
: BOCgroup
- reductionSetID
: ReductionSet, ReductionSubmitMsg, ReductionRegisterMsg
- refCount
: UniqueSetRaw< Elem >
- reg_all_objs
: LdbCoordinator
- rep
: ResizeArray< Elem >
- replace
: ExtForce
- Req
: parm
- requireRegistered
: ReductionSet
- rescaleFreq
: SimParameters
- rescaleTemp
: SimParameters
- rescaleVelocities_numTemps
: Sequencer, Controller
- rescaleVelocities_sumTemps
: Controller
- resendCoordinates
: ComputeGlobalResultsMsg
- resID
: BasicAtomInfo
- resname
: atom_name_info
- resNameIdx
: BasicAtomInfo
- resnameIdx
: AtomNameIdx
- ResNames
: parm
- restartFilename
: SimParameters
- restartFrequency
: SimParameters
- restartSave
: SimParameters
- results
: Patch
- right
: indexed_vdw_pair, vdw_params, angle_params, bond_params
- rigidBonds
: SimParameters
- rigidDie
: SimParameters
- rigidIter
: SimParameters
- rigidTol
: SimParameters
- Rk
: parm
- rotConsAxis
: SimParameters
- rotConsPivot
: SimParameters
- rotConstraintsOn
: SimParameters
- rotConsVel
: SimParameters
- rotDragAxisFile
: SimParameters
- rotDragFile
: SimParameters
- rotDragGlobVel
: SimParameters
- rotDragOn
: SimParameters
- rotDragPivotFile
: SimParameters
- rotDragVelFile
: SimParameters
- savePairlists
: Flags, nonbonded
- scale
: Lattice, GridforceGrid::box, ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
- scale14
: SimParameters, ComputeNonbondedUtil
- scaling
: ComputeNonbondedUtil
- scor_table
: ComputeNonbondedUtil
- scriptArg1
: SimParameters
- scriptArg2
: SimParameters
- scriptArg3
: SimParameters
- scriptArg4
: SimParameters
- scriptArg5
: SimParameters
- scriptBarrier
: Node, ControllerBroadcasts
- segNameIdx
: BasicAtomInfo
- selectConstraintsOn
: SimParameters
- send_order
: PmePencil< T >
- seq
: CollectionMgr::CollectVectorInstance, CollectVectorMsg, CollectionMaster::CollectVectorInstance
- sequence
: Compute, Flags, PmePencil< T >, PmeTransMsg, PmeGridMsg
- sequenceNumber
: ReductionSetData, ReductionSubmitMsg
- sequencerThreads
: LdbCoordinator
- shiftIOToOne
: SimParameters
- sigId
: CompAtomExt
- sigma
: vdw_val, vdw_params
- sigma14
: vdw_val, vdw_params
- simParameters
: Node
- simParams
: Sequencer, Controller
- sizes
: ProxyTree
- sldata
: ParseOptions::DataElement
- slow_table
: ComputeNonbondedUtil
- slowFreq
: Sequencer, Controller
- slptr
: ParseOptions::DataElement
- SMDDir
: SimParameters
- SMDFile
: SimParameters
- SMDk
: SimParameters
- SMDk2
: SimParameters
- SMDOn
: SimParameters
- SMDOutputFreq
: SimParameters
- SMDVel
: SimParameters
- smooth2_avg
: Controller
- smooth2_avg2
: Controller
- sock
: GlobalMasterIMD
- Solty
: parm
- sortVal
: HydrogenGroupID
- sourceNode
: ReductionSubmitMsg, ReductionRegisterMsg, PmeUntransMsg, PmeTransMsg, PmeGridMsg, ExtCoordMsg
- sphericalBCexp1
: SimParameters
- sphericalBCexp2
: SimParameters
- sphericalBCk1
: SimParameters
- sphericalBCk2
: SimParameters
- sphericalBCOn
: SimParameters
- sphericalBCr1
: SimParameters
- sphericalBCr2
: SimParameters
- sphericalCenter
: SimParameters
- splitPatch
: SimParameters
- sptr
: ParseOptions::DataElement
- srcPatchID
: MigrateAtomsCombinedMsg, MigrateAtomsMsg
- start
: PmeGridMsg
- state
: Node, Controller
- status
: UniqueSetIter< T >, NamdState, AtomCstInfo, atom_constants
- step
: Flags, GlobalMaster, ComputeGlobalDataMsg
- stepsPerCycle
: SimParameters
- stepsPerLdbCycle
: LdbCoordinator
- stirAxis
: SimParameters
- stirFilename
: SimParameters
- stirK
: SimParameters
- stirOn
: SimParameters
- stirPivot
: SimParameters
- stirStartingTheta
: SimParameters
- stirVel
: SimParameters
- strainRate
: SimParameters
- strainRate2
: SimParameters
- strategyName
: Rebalancer
- submitLoadStats
: HomePatch, Flags
- surfaceTensionTarget
: SimParameters
- suspended
: BroadcastClient
- switchingActive
: SimParameters
- switchingDist
: SimParameters
- switchOn
: ComputeNonbondedUtil
- switchOn2
: ComputeNonbondedUtil
- switchOn_1
: ComputeNonbondedUtil
- sync
: BOCgroup
- T
: IMDEnergies
- table_alloc
: ComputeNonbondedUtil
- table_noshort
: ComputeNonbondedUtil
- table_short
: ComputeNonbondedUtil
- tag
: StreamMessage, TaggedMsg
- taggedMsg
: BOID
- takingLdbData
: LdbCoordinator
- tavg_count
: Controller
- tclBCArgs
: SimParameters
- tclBCOn
: SimParameters
- tclBCScript
: SimParameters
- tclForcesOn
: SimParameters
- tcoupleCoefficient
: ControllerBroadcasts
- tCoupleOn
: SimParameters
- tCoupleTemp
: SimParameters
- temp_avg
: Controller
- temperature
: Controller
- Teq
: parm
- testOn
: SimParameters
- tf
: ComputeGlobalDataMsg
- theLbdb
: LdbCoordinator
- thermInt
: SimParameters, ComputeNonbondedUtil
- theta0
: AngleValue
- thread
: BroadcastClient
- threadIsWaiting
: ReductionSet
- tiElecLambdaStart
: SimParameters
- tiEquilSteps
: SimParameters
- tiFile
: Controller
- tiLambda
: SimParameters
- timestep
: EnqueueDataMsg
- TiNo
: Controller
- tiOutFile
: SimParameters
- tiOutFreq
: SimParameters
- tiTemp
: SimParameters
- tiVdwLambdaEnd
: SimParameters
- tiVdwShiftCoeff
: SimParameters
- Tk
: parm
- TMDFile
: SimParameters
- TMDFinalRMSD
: SimParameters
- TMDFirstStep
: SimParameters
- TMDInitialRMSD
: SimParameters
- TMDk
: SimParameters
- TMDLastStep
: SimParameters
- TMDOn
: SimParameters
- TMDOutputFreq
: SimParameters
- to
: LdbMigrateMsg
- totalAtoms
: SimParameters, MigrateAtomsCombinedMsg
- totalEnergy
: Controller
- totalStepsDone
: LdbCoordinator
- trans
: ComputeMap, ComputePatchPair, ComputeMap::PatchRec
- transform
: FullAtom
- tree
: ProxySpanningTreeMsg
- TreeJoin
: parm
- trees
: ProxyTree
- tstep
: IMDEnergies
- tupleList
: ComputeHomeTuples< T, S, P >
- tupleParamType
: TupleSignature
- tuplePatchList
: ComputeHomeTuples< T, S, P >
- tupleType
: TupleSignature
- twoAwayX
: SimParameters
- twoAwayY
: SimParameters
- twoAwayZ
: SimParameters
- type
: PDBData, ComputeMap, Compute, ParseOptions::DataElement, IMDheader, ComputeMap::ComputeData
- value
: ScriptParamMsg, ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
- values
: ImproperValue, DihedralValue, crossterm_params, improper_params, dihedral_params
- vdata
: ParseOptions::DataElement
- vdef
: ParseOptions::DataElement
- vdw_array
: Parameters
- vdw_pair_tree
: Parameters
- vdw_type
: AtomCstInfo, atom_constants
- vdwa_table
: ComputeNonbondedUtil
- vdwb_table
: ComputeNonbondedUtil
- vdwGeometricSigma
: SimParameters
- vdwscale14
: SimParameters
- vdwType
: CompAtomExt
- vdwtype_array
: ComputeNonbondedWorkArrays
- velDcdFilename
: SimParameters
- velDcdFrequency
: SimParameters
- velocity
: Output, FullAtom
- velocityRescaleFactor
: ControllerBroadcasts
- virial
: ExtForceMsg
- vptr
: ParseOptions::DataElement
- x
: Vector, FloatVector, PmeParticle, minpoint, TuplePatchElem, PatchElem, EwaldParticle, AtomsForcesMsg, AtomsCoorMsg
- x0
: NonbondedExclValue, BondValue
- x_avg
: TuplePatchElem
- x_start
: LocalPmeInfo, PmeTransMsg
- xBlocks
: PmePencilInitMsgData
- Xcap
: parm
- xPencil
: PmePencilInitMsgData
- xstFile
: Controller
- xstFilename
: SimParameters
- xstFrequency
: SimParameters
- xx
: Tensor
- xy
: Tensor
- xz
: Tensor