NAMD: Class Members

_ | a | b | c | d | e | f | g | h | i | j | k | l | m | n | o | p | q | r | s | t | u | v | w | x | y | z | ~

Here is a list of all class members with links to the classes they belong to:

- _ -

_hasNewAtoms : Patch

- a -

A : indexed_vdw_pair, vdw_pair_params, LJTable::TableEntry
a() : Lattice
A14 : indexed_vdw_pair, vdw_pair_params
a_p() : Lattice
a_r() : Lattice
a_total : nodesort
aaAngleExp : SimParameters
Accumulate() : ALambdaManager, ALambdaControl
activate_pencils() : ComputePmeMgr
actualNumAtoms : AtomStaticInfoMsg
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
addToRemoteSequenceNumber : ReductionSet
addType() : VDWTable, DihedralTable, AngleTable, BondTable, AtomTable
addVelocityToPosition() : Sequencer, HomePatch
ADiheRestraint() : ADiheRestraint
ADistRestraint() : ADistRestraint
adjustBackgroundLoadAndComputeAverage() : Rebalancer
AGroup() : AGroup
aid : ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeGlobalConfigMsg, ComputeConsForceMsg, CollectionMgr::CollectVectorInstance, CollectVectorMsg
ALambdaControl() : ALambdaControl
ALambdaManager() : ALambdaManager
Alg7() : Alg7
AlgNbor() : AlgNbor
algorithm() : Sequencer, Controller
AlgRecBisection() : AlgRecBisection
AlignVector() : AlignVector
alloc() : ReductionSubmitMsg
allocateCids() : ComputeMap
allocateMap() : AtomMap
alternatelocation() : PDBAtom
amberOn : SimParameters
AnAngleRestraint() : AnAngleRestraint
angle : angle_params
angle_array : Parameters
angle_type : angle
AngleAt1 : parm
AngleAt2 : parm
AngleAt3 : parm
angleCnt : AtomSignature
AngleElem : AngleElem, Molecule
angleEnergyIndex : AngleElem
AngleHAt1 : parm
AngleHAt2 : parm
AngleHAt3 : parm
AngleHNum : parm
AngleNum : parm
angleSigIndices : AtomSigInfo
angleSigs : AtomSignature
ANISOU : PDBData
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 : PDBData
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
atom_type_name() : Parameters
atomcharge() : Molecule
ATOMDISNUM : AtomsDisInfo
atomFixed : CompAtom
atomid : MoveAtomMsg
atomID : HydrogenGroupID, ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
atomIDList : ProxyAtomsMsg
atomIndex : ResidueLookupElem
atomMap : Node, ComputeHomeTuples< T, S, P >
AtomMap() : AtomMap
atommass() : Molecule
atomname : atom_name_info, vdw_params
atomNameIdx : BasicAtomInfo
atomnameIdx : AtomNameIdx
AtomNames : parm
AtomRes : parm
atoms : PDB, AtomStaticInfoMsg
atomsCnt : AtomsDisInfo
AtomsDisInfo() : AtomsDisInfo
atomSigIdx : BasicAtomInfo
AtomSigInfo() : AtomSigInfo
AtomSignature() : AtomSignature
atomsInGroup : HydrogenGroupID
AtomSym : parm
AtomTree : parm
atomtype : atom_name_info
atomTypeIdx : BasicAtomInfo
atomtypeIdx : AtomNameIdx
atomUpdate() : ComputePatchPair, ComputePatch, ComputeHomeTuples< T, S, P >, ComputeHomePatches, ComputeHomePatch, Compute
atomvdwtype() : Molecule
AUTHOR : PDBData
auxFilename : SimParameters
available : processorInfo
AVector() : AVector
averageLoad : Rebalancer
avg_count : Controller
avgPlLen : ProxyDataMsg
avgPositionBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair, TuplePatchElem, PatchElem
avgPositionBoxClosed() : Patch
avgPositionComputeList : Patch
avgPositionList : ProxyDataMsg
avgPositionPtrBegin : Patch
avgPositionPtrEnd : Patch
awaitBOCCheckIn() : Node
awaken() : Sequencer, Controller, BroadcastClient, BackEnd
awakenSequencers() : LdbCoordinator

- b -

b : Lattice, netint, GridforceGrid::box
B : indexed_vdw_pair, vdw_pair_params, LJTable::TableEntry
B14 : indexed_vdw_pair, vdw_pair_params
b_p() : Lattice
b_r() : Lattice
b_total : nodesort
backgroundLoad : processorInfo
backward_fft() : PmeXPencil, PmeYPencil, PmeZPencil
barrier() : LdbCoordinator, BackEnd
base_init() : PmePencil< T >
basenode() : PatchMap
basePatchIDList() : PatchMap
basePriority : Compute
begin() : UniqueSetIter< T >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ResizeArray< Elem >, Array< Elem, Size >
berendsenPressure() : Sequencer, Controller
berendsenPressure_avg : Controller
berendsenPressure_count : Sequencer, Controller
berendsenPressureCompressibility : SimParameters
berendsenPressureFreq : SimParameters
berendsenPressureOn : SimParameters
berendsenPressureRelaxationTime : SimParameters
berendsenPressureTarget : SimParameters
binaryOutput : SimParameters
binaryRefine() : RefineTorusLB
binaryRestart : SimParameters
block1 : PmeGrid
block2 : PmeGrid
block3 : PmeGrid
BOCCheckIn() : Node
BOID() : BOID
bond_array : Parameters
bond_type : bond
BondAt1 : parm
BondAt2 : parm
bondCnt : AtomSignature
BondElem : BondElem, Molecule
bondEnergyIndex : BondElem
BondHAt1 : parm
BondHAt2 : parm
BondHNum : parm
BondNum : parm
bondSigIndices : AtomSigInfo
bondSigs : AtomSignature
BOOL : ParseOptions::DataElement
Boundary : parm
Box : parm, GridforceGrid
Box<Owner,Data> : OwnerBox< Owner, Data >
boxClosed() : ProxyPatch, Patch, HomePatch
boxesOpen : Patch
brickDim() : Rebalancer
broadcast : Sequencer, Controller
broadcastClient : BroadcastClientElem
BroadcastClient() : BroadcastClient
BroadcastClientElem() : BroadcastClientElem
broadcastMgr : BOCgroup
BroadcastMgr : BroadcastMgr, BroadcastMsg
BroadcastMsg() : BroadcastMsg
broadcastSet : BOID
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
bytesPerAtom : Rebalancer

- c -

c : Lattice, Rebalancer::pcpair, CrosstermValue
c0 : ComputeNonbondedUtil
c1 : ComputeNonbondedUtil
c3 : ComputeNonbondedUtil
c5 : ComputeNonbondedUtil
c6 : ComputeNonbondedUtil
c7 : ComputeNonbondedUtil
c8 : ComputeNonbondedUtil
c_p() : Lattice
c_r() : Lattice
c_total : nodesort
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_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_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_fullelect() : ComputeNonbondedUtil
calc_pair_fullelect_les() : ComputeNonbondedUtil
calc_pair_fullelect_pprof() : ComputeNonbondedUtil
calc_pair_les() : ComputeNonbondedUtil
calc_pair_merge_fullelect() : ComputeNonbondedUtil
calc_pair_merge_fullelect_les() : ComputeNonbondedUtil
calc_pair_merge_fullelect_pprof() : ComputeNonbondedUtil
calc_pair_pprof() : ComputeNonbondedUtil
calc_pair_slow_fullelect() : ComputeNonbondedUtil
calc_pair_slow_fullelect_les() : ComputeNonbondedUtil
calc_pair_slow_fullelect_pprof() : 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_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_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_fullelect() : ComputeNonbondedUtil
calc_self_fullelect_les() : ComputeNonbondedUtil
calc_self_fullelect_pprof() : ComputeNonbondedUtil
calc_self_les() : ComputeNonbondedUtil
calc_self_merge_fullelect() : ComputeNonbondedUtil
calc_self_merge_fullelect_les() : ComputeNonbondedUtil
calc_self_merge_fullelect_pprof() : ComputeNonbondedUtil
calc_self_pprof() : ComputeNonbondedUtil
calc_self_slow_fullelect() : ComputeNonbondedUtil
calc_self_slow_fullelect_les() : ComputeNonbondedUtil
calc_self_slow_fullelect_pprof() : ComputeNonbondedUtil
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
calculate() : GlobalMasterTest, GlobalMasterTcl, GlobalMasterIMD, GlobalMaster
cellBasisVector1 : SimParameters
cellBasisVector2 : SimParameters
cellBasisVector3 : SimParameters
cellOrigin : SimParameters
cg : PmeParticle, EwaldParticle
chain() : PDBAtom
changedAtoms() : GlobalMaster
changedForces() : GlobalMaster
changedGroups() : GlobalMaster
charge : atom_constants, CompAtom
chargeIdx : BasicAtomInfo
Charges : parm
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
checkpoint_berendsenPressure_avg : Controller
checkpoint_berendsenPressure_count : Sequencer, Controller
checkpoint_langevinPiston_strainRate : Controller
checkpoint_lattice : Controller
checkpoint_stored : Controller
checksum : StreamMessage
cid : PatchMap, Compute
Clear() : ALambdaManager, AGroup
clear() : UniqueSetRaw< Elem >, EntryGlob< Elem >, Entry< Elem >, UniqueSet< Elem >
clearChain() : EntryGlob< Elem >, Entry< Elem >
clearChanged() : GlobalMaster
clearMap() : AtomMap
clients : GlobalMasterIMD
close() : PositionOwnerBox< Owner >, PositionBox< Owner >, OwnerBox< Owner, Data >, Box< Owner, Data >
Cn1 : parm
Cn2 : parm
Cno : parm
COLDOn : SimParameters
COLDRate : SimParameters
COLDTemp : SimParameters
collection : Sequencer, Controller
CollectionMaster() : CollectionMaster
CollectionMasterHandler() : CollectionMasterHandler
collectionMgr : BOCgroup
CollectionMgr() : CollectionMgr
CollectVectorInstance() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
COLUMNS : PDBData
commOnly : SimParameters, ComputeNonbondedUtil
comMove : SimParameters
Communicate() : Communicate
compare() : ProxyUsageKey
compareChecksums() : Controller
CompAtom() : CompAtom
CompAtomExt() : CompAtomExt
COMPND : PDBData
compute : ComputeMap, LocalWorkMsg, ComputeMap::ComputeData
Compute() : Compute
compute_energy() : PmeKSpace
compute_forces() : PmeRealSpace
ComputeAngles() : ComputeAngles
computeArray : LdbCoordinator
computeAverage() : Rebalancer
computeBgPairHeap : Rebalancer
computeBgSelfHeap : Rebalancer
ComputeBonds() : ComputeBonds
computeChecksum : Controller
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 : BOCgroup
ComputeExtMgr() : ComputeExtMgr
computeForce() : ImproperElem, DihedralElem, CrosstermElem, BondElem, AngleElem
ComputeFullDirect() : ComputeFullDirect
ComputeGlobal : ComputeGlobal, HomePatch
ComputeGlobalConfigMsg() : ComputeGlobalConfigMsg
ComputeGlobalDataMsg() : ComputeGlobalDataMsg
computeGlobalObject : ComputeMgr
ComputeGlobalResultsMsg() : ComputeGlobalResultsMsg
ComputeGridForce() : ComputeGridForce
ComputeHomePatch() : ComputeHomePatch
ComputeHomePatches() : ComputeHomePatches
ComputeHomeTuples() : ComputeHomeTuples< T, S, P >
ComputeImpropers() : ComputeImpropers
computeLoad : processorInfo
ComputeMap() : ComputeMap
computeMap : Node, LdbCoordinator
computeMapData : MapDistribMsg
computeMax() : Rebalancer
computeMgr : Node, BOCgroup
ComputeMgr : ComputeMgr, ComputeMap
ComputeNonbondedPair() : ComputeNonbondedPair
ComputeNonbondedSelf() : ComputeNonbondedSelf
ComputeNonbondedUtil() : ComputeNonbondedUtil
computePairHeap : Rebalancer
ComputePatch() : ComputePatch
ComputePatchPair() : ComputePatchPair
ComputePme : ComputePme, ComputePmeMgr
ComputePmeMgr() : ComputePmeMgr
computePmeMgr : BOCgroup
ComputeRestraints() : ComputeRestraints
computes : Rebalancer
ComputeSelfAngles() : ComputeSelfAngles
ComputeSelfBonds() : ComputeSelfBonds
ComputeSelfCrossterms() : ComputeSelfCrossterms
ComputeSelfDihedrals() : ComputeSelfDihedrals
computeSelfHeap : Rebalancer
ComputeSelfImpropers() : ComputeSelfImpropers
ComputeSelfTuples() : ComputeSelfTuples< T, S, P >
computeSet : processorInfo
ComputeSphericalBC() : ComputeSphericalBC
ComputeStir() : ComputeStir
ComputeTclBC() : ComputeTclBC
CONECT : PDBData
config : GlobalMasterEasy
configFileInit() : NamdState
ConfigList() : ConfigList
configList : Node
configListInit() : NamdState
ConfigListNode() : ConfigList::ConfigListNode
consForce : Molecule
consForceFile : SimParameters
consForceIndexes : Molecule
consForceOn : SimParameters
consForceScaling : SimParameters
const_begin() : ResizeArray< Elem >, Array< Elem, Size >
const_end() : ResizeArray< Elem >, Array< Elem, Size >
const_iterator : ResizeArray< Elem >, Array< Elem, Size >
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
Controller : Controller, NamdState
ControllerBroadcasts() : ControllerBroadcasts
controllerExpected : LdbCoordinator
controllerReported : LdbCoordinator
controllerThread : LdbCoordinator
controlNumDegFreedom : Controller
controlPressure : Controller
controlPressure_nbond : Controller
controlPressure_normal : Controller
controlPressure_slow : Controller
coord : MoveAtomMsg, ExtCoordMsg
coordinate() : Output
coordinateNeeded() : Output
coordinates() : PDBAtom
coords : Node
coordtmp : GlobalMasterIMD
coordtmpsize : GlobalMasterIMD
copyPencils() : ComputePme
copyResults() : ComputePme
corr_table : ComputeNonbondedUtil
correctMomentum() : Sequencer, Controller
counter : TaggedMsg
create() : Lattice
createAtomLists() : WorkDistrib
createComputes() : ComputeMgr
createHomePatch() : PatchMgr
createHomePatches() : WorkDistrib
createLoadBalancer() : LdbCoordinator
createProxies() : ProxyMgr
createProxy() : ProxyMgr
createSpanningTree() : Rebalancer
cross() : Vector, AVector
crossterm_array : Parameters
crossterm_params() : crossterm_params
crossterm_type : crossterm
crosstermCnt : AtomSignature
CrosstermElem : CrosstermElem, Molecule
crosstermEnergyIndex : CrosstermElem
crosstermSigIndices : AtomSigInfo
crosstermSigs : AtomSignature
CRYST1 : PDBData
Cutcap : parm
cutoff : SimParameters, ComputeNonbondedUtil
cutoff2 : ComputeNonbondedUtil
cycleBarrier() : Sequencer, Controller
cylindricalBCAxis : SimParameters
cylindricalBCexp1 : SimParameters
cylindricalBCexp2 : SimParameters
cylindricalBCk1 : SimParameters
cylindricalBCk2 : SimParameters
cylindricalBCl1 : SimParameters
cylindricalBCl2 : SimParameters
cylindricalBCOn : SimParameters
cylindricalBCr1 : SimParameters
cylindricalBCr2 : SimParameters
cylindricalCenter : SimParameters

- d -

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
data_types : ParseOptions::DataElement
DataElement() : ParseOptions::DataElement
dataQueue : ReductionSet
dataSize : ReductionSetData, ReductionSubmitMsg
datastream() : datastream
dcdFilename : SimParameters
dcdFrequency : SimParameters
dcdUnitCell : SimParameters
deAssign() : Rebalancer
decrement() : ProxyUsage
decrSTLoad() : Rebalancer
default_coor : PDBAtom
default_occupancy : PDBAtom
default_residueseq : PDBAtom
default_serial : PDBAtom
default_temperaturefactor : PDBAtom
defined() : ParseOptions
del() : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ResizeArrayRaw< Elem >, ResizeArray< Elem >
delData() : ReductionSet
deleted : heapRecord
deleteMax() : maxHeap
deleteMin() : minHeap
delta : Lattice, four_body_consts
delTmpPatchAtomsList() : PatchMap
depositCombinedResultMsg() : ProxyPatch
depositMigration() : HomePatch
destNodeID : MigrationInfo
destPatchID : MigrationInfo, MigrateAtomsCombinedMsg, MigrateAtomsMsg
destroy() : Lattice
dG : Controller
dhaCutoffAngle : SimParameters
dhaOffAngle : SimParameters
dhaOnAngle : SimParameters
diagonal() : Tensor
dielectric : SimParameters
dielectric_1 : ComputeNonbondedUtil
DihAt1 : parm
DihAt2 : parm
DihAt3 : parm
DihAt4 : parm
dihedral_array : Parameters
dihedral_params() : dihedral_params
dihedral_type : dihedral
dihedralCnt : AtomSignature
DihedralElem : DihedralElem, Molecule
dihedralEnergyIndex : DihedralElem
dihedralOn : SimParameters
dihedralSigIndices : AtomSigInfo
dihedralSigs : AtomSignature
DihHAt1 : parm
DihHAt2 : parm
DihHAt3 : parm
DihHAt4 : parm
DihHNum : parm
DihNum : parm
dim : CrosstermValue
dim2 : PmeGrid
dim3 : PmeGrid
dimension : crossterm_params
disAtoms : AtomsDisInfo
disposePositions() : CollectionMaster
disposeVelocities() : CollectionMaster
Dist() : AVector
distance : bond_params
distAttExp : SimParameters
distRepExp : SimParameters
distribute() : MigrateAtomsCombinedMsg
DistributeForce() : ARestraint
distributeHomePatches() : WorkDistrib
DistSqr() : AVector
doAtomMigration() : HomePatch
doEnergy : Flags
doForce() : ComputeStir, ComputeSphericalBC, ComputeRestraints, ComputePatchPair, ComputePatch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomePatch, ComputeGridForce, ComputeEField, ComputeCylindricalBC, ComputeConsTorque, ComputeConsForce
doFullElectrostatics : Flags
doGroupSizeCheck() : HomePatch
doLoadTuples : ComputeHomeTuples< T, S, P >
doMarginCheck() : HomePatch
doMolly : Flags
done_reading_files() : Parameters
done_reading_structure() : Parameters
doneSaveComputeMap() : WorkDistrib
doneUpdateLocalComputes() : ComputeMgr
doNonbonded : Flags
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
dt : SimParameters
dudx : minpoint
dummy : SimParameters

- e -

Eangle : IMDEnergies
EarlyExit() : ARestraint
earlyExit() : Node
easy_calc() : GlobalMasterMisc, GlobalMasterEasy
easy_init() : GlobalMasterMisc, GlobalMasterEasy
Ebond : IMDEnergies
Edihe : IMDEnergies
Eelec : IMDEnergies
eField : SimParameters
eFieldFreq : SimParameters
eFieldOn : SimParameters
eFieldPhase : SimParameters
eik : ComputeEwaldMsg
Eimpr : IMDEnergies
electEnergy : Controller
electEnergy_f : Controller
electEnergyIndex : ComputeNonbondedUtil
electEnergyIndex_s : ComputeNonbondedUtil
electEnergySlow : Controller
electEnergySlow_f : Controller
element() : PDBAtom
enableEarlyExit() : Node
enableExitScheduler() : Node
enableScriptBarrier() : Node
END : PDBData
end() : UniqueSetIter< T >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ResizeArray< Elem >, MOStream, Array< Elem, Size >
endd() : datastream
endi() : infostream
ENDMDL : PDBData
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
EntryGlob<Elem> : Entry< Elem >
Epot : IMDEnergies
epsilon : vdw_val, vdw_params
epsilon14 : vdw_val, vdw_params
error_message : ParseOptions::DataElement
Etot : IMDEnergies
Evdw : IMDEnergies
eventsRegistered : ReductionSet
eventsRemaining : ReductionSetData
evir : PmePencil< T >, PmeUntransMsg, PmeGridMsg
ewaldcof : ComputeNonbondedUtil
ExclAt : parm
exclChecksumIndex : ComputeNonbondedUtil
exclId : CompAtomExt
exclSigIdx : BasicAtomInfo
ExclSigInfo() : ExclSigInfo
exclude : SimParameters
excludeFromPressure : SimParameters
Exclusion() : Exclusion
ExclusionCheck() : ExclusionCheck
ExclusionSignature() : ExclusionSignature
ExecuteMigrations() : LdbCoordinator
exists() : ParseOptions
exit() : BackEnd
ExitSchedOn() : BackEnd
exitScheduler() : Node
exp_dE_ByRT : Controller
EXPDTA : PDBData
ExpectMigrate() : LdbCoordinator
extCoordFilename : SimParameters
ExtForce() : ExtForce
extForceFilename : SimParameters
extForcesCommand : SimParameters
extForcesOn : SimParameters
extraBondsOn : SimParameters

- f -

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
fft_init() : PmeXPencil, PmeYPencil, PmeZPencil
FFTWEstimate : SimParameters
FFTWUseWisdom : SimParameters
FFTWWisdomFile : SimParameters
FFTWWisdomString : SimParameters
fgrid : PmeGridMsg
fid : ComputeGlobalDataMsg
field() : PDBData
FIELDS : PDBData
file : FileStack
filename : FileStack
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
firstAssignInRefine : Rebalancer
firstLdbStep : SimParameters, LdbCoordinator
firstResid : ResidueLookupElem
firstTime : GlobalMasterMisc
firstTimestep : SimParameters
firstwat() : parm
fixedAtomsForces : SimParameters
fixedAtomsOn : SimParameters, ComputeNonbondedUtil
fixedPosition : FullAtom
fixglist : ComputeNonbondedWorkArrays
flags : ProxyDataMsg, Patch, ExclusionCheck
flLen : ProxyResultVarsizeMsg
FLOAT : ParseOptions::DataElement
floatcomplex() : floatcomplex
FloatVector() : FloatVector
FMAFFTBlock : SimParameters
FMAFFTOn : SimParameters
FMALevels : SimParameters
FMAMp : SimParameters
FMAOn : SimParameters
fmaTheta : SimParameters
footnote() : PDBAtom
force : ExtForce, vmdforce, ExtForceMsg
forceArr : ProxyResultVarsizeMsg
forceBox : Patch, ProxyListElem, ComputePatchPair, TuplePatchElem, PatchElem
forceBoxClosed() : Patch
forceComputeList : Patch
forceconstant : angle_params, bond_params
forcedAtoms() : GlobalMaster
forceList : ProxyCombinedResultMsg, ProxyResultMsg
forces : ComputeDPMEResultsMsg
FORMUL : PDBData
forward_fft() : PmeXPencil, PmeYPencil, PmeZPencil
found : SortedArray< Elem >
fptr : ParseOptions::DataElement
free() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
freeEnergyOn : SimParameters
from : LdbMigrateMsg
fromNodeID : MovePatchesMsg, MigrateAtomsCombinedMsg, MigrateAtomsMsg
FTNOTE : PDBData
full_table : ComputeNonbondedUtil
fullDirectOn : SimParameters
fullElectEnergyIndex : ComputeNonbondedUtil
fullElectEnergyIndex_s : ComputeNonbondedUtil
fullElectFrequency : SimParameters
fullElectVirialIndex : ComputeNonbondedUtil
fullExclCnt : ExclusionSignature
fullExclOffset : ExclSigInfo
fullf : nonbonded
fullf_0 : ComputeNonbondedWorkArrays
fullOffset : ExclusionSignature

- g -

gather_coordinates() : IMDOutput
gather_energies() : IMDOutput
gaussian() : Random
gaussian_vector() : Random
gcom : ComputeGlobalDataMsg
gdef : ComputeGlobalConfigMsg
genclose() : parm
genCompressedPsf : SimParameters
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() : 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
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
gforce : ComputeGlobalResultsMsg
globalForcesOn : SimParameters
GlobalMaster() : GlobalMaster
GlobalMasterEasy() : GlobalMasterEasy
GlobalMasterFreeEnergy() : GlobalMasterFreeEnergy
GlobalMasterIMD() : GlobalMasterIMD
GlobalMasterMisc() : GlobalMasterMisc
GlobalMasterServer() : GlobalMasterServer
GlobalMasterSMD() : GlobalMasterSMD
GlobalMasterTcl() : GlobalMasterTcl
GlobalMasterTMD() : GlobalMasterTMD
globalOn : SimParameters
globHead : UniqueSetRaw< Elem >
goodglist : ComputeNonbondedWorkArrays
gotoUsed() : UniqueSetIter< T >
GPID : HydrogenGroupID
gradU() : ADiheRestraint
grid : PmePencilInitMsgData
gridCalc1() : ComputePmeMgr
gridCalc2() : ComputePmeMgr
gridCalc3() : ComputePmeMgr
gridforceCont : SimParameters
GridforceGrid() : GridforceGrid
gridforceOn : SimParameters
gridforceScale : SimParameters
gridforceVOffset : SimParameters
gridforceVolts : SimParameters
gridsize_a() : PatchMap
gridsize_b() : PatchMap
gridsize_c() : PatchMap
gromacsOn : SimParameters
GromacsTopFile() : GromacsTopFile
group : GroupInitMsg
groupFixed : CompAtom
groupForces() : GlobalMaster
grouplist : ComputeNonbondedWorkArrays
groupplcutoff : nonbonded
groupPressure : Controller
groupPressure_avg : Controller
groupPressure_nbond : Controller
groupPressure_normal : Controller
groupPressure_slow : Controller
groupPressure_tavg : Controller

- h -

haAngleExp : SimParameters
handle : LdbMigrateMsg, computeInfo
has_default : ParseOptions::DataElement
has_evir : PmeUntransMsg
hasData : PmePencil< T >, PmeTransMsg, PmeGridMsg
hash() : Exclusion, ProxyUsageKey, ProxyElem, ImproperElem, TuplePatchElem, DihedralElem, CrosstermElem, BondElem, AngleElem, BOID, TaggedMsg, BroadcastClientElem
hasNewAtoms() : Patch
hasPatchZero : ComputeHomePatches
HB12 : parm
HB6 : parm
head() : ConfigList
HEADER : PDBData
header : StreamMessage
HELIX : PDBData
HET : PDBData
HETATM : PDBData
hgroupCutoff : SimParameters
high : netint
highest : netint
holdComputes() : Sync
HomePatch : Sequencer
homePatch : PatchMgr, PatchMap, ComputeHomePatch
HomePatchElem() : HomePatchElem
homePatchIDList() : PatchMap
homePatchList() : PatchMap
htable : ProxyUsage
HydrogenBonds : SimParameters
hydrogenGroup : Molecule
HydrogenGroupID() : HydrogenGroupID
hydrogenGroupSize : CompAtom
hydrogenList : AtomCstInfo, atom_constants

- i -

i : doublecomplex, Transform, netint, floatcomplex
Iac : parm
Iblo : parm
id : Iterator, CompAtom, BOID, BroadcastClient
Id : InfoRecord
idata : ParseOptions::DataElement
idef : ParseOptions::DataElement
identity() : Tensor, Matrix4
idleTime : processorInfo
IfBox : parm
IfCap : parm
imd : Node
IMDfreq : SimParameters
IMDignore : SimParameters, GlobalMasterIMD
IMDon : SimParameters
IMDOutput() : IMDOutput
IMDport : SimParameters
IMDwait : SimParameters, GlobalMasterIMD
improper_array : Parameters
improper_type : improper
improperCnt : AtomSignature
ImproperElem : ImproperElem, Molecule
improperEnergyIndex : ImproperElem
improperSigIndices : AtomSigInfo
improperSigs : AtomSignature
imsg : PmePencil< T >
IncCurrStep() : ALambdaManager, ALambdaControl
increment() : ProxyUsage
incrSTLoad() : Rebalancer
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
index_a() : PatchMap
index_b() : PatchMap
index_c() : PatchMap
info : listNode, heapRecord
infostream() : infostream
Init() : ALambdaControl
init() : SortableResizeArray< Elem >, Random, BackEnd
initAndSendHomePatch() : WorkDistrib
initdata : PmePencil< T >
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
initialTemp : SimParameters
InitProxyUsage() : Rebalancer
initTmpPatchAtomsList() : PatchMap
inMigration : HomePatch
ins() : ResizeArrayRaw< Elem >
insert() : UniqueSortedArray< Elem >, SortedArray< Elem >, Set, ResizeArray< Elem >, maxHeap, minHeap
insertioncode() : PDBAtom
Instance() : PatchMap, ComputeMap, AtomMap
INT : ParseOptions::DataElement
integer() : Random
integrate() : Sequencer, Controller
Integrate_MCTI() : ALambdaManager, ALambdaControl
Ipatm : parm
Ipres : parm
iptr : ParseOptions::DataElement
Iptres : parm
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_defined : ParseOptions::DataElement
is_group_fixed() : Molecule
is_hydrogen() : Molecule
is_hydrogenGroupParent() : Molecule
is_lp() : Molecule
is_optional : ParseOptions::DataElement
is_oxygen() : Molecule
is_water() : Molecule
IsActive() : ALambdaControl
isAtomBased() : ComputeMap
isAvailableO