Main Page Class Hierarchy Alphabetical List Compound List File List Compound Members File Members

NAMD Compound 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 class documentation for each member:

- _ -

_hasNewAtoms : Patch

- a -

a() : Lattice
A : indexed_vdw_pair, vdw_pair_params, LJTable::TableEntry
A14 : indexed_vdw_pair, vdw_pair_params
a_p() : Lattice
a_r() : Lattice
a_total : nodesort
aaAngleExp : SimParameters
Accumulate() : ALambdaManager, ALambdaControl
add() : Vector, UniqueSortedArray< Elem >, UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ResizeArray< Elem >, MigrateAtomsCombinedMsg
Add() : ARestraintManager, ALambdaManager, AGroup
add14Type() : VDWTable
add_const() : Vector
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
AGroup() : AGroup
aid : ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeGlobalConfigMsg, CollectionMgr::CollectVectorInstance, CollectVectorMsg
ALambdaControl() : ALambdaControl
ALambdaManager() : ALambdaManager
Alg7() : Alg7
AlgNbor() : AlgNbor
algorithm() : Sequencer, Controller
AlgRecBisection() : AlgRecBisection
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
AngleElem : AngleElem, Molecule
angleEnergyIndex : AngleElem
AngleHAt1 : parm
AngleHAt2 : parm
AngleHAt3 : parm
AngleHNum : parm
AngleNum : parm
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_dihedral_index() : Parameters
assign_improper_index() : Parameters
assign_vdw_index() : Parameters
assignNode() : PatchMap
assignNodeToPatch() : WorkDistrib
assignToPatch() : PatchMap
ATOM : PDBData
atom : PDB, MovePatchesMsg
atom1 : Exclusion, improper, dihedral, angle, bond
atom1name : vdw_pair_params, improper_params, dihedral_params, angle_params, bond_params
atom1wild : dihedral_params
atom2 : Exclusion, improper, dihedral, angle, bond
atom2name : vdw_pair_params, improper_params, dihedral_params, angle_params, bond_params
atom2wild : dihedral_params
atom3 : improper, dihedral, angle
atom3name : improper_params, dihedral_params, angle_params
atom3wild : dihedral_params
atom4 : improper, dihedral
atom4name : improper_params, dihedral_params
atom4wild : dihedral_params
atom_type_name() : Parameters
atomcharge() : Molecule
atomFixed : CompAtom
atomid : MoveAtomMsg
atomID : HydrogenGroupID, ImproperElem, DihedralElem, BondElem, AngleElem
atomIDList : ProxyAtomsMsg
atomIndex : ResidueLookupElem
atomMap : Node, ComputeHomeTuples< T, S, P >
AtomMap() : AtomMap
atommass() : Molecule
atomname : atom_name_info, vdw_params
AtomNames : parm
AtomRes : parm
atoms() : PDB
atomsInGroup : HydrogenGroupID
AtomSym : parm
AtomTree : parm
atomtype : atom_name_info
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
avgPositionBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair, TuplePatchElem, PatchElem
avgPositionBoxClosed() : Patch
avgPositionComputeList : Patch
avgPositionList : ProxyAllMsg, ProxyDataMsg
avgPositionPtr : Patch
awaitBOCCheckIn() : Node
awaken() : Sequencer, Controller, BroadcastClient, BackEnd
awakenSequencers() : LdbCoordinator

- b -

b() : Lattice
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
barrier() : LdbCoordinator, BackEnd
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
binaryRestart : SimParameters
block1 : PmeGrid
block2 : PmeGrid
BOCCheckIn() : Node
BOID() : BOID
bond_array : Parameters
bond_type : bond
BondAt1 : parm
BondAt2 : parm
BondElem : BondElem, Molecule
bondEnergyIndex : BondElem
BondHAt1 : parm
BondHAt2 : parm
BondHNum : parm
BondNum : parm
BOOL : ParseOptions::DataElement
Boundary : parm
Box : parm
Box< Owner, Data > : OwnerBox< Owner, Data >
boxClosed() : ProxyPatch, Patch, HomePatch
boxesOpen : Patch
broadcast : Sequencer, Controller
BroadcastClient() : BroadcastClient
broadcastClient : BroadcastClientElem
BroadcastClientElem() : BroadcastClientElem
BroadcastMgr : BroadcastMgr, BroadcastMsg
broadcastMgr : BOCgroup
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_fep_flags() : Molecule
build_fixed_atoms() : Molecule
build_langevin_params() : Molecule
build_movdrag_params() : Molecule
build_rotdrag_params() : Molecule
buildProxySpanningTree() : ProxyMgr
buildSpanningTree() : HomePatch

- c -

c() : Lattice
c0 : ComputeNonbondedUtil
c1 : ComputeNonbondedUtil
c3 : ComputeNonbondedUtil
c5 : ComputeNonbondedUtil
c6 : ComputeNonbondedUtil
c7 : ComputeNonbondedUtil
c8 : ComputeNonbondedUtil
c_p() : Lattice
c_r() : Lattice
c_total : nodesort
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_les() : 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_les() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect_fep() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect_les() : ComputeNonbondedUtil
calc_pair_fullelect() : ComputeNonbondedUtil
calc_pair_fullelect_les() : ComputeNonbondedUtil
calc_pair_les() : ComputeNonbondedUtil
calc_pair_merge_fullelect() : ComputeNonbondedUtil
calc_pair_merge_fullelect_les() : ComputeNonbondedUtil
calc_pair_slow_fullelect() : ComputeNonbondedUtil
calc_pair_slow_fullelect_les() : 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_les() : 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_les() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect_fep() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect_les() : ComputeNonbondedUtil
calc_self_fullelect() : ComputeNonbondedUtil
calc_self_fullelect_les() : ComputeNonbondedUtil
calc_self_les() : ComputeNonbondedUtil
calc_self_merge_fullelect() : ComputeNonbondedUtil
calc_self_merge_fullelect_les() : ComputeNonbondedUtil
calc_self_slow_fullelect() : ComputeNonbondedUtil
calc_self_slow_fullelect_les() : ComputeNonbondedUtil
calcAngularMomentum() : HomePatch
calcFullPair : ComputeNonbondedUtil
calcFullPairEnergy : ComputeNonbondedUtil
calcFullSelf : ComputeNonbondedUtil
calcFullSelfEnergy : ComputeNonbondedUtil
calcKineticEnergy() : HomePatch
calcMergePair : ComputeNonbondedUtil
calcMergePairEnergy : ComputeNonbondedUtil
calcMergeSelf : ComputeNonbondedUtil
calcMergeSelfEnergy : ComputeNonbondedUtil
calcMomentum() : HomePatch
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
chain() : PDBAtom
changedAtoms() : GlobalMaster
changedForces() : GlobalMaster
changedGroups() : GlobalMaster
charge : atom_constants, CompAtom
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() : UniqueSetRaw< Elem >, EntryGlob< Elem >, Entry< Elem >, UniqueSet< Elem >
Clear() : ALambdaManager, AGroup
clearChain() : EntryGlob< Elem >, Entry< Elem >
clearChanged() : GlobalMaster
clearMap() : AtomMap
clientsock : 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
collectionMgr : BOCgroup
CollectionMgr() : CollectionMgr
CollectVectorInstance() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
COLUMNS : PDBData
commOnly : SimParameters, ComputeNonbondedUtil
comMove : SimParameters
Communicate() : Communicate
compareChecksums() : Controller
CompAtom() : CompAtom
COMPND : PDBData
compute : ComputeMap, LocalWorkMsg, ComputeMap::ComputeData
Compute() : Compute
compute_energy() : PmeKSpace
compute_forces() : PmeRealSpace
ComputeAngles() : ComputeAngles
computeArray : LdbCoordinator
computeAverage() : Rebalancer
ComputeBonds() : ComputeBonds
computeChecksum : Controller
ComputeConsForce() : ComputeConsForce
ComputeConsTorque() : ComputeConsTorque
ComputeCylindricalBC() : ComputeCylindricalBC
ComputeData() : ComputeMap::ComputeData
ComputeDihedrals() : ComputeDihedrals
ComputeDPMEDataMsg() : ComputeDPMEDataMsg
ComputeDPMEResultsMsg() : ComputeDPMEResultsMsg
ComputeEField() : ComputeEField
ComputeExt() : ComputeExt
computeExtMgr : BOCgroup
ComputeExtMgr() : ComputeExtMgr
computeForce() : ImproperElem, DihedralElem, BondElem, AngleElem
ComputeFullDirect() : ComputeFullDirect
ComputeGlobal() : ComputeGlobal
ComputeGlobalConfigMsg() : ComputeGlobalConfigMsg
ComputeGlobalDataMsg() : ComputeGlobalDataMsg
ComputeGlobalResultsMsg() : ComputeGlobalResultsMsg
ComputeHomePatch() : ComputeHomePatch
ComputeHomePatches() : ComputeHomePatches
ComputeHomeTuples() : ComputeHomeTuples< T, S, P >
ComputeImpropers() : ComputeImpropers
computeLoad : processorInfo
computeMap : Node, LdbCoordinator
ComputeMap() : ComputeMap
computeMapData : MapDistribMsg
computeMax() : Rebalancer
ComputeMgr : ComputeMgr, ComputeMap
computeMgr : BOCgroup
ComputeNonbondedPair() : ComputeNonbondedPair
ComputeNonbondedSelf() : ComputeNonbondedSelf
ComputeNonbondedUtil() : ComputeNonbondedUtil
ComputePatch() : ComputePatch
ComputePatchPair() : ComputePatchPair
ComputePme : ComputePme, ComputePmeMgr
computePmeMgr : BOCgroup
ComputePmeMgr() : ComputePmeMgr
ComputeRestraints() : ComputeRestraints
computes : Rebalancer
ComputeSelfAngles() : ComputeSelfAngles
ComputeSelfBonds() : ComputeSelfBonds
ComputeSelfDihedrals() : ComputeSelfDihedrals
ComputeSelfImpropers() : ComputeSelfImpropers
ComputeSelfTuples() : ComputeSelfTuples< T, S, P >
computeSet : processorInfo
computesHeap : Rebalancer
ComputeSphericalBC() : ComputeSphericalBC
CONECT : PDBData
config : GlobalMasterEasy
configFileInit() : NamdState
configList : Node
ConfigList() : ConfigList
configListInit() : NamdState
ConfigListNode() : ConfigList::ConfigListNode
connect() : IMDOutput
consForce : Molecule
consForceIndexes : Molecule
consForceOn : 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
copyResults() : ComputePme
corr_table : ComputeNonbondedUtil
counter : TaggedMsg
create() : Lattice
createAtomLists() : WorkDistrib
createComputes() : ComputeMgr
createHomePatch() : PatchMgr
createHomePatches() : WorkDistrib
createLoadBalancer() : LdbCoordinator
createProxies() : ProxyMgr
createProxy() : ProxyMgr
cross() : Vector, AVector
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 -

daCutoffDist : SimParameters
daOffDist : SimParameters
daOnDist : SimParameters
data : ReductionSetData, ReductionSubmitMsg, PAL, StreamMessage, ConfigList::ConfigListNode, StringList, 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
deAssign() : Rebalancer
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
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_type : dihedral
DihedralElem : DihedralElem, Molecule
dihedralEnergyIndex : DihedralElem
dihedralOn : SimParameters
DihHAt1 : parm
DihHAt2 : parm
DihHAt3 : parm
DihHAt4 : parm
DihHNum : parm
DihNum : parm
dim2 : PmeGrid
dim3 : PmeGrid
disconnect() : IMDOutput
disposePositions() : CollectionMaster
disposeVelocities() : CollectionMaster
Dist() : AVector
distance : bond_params
distAttExp : SimParameters
distRepExp : SimParameters
distribute() : MigrateAtomsCombinedMsg
DistributeForce() : ARestraint
distributeHomePatches() : WorkDistrib
DistSqr() : AVector
div() : Vector
doAtomMigration() : HomePatch
doEnergy : Flags
doForce() : ComputeSphericalBC, ComputeRestraints, ComputePatchPair, ComputePatch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomePatch, 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
dot() : Vector, AVector
downstream() : PatchMap
downstream2() : PatchMap
downstreamNeighbors() : PatchMap
doWork() : ComputeSelfTuples< T, S, P >, ComputePme, ComputePatchPair, ComputePatch, ComputeHomeTuples< T, S, P >, ComputeHomePatch, ComputeGlobal, ComputeFullDirect, ComputeExt, Compute
dt : SimParameters
dudx : minpoint
dummy : SimParameters

- e -

Eangle : IMDEnergies
earlyExit() : Node
EarlyExit() : ARestraint
easy_calc() : GlobalMasterMisc, GlobalMasterEasy
easy_init() : GlobalMasterMisc, GlobalMasterEasy
Ebond : IMDEnergies
Edihe : IMDEnergies
Eelec : IMDEnergies
eField : SimParameters
eFieldOn : SimParameters
Eimpr : IMDEnergies
eleccutoff : SimParameters
elecswitchDist : SimParameters
electEnergy : Controller
electEnergy_f : Controller
electEnergyIndex : ComputeNonbondedUtil
electEnergyIndex_s : ComputeNonbondedUtil
electEnergySlow : Controller
electEnergySlow_f : Controller
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
enqueueDihedrals() : WorkDistrib
enqueueImpropers() : WorkDistrib
enqueuePme() : WorkDistrib
enqueuePositions() : CollectionMaster
enqueueSelfA() : WorkDistrib
enqueueSelfB() : WorkDistrib
enqueueVelocities() : 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 : PmeUntransMsg, PmeGridMsg
ewaldcof : ComputeNonbondedUtil
ExclAt : parm
exclChecksumIndex : ComputeNonbondedUtil
exclude : SimParameters
excludeFromPressure : SimParameters
Exclusion() : Exclusion
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

- f -

f : Results, Patch, TuplePatchElem, PatchElem, ComputeGlobalResultsMsg
fast_table : ComputeNonbondedUtil
fdata : ParseOptions::DataElement, CollectionMgr::CollectVectorInstance, CollectVectorMsg, CollectionMaster::CollectVectorInstance
fdef : ParseOptions::DataElement
fepEquilSteps : SimParameters
fepFile : Controller
FepNo : Controller
fepOn : SimParameters, ComputeNonbondedUtil
fepOutFile : SimParameters
fepOutFreq : SimParameters
fepSum : Controller
ff : nonbonded
FFTWEstimate : SimParameters
FFTWUseWisdom : SimParameters
FFTWWisdomFile : SimParameters
FFTWWisdomString : SimParameters
fgrid : PmeGridMsg
field() : PDBData
FIELDS : PDBData
file : FileStack
filename : FileStack
fill_charges() : PmeRealSpace
find() : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, Set, ConfigList
find_extremes() : PDB
firstLdbStep : SimParameters, LdbCoordinator
firstResid : ResidueLookupElem
firstTime : GlobalMasterMisc
firstTimestep : SimParameters
firstwat() : parm
fixedAtomsForces : SimParameters
fixedAtomsOn : SimParameters, ComputeNonbondedUtil
fixedPosition : FullAtom
flags : ProxyAllMsg, ProxyDataMsg, Patch, ExclusionCheck
FLOAT : ParseOptions::DataElement
FloatVector() : FloatVector
FMAFFTBlock : SimParameters
FMAFFTOn : SimParameters
FMALevels : SimParameters
FMAMp : SimParameters
FMAOn : SimParameters
fmaTheta : SimParameters
footnote() : PDBAtom
force : ExtForce, vmdforce, ExtForceMsg
forceBox : Patch, ProxyListElem, ComputePatchPair, TuplePatchElem, PatchElem
forceBoxClosed() : Patch
forceComputeList : Patch
forceconstant : angle_params, bond_params
forcedAtoms() : GlobalMaster
forceList : ProxyCombinedResultMsg, ProxyResultMsg
forces : ComputeDPMEResultsMsg
FORMUL : PDBData
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
fullf : nonbonded

- g -

gather_coordinates() : IMDOutput
gather_energies() : IMDOutput
gaussian() : Random
gaussian_vector() : Random
gcom : ComputeGlobalDataMsg
gdef : ComputeGlobalConfigMsg
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_cluster() : Molecule
get_clusterSize() : Molecule
get_cons_params() : Molecule
get_constorque_params() : 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_groupSize() : Molecule
get_improper() : Molecule
get_improper_multiplicity() : Parameters
get_improper_params() : Parameters
get_impropers_for_atom() : Molecule
get_mother_atom() : Molecule
get_movdrag_params() : Molecule
get_num_vdw_params() : Parameters
get_residue_size() : Molecule
get_rotdrag_params() : Molecule
get_vdw_pair_params() : Parameters
get_vdw_params() : Parameters
get_vmd_forces() : GlobalMasterIMD
GetAccumulation() : ALambdaManager, ALambdaControl
getAngle() : GromacsTopFile, GenericMol
GetAngle() : ARestraint
getAngleParams() : GromacsTopFile
GetAngleTarget() : AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AnAngleRestraint
getAtom() : GromacsTopFile, GenericMol
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
getBond() : GromacsTopFile, GenericMol
getBondParams() : GromacsTopFile
GetBound() : ABoundAngleRestraint, ABoundDistRestraint, ABoundPosRestraint
getbuf() : BroadcastMgr
getCharge() : GenericAtom
getData() : ReductionSet
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
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
getMessage() : Communicate
getMol() : MolInst
getMoleculePointers() : ImproperElem, DihedralElem, 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
getNumComputeGlobals() : WorkDistrib
getNumComputes() : Patch
getNumDihedralParams() : GromacsTopFile
getNumDihedrals() : GromacsTopFile, MolInst, GenericMol
GetNumGroups() : ARestraint
GetNumInGroup() : AGroup
GetNumObjects() : ALambdaManager
getNumPatches() : Compute
getNumRes() : MolInst, GenericMol
GetNumRestraints() : ARestraintManager
GetNumSteps() : ALambdaControl
GetNumStepsSoFar() : ALambdaManager, ALambdaControl
GetPaddedTaskStr() : ALambdaControl
getParameterPointers() : ImproperElem, DihedralElem, BondElem, AngleElem
getParams() : VDWTable, DihedralTable, AngleTable, BondTable, AtomTable
getPatchID() : Patch
getPosition() : GlobalMasterFreeEnergy, GlobalMasterEasy
GetPosTarget() : AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, APosRestraint
GetRefAngle() : AFixedDiheRestraint, ABoundAngleRestraint, AFixedAngleRestraint
GetRefDist() : ABoundDistRestraint, AFixedDistRestraint, ABoundPosRestraint
GetRefPos() : ABoundPosRestraint, AFixedPosRestraint
getResNum() : GenericAtom
getResType() : GenericAtom
getScript() : Node
getSpanningTreeChild() : 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
GetTotalNumSteps() : ALambdaManager
getType() : AtomTable, GenericAtom, GenericDihedral, GenericAngle, GenericBond
getTypeNum() : GenericAtom
GetUpperAngle() : ABoundDiheRestraint
getVDWParams() : GromacsTopFile
gforce : ComputeGlobalResultsMsg
globalForcesOn : SimParameters
GlobalMaster() : GlobalMaster
GlobalMasterEasy() : GlobalMasterEasy
GlobalMasterFreeEnergy() : GlobalMasterFreeEnergy
GlobalMasterIMD() : GlobalMasterIMD
GlobalMasterMisc() : GlobalMasterMisc
GlobalMasterServer() : GlobalMasterServer
GlobalMasterSMD() : GlobalMasterSMD
GlobalMasterTcl() : GlobalMasterTcl
globalOn : SimParameters
globHead : UniqueSetRaw< Elem >
gotoUsed() : UniqueSetIter< T >
GPID : HydrogenGroupID
gradU() : ADiheRestraint
gridCalc1() : ComputePmeMgr
gridCalc2() : ComputePmeMgr
gridCalc3() : ComputePmeMgr
gridsize_a() : PatchMap
gridsize_b() : PatchMap
gridsize_c() : PatchMap
gromacsOn : SimParameters
GromacsTopFile() : GromacsTopFile
group : GroupInitMsg
groupcutoff2 : ComputeNonbondedUtil
groupFixed : CompAtom
groupForces() : GlobalMaster
groupPressure : Controller
groupPressure_avg : Controller
groupPressure_nbond : Controller
groupPressure_normal : Controller
groupPressure_slow : Controller

- h -

haAngleExp : SimParameters
handle : LdbMigrateMsg, computeInfo
has_default : ParseOptions::DataElement
hash() : Exclusion, ProxyElem, ImproperElem, TuplePatchElem, DihedralElem, BondElem, AngleElem, BOID, TaggedMsg, BroadcastClientElem
hasNewAtoms() : Patch
HB12 : parm
HB6 : parm
head() : ConfigList
HEADER : PDBData
header : StreamMessage
HELIX : PDBData
HET : PDBData
HETATM : PDBData
hgroupCutoff : SimParameters
holdComputes() : Sync
homePatch : PatchMgr, PatchMap, ComputeHomePatch
HomePatch : Sequencer
HomePatchElem() : HomePatchElem
homePatchIDList() : PatchMap
homePatchList() : PatchMap
HydrogenBonds : SimParameters
hydrogenGroup : Molecule
HydrogenGroupID() : HydrogenGroupID
hydrogenGroupSize : CompAtom
hydrogenList : atom_constants

- i -

i : doublecomplex, Transform
Iac : parm
Iblo : parm
id : Iterator, CompAtom, BOID, BroadcastClient
Id : InfoRecord
idata : ParseOptions::DataElement
idef : ParseOptions::DataElement
identity() : Tensor
IfBox : parm
IfCap : parm
imd : Node
IMDfreq : SimParameters
IMDignore : SimParameters
IMDon : SimParameters
IMDOutput() : IMDOutput
IMDport : SimParameters
IMDwait : SimParameters, GlobalMasterIMD
improper_array : Parameters
improper_type : improper
ImproperElem : ImproperElem, Molecule
improperEnergyIndex : ImproperElem
IncCurrStep() : ALambdaManager, ALambdaControl
ind1 : indexed_vdw_pair
ind2 : indexed_vdw_pair
index : SortedArray< Elem >, Lattice, ParseOptions::DataElement, vdw_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() : SortableResizeArray< Elem >, Random, BackEnd
Init() : ALambdaControl
initialize() : PatchMap, LdbCoordinator, ComputeSelfTuples< T, S, P >, ComputePmeMgr, ComputePatchPair, ComputePatch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >, ComputeHomePatches, ComputeHomePatch, Compute
initialize_config_data() : SimParameters
initialTemp : SimParameters
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_movdragged() : Molecule
is_atom_rotdragged() : Molecule
is_defined : ParseOptions::DataElement
is_group_fixed() : Molecule
is_hydrogen() : Molecule
is_hydrogenGroupParent() : Molecule
is_optional : ParseOptions::DataElement
is_oxygen() : Molecule
is_water() : Molecule
IsActive() : ALambdaControl
isAtomBased() : ComputeMap
isAvailableOn() : Rebalancer
isBasePatch : ComputeHomeTuples< T, S, P >
IsEndOf_MCTI() : ALambdaManager, ALambdaControl
IsEndOf_MCTI_Step() : ALambdaManager, ALambdaControl
IsFirstStep() : ALambdaManager, ALambdaControl
IsForcing() : AForcingDiheRestraint, AForcingAngleRestraint, AForcingDistRestraint, AForcingPosRestraint, ARestraint
isGP : HydrogenGroupID
isOpen() : PositionOwnerBox< Owner >, OwnerBox< Owner, Data >
isPatchBased() : ComputeMap
isPmeProcessor() : ComputePmeMgr
isSorted : SortedArray< Elem >
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 >
ititl : parm

- j -

j : Transform
JRNL : PDBData

- k -

k : NonbondedExclValue, four_body_consts, AngleValue, BondValue, Transform
K1 : PmeGrid
K2 : PmeGrid
K3 : PmeGrid
k_ub : AngleValue, angle_params
kineticEnergy : Controller
kineticEnergyCentered : Controller

- l -

lambda : SimParameters, ComputeNonbondedUtil
lambda2 : SimParameters, ComputeNonbondedUtil
lambda_table : ComputeNonbondedUtil
langevin_force_val() : Molecule
langevin_param() : Molecule
langevinDamping : SimParameters
langevinHydrogen : SimParameters
langevinOn : SimParameters
langevinPiston() : Sequencer
langevinPiston1() : Controller
langevinPiston2() : Controller
langevinPiston_strainRate : Controller
langevinPistonDecay : SimParameters
langevinPistonOn : SimParameters
langevinPistonPeriod : SimParameters
langevinPistonTarget : SimParameters
langevinPistonTemp : SimParameters
langevinTemp : SimParameters
langevinVelocities() : Sequencer
langevinVelocitiesBBK1() : Sequencer
langevinVelocitiesBBK2() : Sequencer
lastResid : ResidueLookupElem
latqueue : CollectionMaster::CollectVectorSequence
Lattice() : Lattice
lattice : SimParameters, Flags, Patch, PmeTransMsg, PmeGridMsg, ExtCoordMsg, CollectionMaster::CollectVectorInstance
ldBarrierHandle : LdbCoordinator
ldbBackgroundScaling : SimParameters
LdbCoordinator() : LdbCoordinator
ldbCoordinator : Node, BOCgroup
ldbCycleNum : LdbCoordinator
ldbHomeBackgroundScaling : SimParameters
ldbPeriod : SimParameters
ldbPMEBackgroundScaling : SimParameters
ldbStatsFP : LdbCoordinator
ldbSteps : Sequencer, Controller
ldbStrategy : SimParameters
ldbUnloadPME : SimParameters
ldbUnloadRank : SimParameters
ldbUnloadSMP : SimParameters
ldbUnloadZero : SimParameters
left : indexed_vdw_pair, vdw_params, angle_params, bond_params
len : StreamMessage, PmeGridMsg
length : Vector, IMDheader
length2() : Vector
lesFactor : SimParameters, ComputeNonbondedUtil
lesOn : SimParameters, ComputeNonbondedUtil
lesScaling : ComputeNonbondedUtil
linenumber : FileStack
List() : AGroup
ljEnergy : Controller
ljEnergy_f : Controller
LJTable() : LJTable
ljTable : ComputeNonbondedUtil
load : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ScriptTcl, InfoRecord
loadTuples() : ComputeHomeTuples< T, S, P >
loadTuplesForAtom() : ImproperElem, DihedralElem, BondElem, AngleElem
localID() : AtomMap
localIndex : ImproperElem, DihedralElem, BondElem, AngleElem
LOCALMOD() : infostream, datastream
localWorkMsg : Compute
longSplitting : SimParameters
lookup() : ResidueLookupElem

- m -

m14 : nonbonded
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
main() : main
makeHeaps() : Rebalancer
many_allowed : ParseOptions::DataElement
mapComputes() : WorkDistrib
margin : SimParameters
marginViolations : HomePatch, Controller
mass : atom_constants, FullAtom
Masses : parm
MASTER : PDBData
master : SlaveInitMsg
MathArray() : MathArray< Elem, Size >
max : ExclusionCheck
max_a() : PatchMap
max_b() : PatchMap
max_c() : PatchMap
maxForceMerged : Flags
maxForceUsed : Flags
maxHeap() : maxHeap
maximumMove : Sequencer, SimParameters
maxNumForces : Results
MaxOneAway : PatchMap
MaxOneOrTwoAway : PatchMap
maxPairPart : SimParameters
maxPart : nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair
maxSelfPart : SimParameters
MaxTwoAway : PatchMap
Mbona : parm
measure() : ScriptTcl
memusage : memusageinit
memusageinit() : memusageinit
messageBOCCheckIn() : Node
messageEnqueueWork() : WorkDistrib
messageRun() : Node
messageStartUp() : Node
Migrate() : LdbCoordinator
MigrateAtomsCombinedMsg() : MigrateAtomsCombinedMsg
MigrateAtomsMsg() : MigrateAtomsMsg
migrationList : MigrateAtomsCombinedMsg, MigrateAtomsMsg
migrations : LdbCoordinator
min : ExclusionCheck
min_a() : PatchMap
min_b() : PatchMap
min_c() : PatchMap
min_energy : Controller
min_f_dot_f : Controller
min_f_dot_v : Controller
min_huge_count : Controller
min_v_dot_v : Controller
minBabyStep : SimParameters
minHeap() : minHeap
minimizationQuenchVelocity() : Sequencer
minimize() : Sequencer, Controller
minimizeCGOn : SimParameters
minimizeCoefficient : ControllerBroadcasts
minimizeOn : SimParameters
minLineGoal : SimParameters
minPart : nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair
minpoint() : minpoint
minTinyStep : SimParameters
miscForcesOn : SimParameters
MIStream() : MIStream
mList : MigrationInfo
MODEL : PDBData
modified : Exclusion
modifyAppliedForces() : GlobalMaster
modifyForcedAtoms() : GlobalMaster
modifyGroupForces() : GlobalMaster
modifyRequestedAtoms() : GlobalMaster
modifyRequestedGroups() : GlobalMaster
mol : ComputeNonbondedUtil
Molecule() : Molecule
molecule : Node
MolInst() : MolInst
mollyAverage() : HomePatch
mollyIter : SimParameters
mollyMollify() : HomePatch
mollyOn : SimParameters
mollyTol : SimParameters
MOStream() : MOStream
movDragFile : SimParameters
movDragGlobVel : SimParameters
movDragOn : SimParameters
movDragVelFile : SimParameters
moveAtom() : PatchMgr
MovePatch() : MovePatch
movePatch() : PatchMgr
MovePatchesMsg() : MovePatchesMsg
moveto : parm, MoveAtomMsg
moveToNode : ComputeMap::ComputeData
movingConstraintsOn : SimParameters
movingConsVel : SimParameters
Mphia : parm
msg : TaggedMsg
msgbuf : HomePatch
msgSize : TaggedMsg
Mtheta : parm
MTRIX : PDBData
MTSAlgorithm : SimParameters
mult() : Vector
multiplicity : ImproperValue, DihedralValue, improper_params, dihedral_params
multirefine() : Rebalancer
myHandle : LdbCoordinator
myid() : Node
myOMid : LdbCoordinator
myRemove() : Set
mySegid : ResidueLookupElem

- n -

N : SimParameters
n : four_body_consts
Namd : NamdState
NamdCentLB() : NamdCentLB
NamdNborLB() : NamdNborLB
NamdState() : NamdState
name : PDBAtom, ParseOptions::DataElement, ConfigList::ConfigListNode
Nat3 : parm
Natcap : parm
Natom : parm
Natyp : parm
Nbona : parm
nbond : Results
nbondFreq : Controller
Nbonh : parm
nComputesExpected : LdbCoordinator
nComputesReported : LdbCoordinator
nearest() : Lattice
net_dE : Controller
newaid : ComputeGlobalResultsMsg
newCid() : PatchMap
newgdef : ComputeGlobalResultsMsg
newInputStream() : Communicate
newMinimizeDirection() : Sequencer
newMinimizePosition() : Sequencer
newNode() : ComputeMap
newNodes : ComputeMapChangeMsg
newOutputStream() : Communicate
newPid() : ComputeMap
next : EntryGlob< Elem >, Entry< Elem >, Set, maxHeap, minHeap, Iterator, listNode, ReductionSetData, PAL, vdw_pair_params, improper_params, dihedral_params, StreamMessage, ResidueLookupElem, heapIterator, ConfigList::ConfigListNode, StringList, FileStack
nextSequenceNumber : ReductionSet
Nhparm : parm
nLdbSteps : LdbCoordinator
nLocalComputes : LdbCoordinator
nLocalPatches : LdbCoordinator
Nmxrs : parm
Nnb : parm
node : PatchMap, ComputeMap, nodesort, ProxySpanningTreeMsg, ProxyResultMsg, UnregisterProxyMsg, RegisterProxyMsg, ProxyListElem, ComputeMap::ComputeData, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, Compute, BOCgroup
Node : Node, NamdState
nodeDone() : LdbCoordinator
nodeID : MovePatch
nodes : ProxyCombinedResultMsg
nodesDone : LdbCoordinator
nodesort() : nodesort
nonbondedFrequency : SimParameters
nonbondedGroupIsAtom : CompAtom
nonbondedScaling : SimParameters
normal : Results
notfree() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
noWork() : ComputeNonbondedPair, Compute
Nparm : parm
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
num() : ParseOptions
num_atoms() : PDB
numAcceptors : Molecule
Numang : parm
numAngles : Molecule
numAtomBased() : ComputeMap
numAtoms : Patch, Molecule, MigrateAtomsCombinedMsg, patchInfo, ComputePatchPair, ComputePatch, nonbonded, ComputeHomePatch, ExtCoordMsg
numAtomsPair : SimParameters
numAtomsPair2 : SimParameters
numAtomsSelf : SimParameters
numAvailable() : Rebalancer
numaway_a() : PatchMap
numaway_b() : PatchMap
numaway_c() : PatchMap
Numbnd : parm
numBonds : Molecule
numCalcAngles : Molecule
numCalcBonds : Molecule
numCalcDihedrals : Molecule
numCalcExclusions : Molecule
numCalcImpropers : Molecule
numCids() : PatchMap
numComputes : ComputeMap, Rebalancer
numConsForce : Molecule
numConsTorque : Molecule
numConstraints : Molecule
numDegFreedom : Controller
numDihedrals : Molecule
numDonors : Molecule
numElements() : Set, maxHeap, minHeap
numExclusions : Molecule
numExPressureAtoms : Molecule
numFepFinal : Molecule
numFepInitial : Molecule
numFixedAtoms : Molecule
numFixedGroups : Molecule
numFixedRigidBonds : Molecule
numHomePatches() : PatchMap
numHydrogenGroups : Molecule
numImpropers : Molecule
numMlBuf : HomePatch
numMovDrag : Molecule
numMultipleDihedrals : Molecule
numMultipleImpropers : Molecule
numNewNodes : ComputeMapChangeMsg
numNodes() : Node
numNodesWithPatches() : PatchMap
numParticles : ComputeDPMEResultsMsg, ComputeDPMEDataMsg
numPartitions : ComputeMap, ComputeMap::ComputeData
numParts : nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair
numPatchBased() : ComputeMap
numPatches : PatchMap, Rebalancer
numPatchesAvail() : Rebalancer
numPatchesOnNode() : PatchMap
numPesAvailable : Rebalancer
numPids : ComputeMap, ComputeMap::ComputeData
numPidsAllocated : ComputeMap::ComputeData
numProxies : ProxyMgr, Rebalancer
numProxiesAvail() : Rebalancer
numRigidBonds : Molecule
numRotDrag : Molecule
numTotalExclusions : Molecule
nx : LocalPmeInfo, PmeTransMsg
ny : PmeUntransMsg
ny_after_transpose : LocalPmeInfo

- o -

obj : Entry< Elem >
Object() : Sync, ReductionMgr, ProxyMgr, PatchMgr, PatchMap, Node, LdbCoordinator, ComputeMap, CollectionMgr, CollectionMaster, BroadcastMgr, AtomMap
ObjectArena() : ObjectArena< Type >
objHandles : LdbCoordinator
OBSLTE : PDBData
occupancy() : PDBAtom
off_diagonal : Tensor
okay() : ConfigList
oldProcessor : computeInfo
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
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
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, BondElem, AngleElem
operator<<() : infostream, datastream
operator=() : Vector, UniqueSortedArray< Elem >, UniqueSetRaw< Elem >, Entry< Elem >, UniqueSetIter< T >, UniqueSet< Elem >, Tensor, SortedArray< Elem >, SortableResizeArray< Elem >, ResizeArrayRaw< Elem >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ResizeArray< Elem >, CompAtom, MathArray< Elem, Size >, HomePatchElem, vmdforce, AVector, ALambdaControl, AGroup, Array< Elem, Size >
operator==() : nodesort, Vector, UniqueSetIter< T >, Tensor, Exclusion, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ProxyElem, MovePatch, HydrogenGroupID, HomePatchElem, vmdforce, ImproperElem, TuplePatchElem, PatchElem, DihedralElem, BondElem, AngleElem, BOID, TaggedMsg, BroadcastClientElem
operator[]() : Vector, ResizeArrayRaw< Elem >, ResizeArray< Elem >, AVector, ARestraintManager, ALambdaManager, AGroup, Array< Elem, Size >
optional() : ParseOptions
optionalB() : ParseOptions
order : PmeGrid
origin() : PatchMap, Lattice
originalPosition : GlobalMasterMisc
ORIGX : PDBData
orthogonal() : Lattice
Out() : AVector
outer : Tensor
output : Node
Output() : Output, AVector
outputEnergies : SimParameters
outputExtendedSystem() : Controller
outputFepEnergy() : Controller
outputFilename : SimParameters
outputMomenta : SimParameters
outputPressure : SimParameters
outputTiming : SimParameters
overLoad : Rebalancer
OwnerBox() : OwnerBox< Owner, Data >
OwnerBox< Owner, Data > : Box< Owner, Data >

- p -

P : Rebalancer
p : Patch, nonbonded, ImproperElem, TuplePatchElem, PatchElem, ComputeGlobalDataMsg, DihedralElem, BondElem, AngleElem
p_avg : Patch
p_ij : nonbonded
pack() : ReductionSubmitMsg, ProxySpanningTreeMsg, ProxyCombinedResultMsg, ProxyResultMsg, ProxyAllMsg, ProxyDataMsg, ProxyAtomsMsg, MovePatchesMsg, PatchMap, MigrateAtomsCombinedMsg, MigrateAtomsMsg, ComputeMap, ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeGlobalConfigMsg, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, DataStreamMsg, CollectVectorMsg
packSize() : PatchMap, ComputeMap
pairElectForceIndex : ComputeNonbondedUtil
pairInteractionGroup1 : SimParameters
pairInteractionGroup2 : SimParameters
pairInteractionOn : SimParameters, ComputeNonbondedUtil
pairInteractionSelf : SimParameters, ComputeNonbondedUtil
pairlistDist : SimParameters
pairVDWForceIndex : ComputeNonbondedUtil
param : ScriptParamMsg
parameters : Node
Parameters() : Parameters
paraTypeCharmmOn : SimParameters
paraTypeXplorOn : SimParameters
parent : ParseOptions::DataElement
parent_ptr : ParseOptions::DataElement
parm() : parm
parse() : PDBAtom
ParseOptions() : ParseOptions
particles : ComputeDPMEDataMsg
partition : RecBisection, ComputeMap, CompAtom, ComputeMap::ComputeData
partner : atom_constants
Patch() : Patch
patch : PatchMap, Sequencer, ProxySpanningTreeMsg, ProxyCombinedResultMsg, ProxyResultMsg, ProxyAllMsg, ProxyDataMsg, ProxyAtomsMsg, UnregisterProxyMsg, RegisterProxyMsg, HomePatchElem, ComputePatchPair, ComputePatch, ComputeHomePatch
patch1 : computeInfo
patch2 : computeInfo
patchArray : LdbCoordinator
patchBased : ComputeMap::ComputeData
patchDimension : SimParameters
PatchElem() : PatchElem
patches : Rebalancer
patchHandles : LdbCoordinator
patchID : ProxyElem, Patch, ComputePatchPair, TuplePatchElem, PatchElem
patchList : ComputeHomePatches
patchLoad() : LdbCoordinator
PatchMap : PatchMap, PatchMgr
patchMap : Node, LdbCoordinator, ComputeHomeTuples< T, S, P >, ComputeHomePatches, Compute
patchMapData : MapDistribMsg
patchMapInit() : WorkDistrib
PatchMgr : PatchMgr, HomePatch
patchMgr : BOCgroup
patchNAtoms : LdbCoordinator
PatchReady() : Sync
patchReady() : Compute
PatchRec() : ComputeMap::PatchRec
patchSet : processorInfo
PDB() : PDB
pdb : Node
PDBAtom() : PDBAtom
PDBAtomRecord() : PDBAtomRecord
PDBData() : PDBData
PDBFormatStyle : PDBData
PDBHetatm() : PDBHetatm
PDBNames : PDBData
PDBPossibleAtoms : PDBAtom
PDBType : PDBData
PDBUnknown() : PDBUnknown
PE : StreamMessage
periodic_a() : PatchMap
periodic_b() : PatchMap
periodic_c() : PatchMap
pes : Rebalancer
Phase : parm
pi_ewaldcof : ComputeNonbondedUtil
pid : PatchMap, ComputeMap, MovePatch, MovePatchesMsg, LocalID, HomePatchElem, ComputeMap::PatchRec
pids : ComputeMap::ComputeData
Pk : parm
plMarginCheckOn : SimParameters
PMEBarrier : SimParameters
PMEEwaldCoefficient : SimParameters
PMEGridSizeX : SimParameters
PMEGridSizeY : SimParameters
PMEGridSizeZ : SimParameters
PMEInterpOrder : SimParameters
PmeKSpace() : PmeKSpace
PMEOn : SimParameters
PMEProcessors : SimParameters
PmeRealSpace() : PmeRealSpace
PMETolerance : SimParameters
Pn : parm
popn : parm
position : CompAtom
positionBox : Patch, ComputePatchPair, TuplePatchElem, PatchElem
PositionBox< Owner > : PositionOwnerBox< Owner >
positionBoxClosed() : Patch
positionComputeList : Patch
positionList : ProxyAllMsg, ProxyDataMsg
PositionOwnerBox() : PositionOwnerBox< Owner >
PositionOwnerBox< Owner > : PositionBox< Owner >
positionPtr : Patch
positionRescaleFactor : ControllerBroadcasts
positionsReady() : Patch, HomePatch
preadln() : parm
precisions : CollectionMgr::CollectVectorInstance
pressure : Controller
pressure_avg : Controller
pressure_nbond : Controller
pressure_normal : Controller
pressure_slow : Controller
pressureProfileData : ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >
pressureProfileFreq : SimParameters
pressureProfileMin : SimParameters, ComputeNonbondedUtil, ImproperElem, DihedralElem, BondElem, AngleElem
pressureProfileNonbonded : SimParameters, ComputeNonbondedUtil
pressureProfileOn : SimParameters
pressureProfileReduction : Sequencer, Controller, nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >
pressureProfileSlabs : SimParameters, ComputeNonbondedUtil, ImproperElem, ComputeHomeTuples< T, S, P >, DihedralElem, BondElem, AngleElem
pressureProfileThickness : SimParameters, ComputeNonbondedUtil, ImproperElem, DihedralElem, BondElem, AngleElem
print() : Set, AtomMap
print_angle_params() : Parameters
print_atoms() : Molecule
print_bond_params() : Parameters
print_bonds() : Molecule
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
printPatchMap() : PatchMap
PrintPreInfo() : ARestraintManager
printRequiredProxies() : LdbCoordinator
PrintRestraintInfo() : ARestraintManager
printResults() : Rebalancer
PrintSomeSpaces() : ALambdaManager
printSummary() : Rebalancer
printTiming() : Controller
priority() : Compute
processData() : GlobalMaster
ProcessMigrate() : LdbCoordinator
processor : patchInfo, computeInfo
processorArray : LdbCoordinator
processorInfo() : processorInfo
processors : Rebalancer
procsPerNode : SimParameters
proxies : processorInfo
proxiesOn : patchInfo
ProxyElem() : ProxyElem
ProxyListElem() : ProxyListElem
proxyMgr : BOCgroup
ProxyMgr() : ProxyMgr
ProxyPatch() : ProxyPatch
proxyPatch : ProxyElem
proxyUsage : processorInfo
publish() : SimpleBroadcastObject< T >
put() : MOStream

- q -

qgrid : PmeUntransMsg, PmeTransMsg, PmeGridMsg
quenchVelocities() : Sequencer
queue : CollectionMaster::CollectVectorSequence

- r -

r : doublecomplex, TuplePatchElem, PatchElem
r2_delta : ComputeNonbondedUtil
r2_delta_1 : ComputeNonbondedUtil
r2_delta_exp : ComputeNonbondedUtil
r_ub : AngleValue, angle_params
Random() : Random, AVector
random : Sequencer, Controller
randomSeed : SimParameters
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
readExclusions : SimParameters
readparm() : parm
ready() : CollectionMaster::CollectVectorInstance
reassignFreq : SimParameters
reassignHold : SimParameters
reassignIncr : SimParameters
reassignTemp : SimParameters
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
reconfig : ComputeGlobalResultsMsg
recvAtoms() : PatchMgr
recvBroadcast() : BroadcastMgr
recvComputeDPMEData() : ComputeMgr
recvComputeDPMEResults() : ComputeMgr
recvComputeGlobalConfig() : ComputeMgr
recvComputeGlobalData() : ComputeMgr
recvComputeGlobalResults() : ComputeMgr
recvComputeMapChanges() : WorkDistrib
recvConfig() : ComputeGlobal
recvCoord() : ComputeExtMgr
recvData() : GlobalMasterServer
recvEnableEarlyExit() : Node
recvEnableExitScheduler() : Node
recvForce() : ComputeExtMgr
recvGrid() : ComputePmeMgr
RecvMigrate() : LdbCoordinator
recvMigrateAtoms() : PatchMgr
recvMigrateAtomsCombined() : PatchMgr
recvMovePatches() : PatchMgr
recvProxyAll() : ProxyMgr
recvProxyData() : ProxyMgr
recvRegisterProxy() : ProxyMgr
recvResults() : ProxyMgr, ComputeGlobal
recvSpanningTree() : ProxyMgr
recvTrans() : ComputePmeMgr
recvUngrid() : ComputePmeMgr
recvUnregisterProxy() : ProxyMgr
recvUntrans() : ComputePmeMgr
reduce() : ResizeArray< Elem >
reduction : Sequencer, Controller, ComputeSphericalBC, ComputeRestraints, nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >, ComputeEField, ComputeCylindricalBC
reductionChecksumLabel : ImproperElem, DihedralElem, BondElem, AngleElem
reductionDataSize : ComputeNonbondedUtil, ImproperElem, DihedralElem, BondElem, AngleElem
reductionMgr : BOCgroup
ReductionMgr : ReductionMgr, RequireReduction, SubmitReduction
ReductionSet() : ReductionSet
ReductionSetData() : ReductionSetData
reductionSetID : ReductionSet, ReductionSubmitMsg, ReductionRegisterMsg
refCount : UniqueSetRaw< Elem >
refine() : Rebalancer
RefineOnly() : RefineOnly
reg_all_objs : LdbCoordinator
registerAvgPositionPickup() : Patch
registerCompute() : ComputeMap
registerForceDeposit() : Patch
registerIDs() : AtomMap
registerPatch() : PatchMap
registerPatchMgr() : PatchMap
registerPositionPickup() : Patch
registerProxy() : ProxyMgr, HomePatch
rehash() : UniqueSetRaw< Elem >, UniqueSet< Elem >
reinitAtoms() : WorkDistrib
reinitVelocities() : Sequencer
REMARK : PDBData
remoteRegister() : ReductionMgr
remoteSubmit() : ReductionMgr
remoteUnregister() : ReductionMgr
remove() : Set
removeProxies() : ProxyMgr
removeProxy() : ProxyMgr
removeReady() : CollectionMaster::CollectVectorSequence
removeSelf() : Entry< Elem >
removeUnusedProxies() : ProxyMgr
reorder() : Random
rep : ResizeArray< Elem >
replace : ExtForce
replaceForces() : HomePatch
Req : parm
requestAtom() : GlobalMasterFreeEnergy, GlobalMasterEasy
requestedAtoms() : GlobalMaster
requestedGroups() : GlobalMaster
require() : RequireReduction, ParseOptions
requireB() : ParseOptions
requiredProxies() : LdbCoordinator
RequireReduction : ReductionMgr
requireRegistered : ReductionSet
rescale() : Lattice
rescaleFreq : SimParameters
rescaleTemp : SimParameters
rescaleVelocities() : Sequencer, Controller
rescaleVelocities_numTemps : Sequencer, Controller
rescaleVelocities_sumTemps : Controller
resendCoordinates : ComputeGlobalResultsMsg
reset() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
ResidueLookupElem() : ResidueLookupElem
residuename() : PDBAtom
residueseq() : PDBAtom
resize() : ResizeArrayRaw< Elem >, ResizeArray< Elem >, ReductionSetData
ResizeArray() : ResizeArray< Elem >
ResizeArray< Elem > : ResizeArrayRaw< Elem >
ResizeArrayIter() : ResizeArrayIter< T >
ResizeArrayIter< Elem > : ResizeArrayRaw< Elem >, ResizeArray< Elem >
ResizeArrayPrimIter() : ResizeArrayPrimIter< T >
ResizeArrayRaw() : ResizeArrayRaw< Elem >
resname : atom_name_info
ResNames : parm
restartFilename : SimParameters
restartFrequency : SimParameters
restartSave : SimParameters
results : Patch
resume() : LdbCoordinator
resume2() : LdbCoordinator
ResumeFromSync() : LdbCoordinator
resumeReady() : LdbCoordinator
REVDAT : PDBData
reverse_transform() : Lattice
revert() : HomePatch
right : indexed_vdw_pair, vdw_params, angle_params, bond_params
rigid_bond_length() : Molecule
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
run() : Sequencer, ScriptTcl, Node, Controller
runComputeObjects() : Sequencer
runController() : NamdState
runSequencer() : HomePatch

- s -

saveComputeMapChanges() : WorkDistrib
saveForce() : Sequencer, HomePatch
saveMaps() : WorkDistrib
saveMolDataPointers() : Node
saveResults() : ComputeExt
scale : Lattice, ImproperElem, DihedralElem, BondElem, AngleElem
SCALE : PDBData
Scale() : AVector
scale14 : SimParameters, ComputeNonbondedUtil
scaling : ComputeNonbondedUtil
scan() : PDBData
scor_table : ComputeNonbondedUtil
scriptBarrier : Node, ControllerBroadcasts
scriptParam() : Node
scriptSet() : SimParameters
ScriptTcl : ScriptTcl, NamdState, Controller
segmentname() : PDBAtom
select() : ComputeNonbondedUtil
selectConstraintsOn : SimParameters
send() : BroadcastMgr
send_Molecule() : Molecule
send_Parameters() : Parameters
send_SimParameters() : SimParameters
sendAtoms() : PatchMgr
sendComputeDPMEData() : ComputeMgr
sendComputeDPMEResults() : ComputeMgr
sendComputeGlobalConfig() : ComputeMgr
sendComputeGlobalData() : ComputeMgr
sendComputeGlobalResults() : ComputeMgr
sendData() : ComputePme
sendDataStream() : CollectionMgr
sendEnableEarlyExit() : Node
sendEnableExitScheduler() : Node
sendGrid() : ComputePmeMgr
sendMaps() : WorkDistrib
sendMessage() : Communicate
sendMigrationMsg() : PatchMgr
sendMigrationMsgs() : PatchMgr
sendMovePatches() : PatchMgr
sendProxyAll() : ProxyMgr
sendProxyData() : ProxyMgr
sendResults() : ProxyMgr
sendSpanningTree() : ProxyMgr
sendTrans() : ComputePmeMgr
sendTransBarrier() : ComputePmeMgr
sendUngrid() : ComputePmeMgr
sendUntrans() : ComputePmeMgr
seq : CollectionMgr::CollectVectorInstance, CollectVectorMsg, CollectionMaster::CollectVectorInstance
SEQRES : PDBData
sequence : Compute, Flags
sequenceNumber : ReductionSetData, ReductionSubmitMsg
Sequencer : Sequencer, HomePatch
sequencerThreads : LdbCoordinator
serialnumber() : PDBAtom
Set() : Set, AVector
set() : Vector, ParseOptions, Lattice
set_all_positions() : PDB
set_transrate() : IMDOutput
setAlignment() : ObjectArena< Type >
setall() : ResizeArray< Elem >
setBlockSize() : ObjectArena< Type >
SetBound() : ABoundAngleRestraint, ABoundDistRestraint, ABoundPosRestraint, ARestraint
setCompute() : ComputePmeMgr, ComputeExtMgr
SetEqual : AVector
SetGroup() : ARestraint
setGroup() : PatchMgr
SetGroups() : ARestraint
SetIntervalAngle() : ABoundDiheRestraint, ARestraint
SetKf() : ARestraint
SetLambdaKf() : ARestraintManager, ARestraint, ALambdaControl
SetLambdaRef() : ARestraintManager, ARestraint, ALambdaControl
SetLambdas() : ARestraintManager
SetLowerAngle() : ABoundDiheRestraint, ARestraint
setMgr() : ComputePme
setNewNode() : ComputeMap
setNext() : EntryGlob< Elem >, Entry< Elem >
setNode() : ComputeMap, Compute
SetNumAccumSteps() : ALambdaControl
SetNumEquilSteps() : ALambdaControl
setNumPatches() : Compute
SetNumPrintSteps() : ALambdaControl
SetNumRepeats() : ALambdaControl
SetNumSteps() : ALambdaControl
SetRefAngle() : AFixedDiheRestraint, ABoundAngleRestraint, AFixedAngleRestraint, ARestraint
SetRefDist() : ABoundDistRestraint, AFixedDistRestraint, ABoundPosRestraint, ARestraint
SetRefPos() : ABoundPosRestraint, AFixedPosRestraint, ARestraint
setResizeParams() : ResizeArrayRaw< Elem >
setSafeNoDestruction() : UniqueSetRaw< Elem >
setScript() : Node
setSpanningTree() : ProxyPatch
SetStartAngle() : AForcingDiheRestraint, AForcingAngleRestraint, ARestraint
SetStartDist() : AForcingDistRestraint, ARestraint
SetStartPos() : AForcingPosRestraint, ARestraint
SetStartStep() : ALambdaControl
SetStopAngle() : AForcingDiheRestraint, AForcingAngleRestraint, ARestraint
SetStopDist() : AForcingDistRestraint, ARestraint
SetStopPos() : AForcingPosRestraint, ARestraint
SetStopStep() : ALambdaControl
SetTask() : ALambdaControl
SetUpperAngle() : ABoundDiheRestraint, ARestraint
SHEET : PDBData
SIGATM : PDBData
sigma : vdw_val, vdw_params
sigma14 : vdw_val, vdw_params
SIGUIJ : PDBData
simParameters : Node
SimParameters() : SimParameters
simParams : Sequencer, Controller
SimpleBroadcastObject() : SimpleBroadcastObject< T >
SITE : PDBData
size : UniqueSetRaw< Elem >, UniqueSet< Elem >, ResizeArrayRaw< Elem >, ResizeArray< Elem >, DihedralTable, AngleTable, BondTable, AtomTable, ImproperElem, DihedralElem, BondElem, AngleElem
skip() : Random
sldata : ParseOptions::DataElement
slow : Results
slow_table : ComputeNonbondedUtil
slowFreq : Sequencer, Controller
slptr : ParseOptions::DataElement
SMDDir : SimParameters
SMDFile : SimParameters
SMDk : SimParameters
SMDOn : SimParameters
SMDOutputFreq : SimParameters
SMDVel : SimParameters
smooth2_avg : Controller
smooth2_avg2 : Controller
sock : GlobalMasterIMD
Solty : parm
sort() : SortedArray< Elem >, SortableResizeArray< Elem >
SortableResizeArray() : SortableResizeArray< Elem >
SortableResizeArray< Elem > : ResizeArrayRaw< Elem >
SortedArray() : SortedArray< Elem >
sortVal : HydrogenGroupID
SOURCE : PDBData
sourceNode : ReductionSubmitMsg, ReductionRegisterMsg, PmeUntransMsg, PmeTransMsg, PmeGridMsg, ExtCoordMsg
sphericalBCexp1 : SimParameters
sphericalBCexp2 : SimParameters
sphericalBCk1 : SimParameters
sphericalBCk2 : SimParameters
sphericalBCOn : SimParameters
sphericalBCr1 : SimParameters
sphericalBCr2 : SimParameters
sphericalCenter : SimParameters
split() : Random
splitPatch : SimParameters
sprint() : PDBAtom, PDBUnknown, PDBData
sprintcol() : PDBData
SPRSDE : PDBData
sptr : ParseOptions::DataElement
square() : ComputeNonbondedUtil
srcPatchID : MigrateAtomsCombinedMsg, MigrateAtomsMsg
SSBOND : PDBData
start : PmeGridMsg
startUp() : Node
startup() : Node
startWork() : LdbCoordinator
state : Node, Controller
staticMigrateFn() : LdbCoordinator
staticQueryEstLoadFn() : LdbCoordinator
staticReceiveAtSync() : LdbCoordinator
staticResumeFromSync() : LdbCoordinator
staticStatsFn() : LdbCoordinator
status : UniqueSetIter< T >, NamdState, atom_constants
step : Flags
steps() : LdbCoordinator
stepsPerCycle : SimParameters
stepsPerLdbCycle : LdbCoordinator
storeCompute() : ComputeMap
strainRate : SimParameters
strainRate2 : SimParameters
strategy() : Rebalancer
strategyName : Rebalancer
STRING : ParseOptions::DataElement
STRINGLIST : ParseOptions::DataElement
StringList() : StringList
sub() : Vector
submit() : SubmitReduction
submitCollections() : Sequencer
submitData() : CollectionMgr::CollectVectorSequence, CollectionMaster::CollectVectorSequence
submitHalfstep() : Sequencer
submitLoadStats : HomePatch, Flags
submitMinimizeReductions() : Sequencer
submitPositions() : CollectionMgr
submitPressureProfileData() : ComputeNonbondedUtil
SubmitReduction : ReductionMgr
submitReductionData() : ComputeNonbondedUtil, ImproperElem, DihedralElem, BondElem, AngleElem
submitReductions() : Sequencer
submitVelocities() : CollectionMgr
subscribe() : BroadcastMgr
Sum_dU_dLambdas() : ARestraintManager
surfaceTensionTarget : SimParameters
suspend() : Sequencer, BackEnd
suspended : BroadcastClient
suspendFor() : BroadcastClient
switchingActive : SimParameters
switchingDist : SimParameters
switchOn : ComputeNonbondedUtil
switchOn2 : ComputeNonbondedUtil
switchOn_1 : ComputeNonbondedUtil
symmetric() : Tensor
sync : BOCgroup
Sync() : Sync

- t -

T : IMDEnergies
table_alloc : ComputeNonbondedUtil
table_noshort : ComputeNonbondedUtil
table_row() : LJTable
table_short : ComputeNonbondedUtil
table_val() : LJTable
table_val_scale14() : LJTable
tag : StreamMessage, TaggedMsg
TaggedMsg() : TaggedMsg
taggedMsg : BOID
takingLdbData : LdbCoordinator
tclForcesOn : SimParameters
tcoupleCoefficient : ControllerBroadcasts
tCoupleOn : SimParameters
tCoupleTemp : SimParameters
tcoupleVelocities() : Sequencer, Controller
temp_avg : Controller
temperature : Controller
temperaturefactor() : PDBAtom
Tensor() : Tensor
Teq : parm
TER : PDBData
terminate() : Sequencer, Controller
testOn : SimParameters
theLbdb : LdbCoordinator
ThereIsAForcingRestraint() : ARestraintManager
theta0 : AngleValue
thread : BroadcastClient
threadIsWaiting : ReductionSet
Tk : parm
to : LdbMigrateMsg
totalAtoms : SimParameters, MigrateAtomsCombinedMsg
totalComputes : Compute
totalEnergy : Controller
trace : Tensor
trans : ComputePatchPair, ComputeMap::PatchRec
transform : FullAtom
Transform() : Transform
transpose : Tensor
tree : ProxySpanningTreeMsg
TreeJoin : parm
triangular() : Tensor
tstep : IMDEnergies
tupleList : ComputeHomeTuples< T, S, P >
TuplePatchElem() : TuplePatchElem
tuplePatchList : ComputeHomeTuples< T, S, P >
TURN : PDBData
TVECT : PDBData
twoAwayNeighbors() : PatchMap
twoAwayX : SimParameters
twoAwayY : SimParameters
twoAwayZ : SimParameters
TwoTargets() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, ADiheRestraint
type : PDBData, ComputeMap, Compute, ParseOptions::DataElement, IMDheader, ComputeMap::ComputeData

- u -

u : minpoint
uidata : ParseOptions::DataElement
uidef : ParseOptions::DataElement
UINT : ParseOptions::DataElement
uiptr : ParseOptions::DataElement
UNDEF : ParseOptions::DataElement
ungridCalc() : ComputePmeMgr
ungridForces() : ComputePme
uniform() : Random
uniq() : SortableResizeArray< Elem >
UniqueSet() : UniqueSet< Elem >
UniqueSet< Elem > : UniqueSetRaw< Elem >
UniqueSetIter() : UniqueSetIter< T >
UniqueSetIter< Elem > : UniqueSetRaw< Elem >, EntryGlob< Elem >, UniqueSet< Elem >
UniqueSetRaw() : UniqueSetRaw< Elem >
UniqueSetRaw< Elem > : EntryGlob< Elem >, Entry< Elem >
UniqueSortedArray() : UniqueSortedArray< Elem >
unit() : Vector
units : ParseOptions, ParseOptions::DataElement
UNKNOWN : PDBData
unpack() : ReductionSubmitMsg, ProxySpanningTreeMsg, ProxyCombinedResultMsg, ProxyResultMsg, ProxyAllMsg, ProxyDataMsg, ProxyAtomsMsg, MovePatchesMsg, PatchMap, MigrateAtomsCombinedMsg, MigrateAtomsMsg, ComputeMap, ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeGlobalConfigMsg, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, DataStreamMsg, CollectVectorMsg
unregisterAvgPositionPickup() : Patch
unregisterForceDeposit() : Patch
unregisterIDs() : AtomMap
unregisterPatch() : PatchMap
unregisterPositionPickup() : Patch
unregisterProxy() : ProxyMgr, HomePatch
unscale() : Lattice
unsubscribe() : BroadcastMgr
update() : IMDOutput
updateComputes() : ComputeMgr
updateComputes2() : ComputeMgr
updateComputes3() : ComputeMgr
updateComputesReady() : LdbCoordinator
UpdateCOMs() : ARestraintManager, ARestraint
updateLocalComputes() : ComputeMgr
updateLocalComputes2() : ComputeMgr
updateLocalComputes3() : ComputeMgr
updateLocalComputes4() : ComputeMgr
updateLocalComputes5() : ComputeMgr
upstreamNeighbors() : PatchMap
USE_ATOM : PDBAtom
USE_HETATM : PDBAtom
useAntecedent : SimParameters
useAvgPositions : ComputeHomePatches
useConstantArea : SimParameters
useConstantRatio : SimParameters
useController() : NamdState
useDPME : SimParameters
useFlexibleCell : SimParameters
useGroupPressure : SimParameters
useSequencer() : HomePatch
useSettle : SimParameters

- v -

value : ScriptParamMsg, ImproperElem, DihedralElem, BondElem, AngleElem
values : ImproperValue, DihedralValue, improper_params, dihedral_params
vdata : ParseOptions::DataElement
vdef : ParseOptions::DataElement
vdw_array : Parameters
vdw_type : atom_constants
vdwa_table : ComputeNonbondedUtil
vdwb_table : ComputeNonbondedUtil
vdwcutoff : SimParameters
vdwEnergyIndex : ComputeNonbondedUtil
vdwEnergyIndex_s : ComputeNonbondedUtil
vdwscale14 : SimParameters
vdwswitchDist : SimParameters
Vector() : Vector
VECTOR : ParseOptions::DataElement
velDcdFilename : SimParameters
velDcdFrequency : SimParameters
velocity : Output, FullAtom
velocityNeeded() : Output
velocityRescaleFactor : ControllerBroadcasts
virial : ExtForceMsg
virialIndex : ComputeNonbondedUtil, ImproperElem, DihedralElem, BondElem, AngleElem
volume() : Lattice
vptr : ParseOptions::DataElement

- w -

waitForTag : BroadcastClient
waitingForSequenceNumber : ReductionSet
waitingThread : ReductionSet
waterIndex : Molecule
willRequire() : ReductionMgr
willSubmit() : ReductionMgr
WorkDistrib : WorkDistrib, PatchMap, ComputeMap
workDistrib : Node, BOCgroup
wrap_delta() : Lattice
wrap_nearest_delta() : Lattice
wrapAll : SimParameters
wrapNearest : SimParameters
wrapWater : SimParameters
write() : PDB
writeExtendedSystemData() : Controller
writeExtendedSystemLabels() : Controller
writeFepEnergyData() : Controller

- x -

x : Vector, FloatVector, PmeParticle, minpoint, TuplePatchElem, PatchElem
x0 : NonbondedExclValue, BondValue
x_avg : TuplePatchElem
x_start : LocalPmeInfo, PmeTransMsg
Xcap : parm
xcoor() : PDBAtom
xstFile : Controller
xstFilename : SimParameters
xstFrequency : SimParameters
xx : Tensor
xy : Tensor
xz : Tensor

- y -

y : Vector, FloatVector, PmeParticle
y_start : PmeUntransMsg
y_start_after_transpose : LocalPmeInfo
Ycap : parm
ycoor() : PDBAtom
yx : Tensor
yy : Tensor
yz : Tensor

- z -

z : Vector, FloatVector, PmeParticle
Zcap : parm
zcoor() : PDBAtom
ZeroAccumulator() : ALambdaManager, ALambdaControl
zlist : PmeGridMsg
zlistlen : PmeGridMsg
zVector() : zVector
zx : Tensor
zy : Tensor
zz : Tensor

- ~ -

~AGroup() : AGroup
~ALambdaManager() : ALambdaManager
~AngleElem() : AngleElem
~ARestraint() : ARestraint
~ARestraintManager() : ARestraintManager
~Array() : Array< Elem, Size >
~AtomMap() : AtomMap
~BOID() : BOID
~BondElem() : BondElem
~BroadcastClient() : BroadcastClient
~BroadcastClientElem() : BroadcastClientElem
~BroadcastMgr() : BroadcastMgr
~BroadcastMsg() : BroadcastMsg
~CollectionMaster() : CollectionMaster
~CollectionMgr() : CollectionMgr
~Communicate() : Communicate
~Compute() : Compute
~ComputeCylindricalBC() : ComputeCylindricalBC
~ComputeDPMEDataMsg() : ComputeDPMEDataMsg
~ComputeDPMEResultsMsg() : ComputeDPMEResultsMsg
~ComputeEField() : ComputeEField
~ComputeExt() : ComputeExt
~ComputeExtMgr() : ComputeExtMgr
~ComputeFullDirect() : ComputeFullDirect
~ComputeGlobal() : ComputeGlobal
~ComputeGlobalConfigMsg() : ComputeGlobalConfigMsg
~ComputeGlobalDataMsg() : ComputeGlobalDataMsg
~ComputeGlobalResultsMsg() : ComputeGlobalResultsMsg
~ComputeHomePatch() : ComputeHomePatch
~ComputeHomePatches() : ComputeHomePatches
~ComputeHomeTuples() : ComputeHomeTuples< T, S, P >
~ComputeMap() : ComputeMap
~ComputeMgr() : ComputeMgr
~ComputeNonbondedPair() : ComputeNonbondedPair
~ComputeNonbondedSelf() : ComputeNonbondedSelf
~ComputeNonbondedUtil() : ComputeNonbondedUtil
~ComputePatch() : ComputePatch
~ComputePatchPair() : ComputePatchPair
~ComputePme() : ComputePme
~ComputePmeMgr() : ComputePmeMgr
~ComputeRestraints() : ComputeRestraints
~ComputeSelfTuples() : ComputeSelfTuples< T, S, P >
~ComputeSphericalBC() : ComputeSphericalBC
~ConfigList() : ConfigList
~ConfigListNode() : ConfigList::ConfigListNode
~Controller() : Controller
~DataElement() : ParseOptions::DataElement
~datastream() : datastream
~DihedralElem() : DihedralElem
~Entry() : Entry< Elem >
~EntryGlob() : EntryGlob< Elem >
~GlobalMaster() : GlobalMaster
~GlobalMasterEasy() : GlobalMasterEasy
~GlobalMasterFreeEnergy() : GlobalMasterFreeEnergy
~GlobalMasterIMD() : GlobalMasterIMD
~GlobalMasterMisc() : GlobalMasterMisc
~GlobalMasterServer() : GlobalMasterServer
~GlobalMasterSMD() : GlobalMasterSMD
~GlobalMasterTcl() : GlobalMasterTcl
~HomePatch() : HomePatch
~HomePatchElem() : HomePatchElem
~HydrogenGroupID() : HydrogenGroupID
~IMDOutput() : IMDOutput
~ImproperElem() : ImproperElem
~infostream() : infostream
~LdbCoordinator() : LdbCoordinator
~LJTable() : LJTable
~MathArray() : MathArray< Elem, Size >
~maxHeap() : maxHeap
~MigrateAtomsCombinedMsg() : MigrateAtomsCombinedMsg
~minHeap() : minHeap
~MIStream() : MIStream
~Molecule() : Molecule
~MOStream() : MOStream
~MovePatch() : MovePatch
~NamdState() : NamdState
~Node() : Node
~ObjectArena() : ObjectArena< Type >
~Output() : Output
~OwnerBox() : OwnerBox< Owner, Data >
~Parameters() : Parameters
~parm() : parm
~ParseOptions() : ParseOptions
~Patch() : Patch
~PatchElem() : PatchElem
~PatchMap() : PatchMap
~PatchMgr() : PatchMgr
~PDB() : PDB
~PDBAtom() : PDBAtom
~PDBAtomRecord() : PDBAtomRecord
~PDBData() : PDBData
~PDBHetatm() : PDBHetatm
~PDBUnknown() : PDBUnknown
~PmeKSpace() : PmeKSpace
~PmeRealSpace() : PmeRealSpace
~PositionOwnerBox() : PositionOwnerBox< Owner >
~ProxyListElem() : ProxyListElem
~ProxyMgr() : ProxyMgr
~ProxyPatch() : ProxyPatch
~Rebalancer() : Rebalancer
~RecBisection() : RecBisection
~ReductionMgr() : ReductionMgr
~ReductionSetData() : ReductionSetData
~RequireReduction() : RequireReduction
~ResidueLookupElem() : ResidueLookupElem
~ResizeArray() : ResizeArray< Elem >
~ResizeArrayIter() : ResizeArrayIter< T >
~ResizeArrayPrimIter() : ResizeArrayPrimIter< T >
~ResizeArrayRaw() : ResizeArrayRaw< Elem >
~ScriptTcl() : ScriptTcl
~Sequencer() : Sequencer
~Set() : Set
~SimParameters() : SimParameters
~SimpleBroadcastObject() : SimpleBroadcastObject< T >
~SortableResizeArray() : SortableResizeArray< Elem >
~StringList() : StringList
~SubmitReduction() : SubmitReduction
~Sync() : Sync
~TaggedMsg() : TaggedMsg
~Tensor() : Tensor
~TuplePatchElem() : TuplePatchElem
~UniqueSet() : UniqueSet< Elem >
~UniqueSetIter() : UniqueSetIter< T >
~UniqueSetRaw() : UniqueSetRaw< Elem >
~WorkDistrib() : WorkDistrib

Generated on Thu Nov 7 04:01:44 2002 for NAMD by