NAMD
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level
1
2
]
▶
N
AmberParm7Reader
C
Ambertoppar
C
FortranData
C
FortranFormatSpecifier
▶
N
dlloader
C
DLLoader
C
DLLoaderInterface
▶
N
msm
C
Array
C
AtomCoord
C
BlockDiagram
C
BlockIndex
C
BlockSend
C
FoldFactor
C
Grid
C
GridFixed
C
IndexRange
C
Ivec
C
Map
C
PatchData
C
PatchDiagram
C
PatchSend
C
PriorityQueue
C
__sort_entry
C
ABoundAngleRestraint
C
ABoundDiheRestraint
C
ABoundDistRestraint
C
ABoundPosRestraint
C
ADiheRestraint
C
ADistRestraint
C
AFixedAngleRestraint
C
AFixedDiheRestraint
C
AFixedDistRestraint
C
AFixedPosRestraint
C
AForcingAngleRestraint
C
AForcingDiheRestraint
C
AForcingDistRestraint
C
AForcingPosRestraint
C
AGroup
C
ALambdaControl
C
ALambdaManager
C
AlchData
Alchemical datastructure that holds the lambda-relevant paramenters for FEP/TI
C
Alg7
C
AlgNbor
C
AlgRecBisection
C
AlignVector
C
Ambertoppar
C
AnAngleRestraint
C
angle
C
angle_params
C
AngleElem
C
AngleTable
C
AngleValue
C
aniso
C
AnisoElem
C
APosRestraint
C
ARestraint
C
ARestraintManager
C
Array
C
assert_ProxyResultVarsizeMsg
C
atom_constants
C
atom_name_info
C
AtomCstInfo
C
atomData
C
atomID_less
C
AtomMap
C
AtomMapper
C
AtomNameIdx
C
AtomsCntPerPatchMsg
C
AtomSigInfo
C
AtomSignature
C
AtomTable
C
AVector
C
BackEnd
C
BasicAtomInfo
C
BOCgroup
C
BOID
C
bond
C
bond_params
C
BondElem
C
BondTable
C
BondValue
C
BoundingBox
C
Box
C
BroadcastClient
C
BroadcastClientElem
C
BroadcastMgr
C
BroadcastMsg
C
C1Matrix
C
C1Vector
C
CheckpointAtomsMsg
C
CheckpointAtomsReqMsg
C
CheckpointMsg
C
CheckStep
C
CkPrintf_stringbuf
C
ClusterCoorElem
C
ClusterCoorMsg
C
ClusterElem
C
ClusterSizeMsg
▶
C
CollectionMaster
C
CollectVectorInstance
C
CollectVectorInstanceDcdSelection
C
CollectVectorSequence
C
CollectVectorSequenceDcdSelection
▶
C
CollectionMgr
C
CollectVectorInstance
C
CollectVectorSequence
C
CollectLoadsMsg
C
CollectProxyVectorInstance
C
CollectProxyVectorSequence
C
CollectVectorMsg
C
CollectVectorVarMsg
C
colvarproxy_namd
Communication between colvars and NAMD (implementation of
colvarproxy
)
C
Communicate
C
CompAtom
C
CompAtomExt
C
CompAtomExtCopy
C
Compute
C
ComputeAngles
C
ComputeAniso
▶
C
ComputeBondedCUDAKernel
C
BondedVirial
C
ComputeBonds
C
ComputeConsForce
C
ComputeConsForceMsg
C
ComputeConsTorque
C
ComputeCrossterms
C
ComputeCUDAMgr
C
ComputeCylindricalBC
C
ComputeDihedrals
C
ComputeDPMEDataMsg
C
ComputeDPMEResultsMsg
C
ComputeEField
C
ComputeEwald
C
ComputeEwaldMsg
C
ComputeExcls
C
ComputeExt
C
ComputeExtAtom
C
ComputeExtMgr
C
ComputeFmmSerial
C
ComputeFmmSerialAtom
C
ComputeFmmSerialMgr
C
ComputeFullDirect
C
ComputeGBISAtom
C
ComputeGBISser
C
ComputeGBISserMgr
C
ComputeGlobal
C
ComputeGlobalDataMsg
C
ComputeGlobalResultsMsg
C
ComputeGridForce
C
ComputeGromacsPair
C
ComputeHomePatch
C
ComputeHomePatches
C
ComputeHomeTuples
C
ComputeImpropers
C
computeInfo
C
ComputeLCPO
C
ComputeLjPmeSerial
C
ComputeLjPmeSerialMgr
▶
C
ComputeLonepairsCUDA
C
LonepairBisector
C
LonepairColinear
C
LonepairRelative
▶
C
ComputeMap
C
ComputeData
C
PatchRec
C
ComputeMapChangeMsg
C
ComputeMgr
C
ComputeMoa
C
ComputeMsm
C
ComputeMsmMgr
C
ComputeMsmSerial
C
ComputeMsmSerialAtom
C
ComputeMsmSerialMgr
C
ComputeNonbondedPair
C
ComputeNonbondedSelf
C
ComputeNonbondedUtil
C
ComputeNonbondedWorkArrays
C
ComputePatch
C
ComputePatchPair
C
ComputePme
C
ComputePmeCUDA
C
ComputePmeCUDADevice
C
ComputePmeCUDAMgr
▶
C
ComputePmeMgr
C
cuda_submit_charges_args
C
ComputePmeUtil
C
ComputeQM
C
ComputeQMAtom
C
ComputeQMMgr
C
ComputeQMPntChrg
C
ComputeRestraints
C
ComputeSelfAngles
C
ComputeSelfAniso
C
ComputeSelfBonds
C
ComputeSelfCrossterms
C
ComputeSelfDihedrals
C
ComputeSelfExcls
C
ComputeSelfGromacsPair
C
ComputeSelfImpropers
C
ComputeSelfThole
C
ComputeSelfTuples
C
ComputeSphericalBC
C
ComputeStir
C
ComputeTclBC
C
ComputeThole
▶
C
ConfigList
C
ConfigListNode
C
ConstPointer
C
constraintTuple
▶
C
Controller
C
checkpoint
C
CthThreadWrapper
C
ControllerBroadcasts
C
ControllerState
C
cptr_sortop_priority
C
CpuPmeAtomStorage
C
cr_sortop_distance
C
cr_sortop_reverse_priority
C
crossterm
C
crossterm_params
C
CrosstermData
C
CrosstermElem
C
CrosstermValue
C
cuda_args_t
C
CudaAlchFlags
C
CudaAlchLambdas
C
CudaAlchParameters
C
CudaAngle
C
CudaAngleStage
C
CudaAngleValue
C
CudaAtom
C
CudaBond
C
CudaBondStage
C
CudaBondValue
C
CudaComputeGBISKernel
▶
C
CudaComputeNonbonded
C
ComputeRecord
C
PatchRecord
C
CudaComputeNonbondedKernel
C
CudaComputeNonbondedMsg
C
CudaComputeRecord
C
CudaCrossterm
C
CudaCrosstermStage
C
CudaCrosstermValue
C
CudaDihedral
C
CudaDihedralStage
C
CudaDihedralValue
C
CudaExclusion
C
CudaExclusionStage
C
CudaFFTCompute
C
CudaForce
C
CudaGlobalMasterClient
A class for performing calculations on specific atoms selected by atom serial numbers
C
CudaGlobalMasterServer
A class for copying atom information from SequencerCUDA to
CudaGlobalMasterClient
C
CudaLocalRecord
C
CudaMInfo
C
CudaNBConstants
C
CudaNonbondedTables
C
CudaPatchRecord
C
CudaPeerRecord
C
CudaPmeAtomStorage
C
CudaPmeKSpaceCompute
▶
C
CudaPmeOneDevice
C
EnergyVirial
C
CudaPmePencilX
C
CudaPmePencilXY
C
CudaPmePencilXYZ
C
CudaPmePencilY
C
CudaPmePencilZ
C
CudaPmeRealSpaceCompute
C
CudaPmeTranspose
C
CudaPmeXInitMsg
C
CudaPmeXYInitMsg
C
CudaPmeXYZInitMsg
C
CudaRattleElem
C
CudaRattleParam
C
CudaStaticAssert
C
CudaStaticAssert< true >
C
cudaTensor
C
CudaTileListKernel
C
cudaVector
C
DataExchanger
C
DataMessage
C
datastream
C
DataStreamMsg
C
dcd_params
C
DeviceBuffer
C
DeviceCUDA
C
DeviceDataMsg
C
dihedral
C
dihedral_params
C
DihedralElem
C
DihedralTable
C
DihedralValue
C
doublecomplex
C
drude_constants
C
dummyData
C
eABF
C
eABF1D
C
eABF2D
C
Entry
C
EntryGlob
C
EwaldParticle
C
ExchangeAtomsMsg
C
ExchangeAtomsReqMsg
C
ExclElem
C
ExclSigInfo
C
Exclusion
C
ExclusionCheck
C
ExclusionSignature
C
exlist_sortop
C
ExtCoordMsg
C
ExtForce
C
ExtForceMsg
C
FFTCompute
C
FileStack
C
FinishWorkMsg
C
Flags
C
floatcomplex
C
FloatVector
C
FmmSerialCoordMsg
C
FmmSerialForceMsg
C
four_body_consts
C
FullAtom
C
GBISCoordMsg
C
GBISForceMsg
C
GBISParamStruct
C
GenericAngle
C
GenericAtom
C
GenericBond
C
GenericDihedral
C
GenericMol
C
GlobalMaster
C
GlobalMasterEasy
C
GlobalMasterFreeEnergy
C
GlobalMasterIMD
C
GlobalMasterMisc
C
GlobalMasterServer
C
GlobalMasterSMD
C
GlobalMasterSymmetry
C
GlobalMasterTcl
C
GlobalMasterTest
C
GlobalMasterTMD
C
GMWakeMsg
C
go_pair
C
go_val
▶
C
GridforceFullBaseGrid
C
GridIndices
C
GridforceFullMainGrid
C
GridforceFullSubGrid
C
GridforceGrid
C
GridforceLiteGrid
C
GridMsg
C
GroGaussPair
C
GroLJPair
C
gromacsPair
C
GromacsPairElem
C
GromacsPairValue
C
GromacsTopFile
C
GroupInitMsg
C
GroupRestraintList
C
GroupRestraintParam
C
HashPool
C
HashPoolAdaptorT
C
HashReal
C
HashString
C
heapIterator
C
heapRecord
▶
C
HomePatch
C
checkpoint_t
C
RattleList
C
HomePatchElem
C
HydroBasedMsg
C
HydrogenGroupID
C
idIndxStr
C
ijpair
C
ijpair_sortop_bit_reversed
C
IMDEnergies
C
IMDheader
C
IMDOutput
C
improper
C
improper_params
C
ImproperElem
C
ImproperValue
C
indexed_nbthole_pair
C
indexed_table_pair
C
indexed_vdw_pair
C
indexed_vdw_pair_accel
C
InfoRecord
C
infostream
C
InitDeviceMsg
C
InitDeviceMsg2
C
InputAtom
C
Int2
C
Int3
C
InterpParams_t
C
intpair
C
IRSet
C
isEmpty
C
isWater
C
Iterator
C
LargeIRSet
C
Lattice
C
LCPOAtom
C
LCPONeighborList
C
LdbCoordinator
C
LdbMigrateMsg
C
LincsSolver
C
listNode
C
LjPmeCompute
C
LjPmeGrid
C
LjPmeKSpace
C
LjPmeMgr
C
LjPmeRealSpace
C
LjPmeSerialAtom
C
LjPmeSerialCoordMsg
C
LjPmeSerialForceMsg
▶
C
LJTable
C
TableEntry
C
LocalID
C
localIDResult
Helper struct to store the result of query local ID from global ID
C
LocalLBInfoMsg
C
LocalPmeInfo
C
LocalWorkMsg
C
lphost
C
LSSDataStr
C
lssDistSort
C
LSSSubsDat
C
main
C
MathArray
C
Matrix4
4x4 matrix class with numerous operators, conversions, etc
C
Matrix4Symmetry
C
Matrix4TMD
C
maxHeap
C
Measure
C
meMMQMGrp
C
memusageinit
C
MGridforceParams
C
MGridforceParamsList
C
MigrateAtomsCombinedMsg
C
MigrateAtomsMsg
C
MigrationInfo
C
minHeap
C
minpoint
C
MIStream
C
MoaData
C
Molecule
Molecule
stores the structural information for the system
C
MolInfoMsg
C
MolInst
C
MOStream
C
MoveAllByMsg
C
MoveAtomMsg
C
MoveInputAtomsMsg
C
MovePatch
C
MovePatchAtomsMsg
C
MovePatchesMsg
C
MovingAverage
C
MsmBlock
C
MsmBlockKernel
C
MsmBlockMap
C
MsmBlockProxyMsg
C
MsmC1HermiteBlock
C
MsmC1HermiteBlockProxyMsg
C
MsmC1HermiteGridCutoff
C
MsmC1HermiteGridCutoffProxyMsg
C
MsmC1HermiteGridCutoffSetupMsg
C
MsmGridCutoff
C
MsmGridCutoffInitMsg
C
MsmGridCutoffKernel
C
MsmGridCutoffMap
C
MsmGridCutoffProxyMsg
C
MsmGridCutoffSetupMsg
C
MsmInitMsg
C
MsmProfiler
C
MsmSerialCoordMsg
C
MsmSerialForceMsg
C
MsmTimer
C
MStringStrider
C
MultiString
C
NamdCentLB
C
NamdDummyLB
C
NamdHybridLB
C
NamdProfileEvent
C
NamdState
C
nbthole_pair_params
C
nbthole_pair_value
C
netint
Structure used to perform byte swapping operations
C
NL_Msm_t
C
Node
C
NodePmeInfo
C
NodePmeMgr
C
NodeProxyMgr
C
NodeReduction
C
nodesort
C
nonbonded
C
NonbondedExclValue
C
notZero
C
NumDevicesMsg
C
ObjectArena
C
ofstream_namd
C
Output
▶
C
OutputAtomRecord
C
floatVals
C
integerVals
C
shortVals
C
OwnerBox
C
Pairlists
C
PairTable
C
PAL
C
ParallelIOMgr
C
Parameters
▶
C
ParseOptions
C
DataElement
C
Patch
C
patch_sortop_curve_a
C
patch_sortop_curve_b
C
patch_sortop_curve_c
C
PatchData
C
PatchDataSOA
C
patchDataStrc
C
PatchElem
C
patchInfo
C
PatchInfo
C
PatchLevelPmeData
C
PatchMap
C
PatchMapMsg
C
PatchMgr
C
PatchPairRecord
C
PatchProxyListMsg
C
PatchRecord
C
PDB
C
PDBAtom
C
PDBAtomRecord
C
PDBData
C
PDBHetatm
C
PDBUnknown
C
pe_sortop_bit_reversed
C
pe_sortop_coord_x
C
pe_sortop_coord_y
C
per_atom_flags
C
pid_sortop_reverse_priority
C
PluginIOMgr
C
PmeAckMsg
C
PmeAtomFiler
C
PmeAtomMsg
C
PmeAtomPencilMsg
C
PmeAtomStorage
C
PmeBlockMsg
C
PmeDoneMsg
C
PmeEvirMsg
C
PmeForceMsg
C
PmeForcePencilMsg
C
PmeGrid
C
PmeGridMsg
C
PmeKSpace
C
PmeKSpaceCompute
C
PmeLaunchMsg
C
PmeParticle
C
PmePencil
C
PmePencilInitMsg
C
PmePencilInitMsgData
C
PmePencilMap
C
PmePencilX
C
PmePencilXMap
C
PmePencilXY
C
PmePencilXYMap
C
PmePencilXYZ
C
PmePencilXYZMap
C
PmePencilY
C
PmePencilZ
C
PmeRealSpace
C
PmeRealSpaceCompute
C
PmeRunMsg
C
PmeSharedTransMsg
C
PmeSharedUntransMsg
C
PmeStartMsg
C
PmeTransMsg
C
PmeTranspose
C
PmeUntransMsg
C
PmeXPencil
C
PmeYPencil
C
PmeZPencil
C
pntChrgDist
C
Pointer
C
position_index
C
PressureProfileReduction
C
processorInfo
C
ProxyCombinedResultMsg
C
ProxyCombinedResultRawMsg
C
ProxyDataMsg
C
ProxyElem
C
ProxyGBISP1ResultMsg
C
ProxyGBISP2DataMsg
C
ProxyGBISP2ResultMsg
C
ProxyGBISP3DataMsg
C
ProxyListInfo
C
ProxyMgr
C
ProxyNodeAwareSpanningTreeMsg
C
ProxyPatch
C
ProxyResultMsg
C
ProxyResultVarsizeMsg
C
ProxySpanningTreeMsg
C
ProxyTree
C
proxyTreeNode
C
ProxyUsage
C
ProxyUsageKey
C
QMAtomData
C
QMCoordMsg
C
QMForce
C
QMForceMsg
C
QMGrpCalcMsg
C
QMGrpResMsg
C
QMPntChrgMsg
C
qmSolvData
C
Random
C
RattleParam
▶
C
Rebalancer
C
pcpair
C
RecBisection
C
RecvDeviceMsg
C
ReductionMgr
C
ReductionRegisterMsg
C
ReductionSet
C
ReductionSetData
C
ReductionSubmitMsg
C
ReductionValue
C
RefineOnly
C
RefineTorusLB
C
refSelStr
C
RegisterPatchMsg
C
RegisterProxyMsg
C
ReplicaDcdAckMsg
C
ReplicaDcdDataMsg
C
ReplicaDcdInitMsg
C
RequireReduction
C
ResidueLookupElem
C
ResizeArray
C
ResizeArrayIter
C
ResizeArrayPrimIter
C
ResizeArrayRaw
C
Results
C
RunningAverage
C
ScriptParamMsg
▶
C
ScriptTcl
C
SimpleBroadcastObjectWrapper
C
seg_resid
C
Sequencer
C
SetLatticeMsg
C
SettleParameters
C
SimParameters
C
SimpleBroadcastObject
C
SlaveInitMsg
C
SortableResizeArray
C
SortedArray
C
sortop_base
C
sortop_bit_reversed
C
sortop_SOA
C
sortop_x
C
sortop_y
C
sortop_z
C
sparseMatrix
C
SplitComputesMsg
C
StreamMessage
C
StringList
C
SubmitReduction
C
Sync
C
table_pair_params
C
TaggedMsg
C
Tensor
C
thole
C
TholeElem
C
TileExcl
C
TileList
C
TileListStat
C
TileListVirialEnergy
▶
C
TopoManagerWrapper
C
pe_sortop_topo
C
TorusLB
C
Transform
C
TransposeBatch
C
TupleCounts
C
TupleData
C
TupleDataStage
C
TupleDataStagePeer
C
TupleIntArrays
C
TupleIntArraysContiguous
C
TupleIntArraysPeer
C
TuplePatchElem
C
TupleSignature
C
TupleSizes
C
TupleStrider
C
TupleString
C
TupleStringHash
C
TwoLevelParam
C
UniqueSet
C
UniqueSetIter
C
UniqueSetRaw
C
UniqueSortedArray
C
UnregisterProxyMsg
C
validRattle
C
vdw_pair_params
C
vdw_params
C
vdw_val
C
VDWTable
C
vect
C
Vector
C
VirialEnergy
C
vmdforce
C
wkf_timer
C
wkfmsgtimer
▶
C
WorkDistrib
C
pe_sortop_compact
C
pe_sortop_diffuse
C
WorkIndex
C
XXH32_canonical_t
C
XXH64_canonical_t
C
zVector
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