Here is a list of all documented class members with links to the class documentation for each member:
- s -
- s
: BondedInteraction
- sampleCount()
: gmx::AnalysisDataAverageModule
- saveEdsamPointer()
: gmx::Constraints
- sblock
: gmx::shakedata
- scaleAll()
: gmx::AbstractAverageHistogram
- scaleAllByVector()
: gmx::AbstractAverageHistogram
- scaleBox()
: EwaldBoxZScaler
- scaled_lagrange_multiplier
: gmx::shakedata
- scaleOperationOnly()
: gmx::TranslateAndScale
- scaleSingle()
: gmx::AbstractAverageHistogram
- scheduleCheckOfLocalTopology()
: gmx::LocalTopologyChecker
- sci
: nbnxn_sci
- scopedTransform()
: gmx::IKeyValueTreeTransformRules
- SearchMode
: gmx::AnalysisNeighborhood
- seed()
: gmx::ThreeFry2x64General< rounds, internalCounterBits >
- select_on_container_copy_construction()
: gmx::HostAllocationPolicy
- selectDataSet()
: gmx::AnalysisDataStorageFrame
, gmx::AnalysisDataHandle
- selected()
: gmx::SelectionPosition
- Selection()
: gmx::Selection
- selection()
: gmx::SelectionCollection
- SelectionCollection()
: gmx::SelectionCollection
- selectionCollection()
: gmx::AnalysisDataPlotSettings
- SelectionFileOption()
: gmx::SelectionFileOption
- SelectionFileOptionInfo()
: gmx::SelectionFileOptionInfo
- SelectionOption()
: gmx::SelectionOption
- SelectionOptionBehavior()
: gmx::SelectionOptionBehavior
- SelectionOptionInfo()
: gmx::SelectionOptionInfo
- SelectionOptionManager()
: gmx::SelectionOptionManager
- SelectionOptionStorage
: gmx::Selection
, gmx::SelectionOption
, gmx::SelectionOptionManager
- SelectionPosition()
: gmx::SelectionPosition
- selectionText()
: gmx::Selection
- SelectionTopologyProperties()
: gmx::SelectionTopologyProperties
- SelectionTypeOption
: gmx::SelectionCollection
- selectSingleFromArray()
: gmx::AnalysisNeighborhoodPositions
- selfEnergy()
: gmx::CoulombCalculator< KernelCoulombType::RF >
, gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical >
, gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated >
- sendCoordinatesToPmeFromCpu()
: gmx::PmePpCommGpu
- sendCoordinatesToPmeFromGpu()
: gmx::PmePpCommGpu
- sendFToPpGpuAwareMpi()
: gmx::PmeForceSenderGpu
- sendFToPpPeerToPeer()
: gmx::PmeForceSenderGpu
- serialize()
: gmx::WriteCheckpointDataHolder
, StringTableEntry
- serializeParticle()
: SimulationParticle
- serializeStringTable()
: StringTable
- set
: gmx::SimulationSignal
, gmx::FlagsTemplate< FlagType >
- setAcceptBooleanNoPrefix()
: gmx::OptionsAssigner
- setAnyValue()
: gmx::KeyValueTreeValueBuilder
- setAtomProperties()
: nonbonded_verlet_t
- setAtomProperty()
: AtomProperties
- SetAtoms()
: gmx::SetAtoms
- setAverageDataSets()
: gmx::AnalysisDataAverageModule
- SetBox()
: gmx::SetBox
- setBugText()
: gmx::ICommandLineOptionsModuleSettings
- setColumnCount()
: gmx::test::AnalysisDataTestInput
, gmx::AbstractAnalysisData
, gmx::AnalysisData
, gmx::AbstractAnalysisArrayData
- setColumnFirstLineOffset()
: gmx::TextTableFormatter
- setConstraints()
: gmx::Constraints
, gmx::SettleData
- setContinuationChar()
: gmx::TextLineWrapperSettings
- setCumulative()
: gmx::AnalysisDataLifetimeModule
- setCutoff()
: gmx::AnalysisNeighborhood
- setDataSetCount()
: gmx::AbstractAnalysisData
, gmx::AnalysisData
- setDebugLevel()
: gmx::SelectionCollection
- setDefaultNiceLevel()
: gmx::CommandLineModuleSettings
- setDefaultTolerance()
: gmx::test::CommandLineTestBase
, gmx::test::TestReferenceChecker
- setDefaultValue()
: gmx::OptionStorageTemplate< T >
- setDefaultValueIfSet()
: gmx::OptionStorageTemplate< T >
- setDescription()
: gmx::AbstractOption
- setDisplayName()
: gmx::CommandLineProgramContext
- setDynamicMask()
: gmx::SelectionOptionInfo
- setError()
: gmx::AnalysisDataValue
- setErrorsAsSeparateColumn()
: gmx::AbstractPlotModule
- setEvaluateForces()
: gmx::Selection
, gmx::SelectionOptionInfo
- setEvaluateVelocities()
: gmx::Selection
, gmx::SelectionOptionInfo
- setFileAndLineNumber()
: WarningHandler
- setFileName()
: gmx::AbstractPlotModule
- setFirstColumnIndent()
: gmx::TextTableFormatter
- setFirstLineIndent()
: gmx::TextLineWrapperSettings
- setFlag()
: gmx::AbstractOptionStorage
, gmx::AbstractOption
, gmx::TrajectoryAnalysisSettings
- setFlags()
: t_state
, gmx::TrajectoryAnalysisSettings
- setFoldLastColumnToNextLine()
: gmx::TextTableFormatter
- setForceParameter()
: InteractionOfType
- SetForces()
: gmx::SetForces
- setForceSendBuffer()
: gmx::PmeForceSenderGpu
- setFrameFlags()
: gmx::TrajectoryAnalysisSettings
- setGlobalOutputTempDirectory()
: gmx::test::TestFileManager
- setHelpText()
: gmx::CommandLineHelpWriter
, gmx::ICommandLineOptionsModuleSettings
, gmx::TrajectoryAnalysisSettings
- setIndent()
: gmx::TextLineWrapperSettings
- setIndexGroups()
: gmx::SelectionCollection
- setIndicesInDomainDecomposition()
: gmx::LocalAtomSetManager
- setInfo()
: gmx::GromacsException
- setInputAndOutputFile()
: gmx::test::CommandLineTestBase
- setInputDataDirectory()
: gmx::test::TestFileManager
- setInputFile()
: gmx::test::CommandLineTestBase
- setInputFileContents()
: gmx::test::CommandLineTestHelper
, gmx::test::CommandLineTestBase
- setInputLines()
: gmx::test::InteractiveTestHelper
- setInputRedirector()
: gmx::FileNameOptionManager
- setKeepFinalSpaces()
: gmx::TextLineWrapperSettings
- setKnownIssues()
: gmx::CommandLineHelpWriter
- setLastNewline()
: gmx::test::InteractiveTestHelper
- setLegend()
: gmx::AbstractPlotModule
- setLineLength()
: gmx::TextLineWrapperSettings
- setLocalAtomOrder()
: nonbonded_verlet_t
, PairSearch
- setMaxTime()
: gmx::AnalysisDataDisplacementModule
- setMaxValueCount()
: gmx::AbstractOptionStorage
- setMinValueCount()
: gmx::AbstractOptionStorage
- setMode()
: gmx::AnalysisNeighborhood
- setModifiableInputFile()
: gmx::test::CommandLineTestBase
- setModuleDisplayName()
: gmx::CommandLineHelpContext
- setModuleFlag()
: gmx::test::FlagTest
- setMSDHistogram()
: gmx::AnalysisDataDisplacementModule
- setMultipoint()
: gmx::AbstractAnalysisData
, gmx::AnalysisData
- setOmitX()
: gmx::AbstractPlotModule
- setOnlyAtoms()
: gmx::SelectionOptionInfo
- setOnlyStatic()
: gmx::SelectionOptionInfo
- setOptionsModuleSettings()
: gmx::TrajectoryAnalysisSettings
- setOriginalId()
: gmx::Selection
- setOutputFile()
: gmx::test::CommandLineTestHelper
, gmx::test::CommandLineTestBase
- setOutputFileWithGeneratedName()
: gmx::test::CommandLineTestHelper
, gmx::test::CommandLineTestBase
- setOutputPosType()
: gmx::SelectionCollection
- setOutputRedirector()
: gmx::CommandLineModuleManager
- setOutputTempDirectory()
: gmx::test::TestFileManager
- setPBC()
: gmx::TrajectoryAnalysisSettings
- setPlainOutput()
: gmx::AbstractPlotModule
- setPoint()
: gmx::AnalysisDataHandle
- setPoints()
: gmx::AnalysisDataHandle
- SetPrecision()
: gmx::SetPrecision
- setQuiet()
: gmx::CommandLineModuleManager
- setReferencePosType()
: gmx::SelectionCollection
- setReplacement()
: gmx::HelpWriterContext
- setRmPBC()
: gmx::TrajectoryAnalysisSettings
- setRowCount()
: gmx::AbstractAnalysisArrayData
- setScaleFactor()
: gmx::DoubleOptionInfo
, gmx::FloatOptionInfo
- setSearchPathFromEnv()
: gmx::DataFileFinder
- setSelectionCollection()
: gmx::AnalysisDataPlotSettings
- setSelectionOptionValues()
: gmx::test::ModuleSelection
- setSettings()
: gmx::AbstractPlotModule
- setShowHidden()
: gmx::CommandLineHelpContext
- setSignal()
: gmx::CheckpointHandler
, gmx::ResetHandler
, gmx::StopHandler
- setSignals()
: gmx::SimulationSignaller
- setSingleModule()
: gmx::CommandLineModuleManager
- SetStartTime()
: gmx::SetStartTime
- setStoreData()
: gmx::EnergyTerm
- setStoreIsSet()
: gmx::AbstractOption
- setSubtitle()
: gmx::AbstractPlotModule
- setTestSimulationDatabaseDirectory()
: gmx::test::TestFileManager
- SetTimeStep()
: gmx::SetTimeStep
- setTimeUnit()
: gmx::AnalysisDataPlotSettings
, gmx::TimeUnitManager
, gmx::TimeUnitBehavior
- setTimeUnitFromEnvironment()
: gmx::TimeUnitBehavior
- setTimeUnitStore()
: gmx::TimeUnitBehavior
- settings()
: gmx::AbstractAverageHistogram
, gmx::AnalysisDataSimpleHistogramModule
, gmx::AnalysisDataWeightedHistogramModule
, gmx::AnalysisDataBinAverageModule
, gmx::TextLineWrapper
- setTitle()
: gmx::AbstractPlotModule
- SettleData()
: gmx::SettleData
- setTopology()
: gmx::SelectionCollection
- setTopologyExclusions()
: gmx::AnalysisNeighborhood
- setTrimLeadingWhiteSpace()
: gmx::TextReader
- setTrimTrailingComment()
: gmx::TextReader
- setTrimTrailingWhiteSpace()
: gmx::TextReader
- setType()
: PreprocessingAtomTypes
- setup()
: ListedForces
- setupArrayData()
: gmx::test::AnalysisDataTestFixture
- setupDataObject()
: gmx::test::AnalysisDataTestFixture
- setupGpuShortRangeWork()
: nonbonded_verlet_t
- setValue()
: gmx::AnalysisDataStorageFrame
, gmx::KeyValueTreeValueBuilder
, gmx::AnalysisDataValue
- setValueCount()
: gmx::AbstractOption
, gmx::SelectionOptionInfo
- setVector()
: gmx::AbstractOption
- SetVelocities()
: gmx::SetVelocities
- setVirtualSites()
: gmx::VirtualSitesHandler
- setWriteMask()
: gmx::AnalysisDataVectorPlotModule
- setWriteNorm()
: gmx::AnalysisDataVectorPlotModule
- setWriteX()
: gmx::AnalysisDataVectorPlotModule
- setWriteY()
: gmx::AnalysisDataVectorPlotModule
- setWriteZ()
: gmx::AnalysisDataVectorPlotModule
- setXAxis()
: gmx::AbstractAnalysisArrayData
- setXAxisIsTime()
: gmx::AbstractPlotModule
- setXAxisValue()
: gmx::AbstractAnalysisArrayData
- setXFormat()
: gmx::AbstractPlotModule
- setXLabel()
: gmx::AbstractPlotModule
- setXYMode()
: gmx::AnalysisNeighborhood
- setYFormat()
: gmx::AbstractPlotModule
- setYLabel()
: gmx::AbstractPlotModule
- setZero()
: gmx::GaussTransform3D
- shared
: gmx::HardwareTopology::Cache
- shellCompletionWriter()
: gmx::CommandLineHelpContext
- shift
: nbnxn_sci
- shiftForces()
: gmx::ForceWithShiftForces
, ForceHelperBuffers
- shortDescription()
: gmx::ICommandLineModule
, gmx::NonbondedBenchmarkInfo
, gmx::ConvertTprInfo
- showHidden()
: gmx::CommandLineHelpContext
- sig
: gmx::SimulationSignal
- sigma3A
: t_mdatoms
- sigma3B
: t_mdatoms
- sigma_
: gmx::GaussianSpreadKernelParameters::Shape
- sigmaA
: t_mdatoms
- sigmaB
: t_mdatoms
- signalInterSim()
: gmx::SimulationSignaller
- signFactor_
: AtomsAdjacencyListElement
- signsDiffer()
: gmx::test::FloatingPointDifference
- Simd4DBool()
: gmx::Simd4DBool
- Simd4Double()
: gmx::Simd4Double
- Simd4FBool()
: gmx::Simd4FBool
- Simd4Float()
: gmx::Simd4Float
- SimdDBool()
: gmx::SimdDBool
- SimdDIBool()
: gmx::SimdDIBool
- SimdDInt32()
: gmx::SimdDInt32
- SimdDouble()
: gmx::SimdDouble
- SimdFBool()
: gmx::SimdFBool
- SimdFIBool()
: gmx::SimdFIBool
- SimdFInt32()
: gmx::SimdFInt32
- SimdFloat()
: gmx::SimdFloat
- simdInternal_
: gmx::Simd4DBool
, gmx::Simd4Float
, gmx::Simd4FBool
, gmx::SimdDInt32
, gmx::SimdDBool
, gmx::SimdDIBool
, gmx::SimdFInt32
, gmx::SimdFBool
, gmx::SimdFIBool
, gmx::SimdFloat
, gmx::SimdDouble
, gmx::Simd4Double
- similarity()
: gmx::DensitySimilarityMeasure
- simulation_part
: CheckpointHeaderContents
- SimulationAlgorithmSetupError()
: gmx::SimulationAlgorithmSetupError
- simulationComm_
: gmx_multisim_t
- simulationCommunicator_
: gmx::SimulationContext
- SimulationContext()
: gmx::SimulationContext
- simulationIndex_
: gmx_multisim_t
- SimulationInstabilityError()
: gmx::SimulationInstabilityError
- SimulationParticle()
: SimulationParticle
- simulationSetupNotifier_
: gmx::MDModulesNotifiers
- SimulationSignal()
: gmx::SimulationSignal
- SimulationSignaller()
: gmx::SimulationSignaller
- SimulatorConfig()
: gmx::SimulatorConfig
- SimulatorEnv()
: gmx::SimulatorEnv
- SimulatorStateData()
: gmx::SimulatorStateData
- Site()
: gmx::Site
- sites()
: gmx::IRestraintPotential
- size()
: gmx::Range< typename >
, PreprocessingBondAtomType
, gmx::KeyValueTreePath
, PreprocessingAtomTypes
, gmx::HardwareTopology::Cache
, gmx::HashedMap< T >
, gmx::ArrayRef< typename >
, gmx::ArrayRefWithPadding< typename >
, gmx::PaddedVector< T, Allocator >
, JClusterList
, gmx::FixedCapacityVector< typename, size_t >
, gmx::test::AnalysisDataTestInputPointSet
, gmx::ListOfLists< typename >
, InteractionsOfType
, PackedJClusterList
, gmx::EnumerationArray< EnumType, DataType, ArraySize >
- size_
: gmx::PhysicalNodeCommunicator
- size_type
: gmx::ArrayRef< typename >
, gmx::FixedCapacityVector< typename, size_t >
, gmx::ArrayRefWithPadding< typename >
- sizeOfTprBody
: TpxFileHeader
- skewData_
: gmx::MrcDensityMapHeader
- skipRemainingPairsForTestPosition()
: gmx::AnalysisNeighborhoodPairSearch
- skipUnknown()
: gmx::CommandLineParser
- sliced_extents()
: gmx::detail::extents_analyse< R, E0, StaticExtents...>
, gmx::extents< StaticExtents >
, gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...>
- slopeOfLinearFit()
: gmx::EnergyTerm
- sortAtomIds()
: InteractionOfType
- sortBuffer
: PairsearchWork
- sourceLayoutTreeLike_
: gmx::InstallationPrefixInfo
- spaceGroup_
: gmx::MrcDensityMapHeader
- spacing
: gmx::NumericalSplineTableInput
- spawnThreads()
: gmx::Mdrunner
- spreadForces()
: gmx::VirtualSitesHandler
- spreadWidthMultiplesOfSigma_
: gmx::GaussianSpreadKernelParameters::Shape
- sqrt_c6A
: t_mdatoms
- sqrt_c6B
: t_mdatoms
- ssize()
: gmx::ListOfLists< typename >
, gmx::FixedCapacityVector< typename, size_t >
, gmx::ArrayRef< typename >
- standardDeviation()
: gmx::AnalysisDataAverageModule
, gmx::EnergyTerm
- standardError()
: gmx::TextOutputFile
- standardOutput()
: gmx::IFileOutputRedirector
, gmx::test::TestFileOutputRedirector
, gmx::TextOutputFile
- start()
: nbnxn_cycle_t
, gmx::AnalysisHistogramSettingsInitializer
, wallcc_t
, gmx::OptionsAssigner
- startContext()
: gmx::MessageStringCollector
- startData()
: gmx::AnalysisData
- startDataStorage()
: gmx::AnalysisDataStorage
- startFrame()
: gmx::AnalysisDataStorage
, gmx::AnalysisDataHandle
- startFrames()
: gmx::TrajectoryAnalysisModule
- startingBehavior_
: gmx::SimulatorConfig
- startOption()
: gmx::OptionsAssigner
- startPairSearch()
: gmx::AnalysisNeighborhoodSearch
- startParallelDataStorage()
: gmx::AnalysisDataStorage
- startSection()
: gmx::OptionsAssigner
- startSelfPairSearch()
: gmx::AnalysisNeighborhoodSearch
- startSet()
: gmx::AbstractOptionStorage
- startSource()
: gmx::AbstractOptionStorage
- startTimeValue
: gmx::OutputRequirements
- state()
: gmx::ExponentialMovingAverage
- stateChanged
: gmx::StepWorkload
- static_extent()
: gmx::detail::extents_analyse< 0 >
, gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...>
, gmx::extents< StaticExtents >
, gmx::detail::extents_analyse< R, E0, StaticExtents...>
, gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
- status
: DeviceInformation
- stddev()
: gmx::TabulatedNormalDistribution< RealType, tableBits >
, gmx::NormalDistribution< RealType >::param_type
, gmx::NormalDistribution< RealType >
, gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type
- StdioTestHelper()
: gmx::test::StdioTestHelper
- step()
: gmx::EnergyAnalysisFrame
, CheckpointHeaderContents
- step_
: gmx::ForceProviderInput
- stepBegin()
: gmx::EnergyTerm
- stepEnd()
: gmx::EnergyTerm
- stepFactor
: gmx::MtsLevel
- stepping()
: gmx::CpuInfo
- stop()
: nbnxn_cycle_t
- StopConditionSignal()
: gmx::StopConditionSignal
- StopConditionTime()
: gmx::StopConditionTime
- StopHandler()
: gmx::StopHandler
- stoppingAfterCurrentStep()
: gmx::StopHandler
- store()
: gmx::OptionTemplate< T, U >
- storeCount()
: gmx::OptionTemplate< T, U >
- storeData()
: gmx::EnergyTerm
- storeIsSet()
: gmx::OptionTemplate< T, U >
- StorePointer
: gmx::OptionStorageTemplate< T >
- storeVector()
: gmx::OptionTemplate< T, U >
, gmx::RepeatingOptionSection< T >
- stream()
: gmx::DeviceStreamManager
, DeviceStream
- streamIsValid()
: gmx::DeviceStreamManager
- stride()
: gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
, gmx::layout_right::mapping< Extents >
- StringCompare()
: gmx::StringCompare
- StringFormatter()
: gmx::StringFormatter
- StringInputStream()
: gmx::StringInputStream
- StringOption()
: gmx::StringOption
- StringOptionInfo()
: gmx::StringOptionInfo
- StringOptionStorage
: gmx::StringOption
- StringTable()
: StringTable
- StringTableEntry()
: StringTableEntry
- subArray()
: gmx::ArrayRef< typename >
- subscribe()
: gmx::MDModulesNotifier< CallParameter, MDModulesNotifierBase >
- subscribeToPreProcessingNotifications()
: gmx::IMDModule
, gmx::MDModules
, gmx::RestraintMDModule
- subscribeToSimulationSetupNotifications()
: gmx::IMDModule
, gmx::MDModules
, gmx::RestraintMDModule
- substituteMarkupAndWrapToString()
: gmx::HelpWriterContext
- substituteMarkupAndWrapToVector()
: gmx::HelpWriterContext
- sum_dg
: df_history_t
- sum_minvar
: df_history_t
- sum_variance
: df_history_t
- sum_weights
: df_history_t
- supportedSubGroupSizesData
: DeviceInformation
- SupportLevel
: gmx::CpuInfo
- supportLevel()
: gmx::CpuInfo
, gmx::HardwareTopology
- SupportLevel
: gmx::HardwareTopology
- svir_prev
: t_state
- swap()
: gmx::ArrayRefWithPadding< typename >
, gmx::PaddedVector< T, Allocator >
, gmx::ArrayRef< typename >
, gmx::MultiDimArray< TContainer, Extents, LayoutPolicy >
- swapHistory
: ObservablesHistory
- synchronize()
: DeviceStream