- s -

• sampleCoordAndPmf() : gmx::BiasState
• sampleCount() : gmx::AnalysisDataAverageModule , gmx::AnalysisDataFrameAverager
• samplePmf() : gmx::PointState
• sampleProbabilityWeights() : gmx::BiasState
• sampleUmbrellaGridpoint() : gmx::CoordState
• SasaModuleData() : gmx::analysismodules::anonymous_namespace{sasa.cpp}::SasaModuleData
• saveCheckpointState() : gmx::EnergyData::Element , gmx::PullElement , gmx::StatePropagatorData::Element , gmx::ExpandedEnsembleElement , gmx::VelocityScalingTemperatureCoupling , gmx::FirstOrderPressureCoupling , gmx::FreeEnergyPerturbationData::Element , gmx::ICheckpointHelperClient , gmx::MttkData , gmx::NoseHooverChainsData , gmx::ParrinelloRahmanBarostat
• saveEdsamPointer() : gmx::Constraints
• scale() : gmx::MttkData
• scaleAll() : gmx::AbstractAverageHistogram
• scaleAllByVector() : gmx::AbstractAverageHistogram
• scaleBox() : EwaldBoxZScaler
• scaleCoordinates() : gmx::UpdateConstrainGpu::Impl
• scaleInternalToUserInput() : gmx::DimParams
• scaleOperationOnly() : gmx::TranslateAndScale
• scaleSingle() : gmx::AbstractAverageHistogram
• scaleTarget() : gmx::PointState
• scaleUserInputToInternal() : gmx::DimParams
• scaleVelocities() : gmx::UpdateConstrainGpu::Impl
• scheduleCheckOfLocalTopology() : gmx::LocalTopologyChecker
• scheduleTask() : gmx::AndersenTemperatureCoupling , gmx::CheckpointHelper , gmx::CompositeSimulatorElement , gmx::ComputeGlobalsElement< algorithm > , gmx::ConstraintsElement< variable > , gmx::EnergyData::Element , gmx::ExpandedEnsembleElement , gmx::FirstOrderPressureCoupling , gmx::ForceElement , gmx::FreeEnergyPerturbationData::Element , gmx::ISimulatorElement , gmx::MttkElement , gmx::MttkBoxScaling , gmx::NoseHooverChainsElement , gmx::ParrinelloRahmanBarostat , gmx::Propagator< integrationStage > , gmx::PullElement , gmx::StatePropagatorData::Element , gmx::TrajectoryElement , gmx::VelocityScalingTemperatureCoupling
• scopedTransform() : gmx::IKeyValueTreeTransformRules
• secondWorstValue() : gmx::NelderMeadSimplex
• seed() : gmx::AwhParams , gmx::ThreeFry2x64General< rounds, internalCounterBits >
• select_on_container_copy_construction() : gmx::HostAllocationPolicy
• selectDataSet() : gmx::AnalysisDataHandle , gmx::AnalysisDataStorageFrame
• selected() : gmx::SelectionPosition
• selection() : gmx::SelectionCollection
• Selection() : gmx::Selection
• selectionCollection() : gmx::AnalysisDataPlotSettings
• SelectionCollection() : gmx::SelectionCollection
• SelectionData() : gmx::internal::SelectionData
• SelectionFileOption() : gmx::SelectionFileOption
• SelectionFileOptionInfo() : gmx::SelectionFileOptionInfo
• SelectionFileOptionStorage() : gmx::SelectionFileOptionStorage
• SelectionOption() : gmx::SelectionOption
• SelectionOptionBehavior() : gmx::SelectionOptionBehavior
• SelectionOptionInfo() : gmx::SelectionOptionInfo
• SelectionOptionManager() : gmx::SelectionOptionManager
• SelectionOptionStorage() : gmx::SelectionOptionStorage
• SelectionParserSymbolIterator() : gmx::SelectionParserSymbolIterator
• SelectionParserSymbolTable() : gmx::SelectionParserSymbolTable
• SelectionPosition() : gmx::SelectionPosition
• SelectionRequest() : gmx::SelectionOptionManager::Impl::SelectionRequest
• selectionText() : gmx::internal::SelectionData , gmx::Selection
• SelectionTopologyProperties() : gmx::SelectionTopologyProperties
• SelectionTreeElement() : gmx::SelectionTreeElement
• selectSingleFromArray() : gmx::AnalysisNeighborhoodPositions
• SelelemTemporaryValueAssigner() : anonymous_namespace{evaluate.cpp}::SelelemTemporaryValueAssigner
• SelMethodEvalContext() : gmx::SelMethodEvalContext
• sendCoordinatesToPme() : gmx::PmePpCommGpu::Impl
• sendCoordinatesToPmeFromCpu() : gmx::PmePpCommGpu
• sendCoordinatesToPmeFromGpu() : gmx::PmePpCommGpu
• sendEnergies() : gmx::MimicCommunicator
• sendForces() : gmx::MimicCommunicator
• sendFToPpCudaDirect() : gmx::PmeForceSenderGpu , gmx::PmeForceSenderGpu::Impl
• sendFToPpCudaMpi() : gmx::PmeForceSenderGpu , gmx::PmeForceSenderGpu::Impl
• sendInitData() : gmx::MimicCommunicator
• serialize() : gmx::AwhParams , gmx::WriteCheckpointDataHolder , StringTableEntry
• serializeStringTable() : StringTable
• set() : gmx::LincsGpu , gmx::SettleGpu , gmx::UpdateConstrainGpu::Impl , gmx::FlagsTemplate< FlagType >
• setAbsTol() : gmx::test::SimdBaseTest
• setAcceptBooleanNoPrefix() : gmx::OptionsAssigner
• setAllBlocksSizeOne() : gmx::RangePartitioning
• setAllowedValueCount() : gmx::SelectionOptionStorage
• setAnharmPolarization() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setAnyValue() : gmx::KeyValueTreeValueBuilder
• setArg() : PmeSolveKernel< gridOrdering, computeEnergyAndVirial, gridIndex, subGroupSize >
• setAtomProperties() : nonbonded_verlet_t
• setAtomProperty() : AtomProperties
• setAtoms() : gmx::test::SetAtomsTest
• SetAtoms() : gmx::SetAtoms
• SetAtomsTest() : gmx::test::SetAtomsTest
• setAverageDataSets() : gmx::AnalysisDataAverageModule
• setBound() : WorkDivision
• SetBox() : gmx::SetBox
• setBugText() : gmx::ICommandLineOptionsModuleSettings
• setCalculateAtomArea() : gmx::SurfaceAreaCalculator
• setCalculateSurfaceDots() : gmx::SurfaceAreaCalculator
• setCalculateVolume() : gmx::SurfaceAreaCalculator
• setCellIndices() : Nbnxm::Grid
• setCheckpointHandler() : gmx::CheckpointHelperBuilder
• setColumnCount() : gmx::AbstractAnalysisData , gmx::AnalysisData , gmx::AbstractAnalysisArrayData , gmx::AnalysisDataFrameLocalData< ValueType > , gmx::AnalysisDataFrameAverager , gmx::test::AnalysisDataTestInput
• setColumnFirstLineOffset() : gmx::TextTableFormatter
• setConstraints() : gmx::Constraints , gmx::SettleData
• setConsumptionLimits() : GpuEventSynchronizer
• setContinuationChar() : gmx::TextLineWrapperSettings
• setCoordValue() : gmx::BiasState , gmx::CoordState
• setCrossBondAngles() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setCrossBondBonds() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setCubic() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setCumulative() : gmx::AnalysisDataLifetimeModule
• setCutoff() : gmx::AnalysisNeighborhood
• setDataSetCount() : gmx::AbstractAnalysisData , gmx::AnalysisData , gmx::AnalysisDataFrameLocalData< ValueType >
• setDatasetTolerance() : gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
• setDebugLevel() : gmx::SelectionCollection
• setDefaultNiceLevel() : gmx::CommandLineModuleSettings
• setDefaultTolerance() : gmx::test::CommandLineTestBase , gmx::test::TestReferenceChecker
• setDefaultValue() : gmx::OptionStorageTemplate< T >
• setDefaultValueIfSet() : gmx::OptionStorageTemplate< T >
• setDescription() : gmx::AbstractOption
• setDimensions() : Nbnxm::Grid
• setDisplayName() : gmx::CommandLineProgramContext
• setDotCount() : gmx::SurfaceAreaCalculator
• setDynamicMask() : gmx::SelectionOptionInfo
• setEnergyOutputRequest() : gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting
• setError() : gmx::AnalysisDataValue
• setErrorsAsSeparateColumn() : gmx::AbstractPlotModule
• setEtaVelocity() : gmx::MttkData
• setEvaluateForces() : gmx::Selection , gmx::SelectionOptionInfo
• setEvaluateVelocities() : gmx::Selection , gmx::SelectionOptionInfo
• setExpectedDisplayName() : gmx::test::MockModule
• setFene() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setFileName() : gmx::AbstractPlotModule , gmx::analysismodules::anonymous_namespace{select.cpp}::IndexFileWriterModule
• setFirstColumnIndent() : gmx::TextTableFormatter
• setFirstLineIndent() : gmx::TextLineWrapperSettings
• setFitGroupIndices() : gmx::DensityFittingOptions
• setFlag() : gmx::AbstractOption , gmx::AbstractOptionStorage , gmx::TrajectoryAnalysisSettings
• setFlags() : gmx::internal::SelectionData , gmx::TrajectoryAnalysisSettings
• setFoldLastColumnToNextLine() : gmx::TextTableFormatter
• setForceParameter() : InteractionOfType
• SetForces() : gmx::SetForces
• setForceSendBuffer() : gmx::PmeForceSenderGpu , gmx::PmeForceSenderGpu::Impl
• setFrameFlags() : gmx::TrajectoryAnalysisSettings
• setFreeEnergy() : gmx::PointState
• setFreeEnergyPerturbationData() : gmx::StatePropagatorData::Element
• setFromHistory() : gmx::PointState
• setGlobalOutputTempDirectory() : gmx::test::TestFileManager
• setGroup() : anonymous_namespace{indexutil.cpp}::IndexBlockTest
• setHarmonic() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setHelpText() : gmx::CommandLineHelpWriter , gmx::ICommandLineOptionsModuleSettings , gmx::TrajectoryAnalysisSettings
• setHistogramSize() : gmx::HistogramSize
• setIndent() : gmx::TextLineWrapperSettings
• setIndexGroups() : gmx::SelectionCollection
• setIndicesInDomainDecomposition() : gmx::LocalAtomSetManager
• setInfo() : gmx::GromacsException
• setInitialReferenceWeightHistogram() : gmx::PointState
• 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
• setInteraction() : gmx::test::anonymous_namespace{nb_free_energy.cpp}::ListInput
• setKeepFinalSpaces() : gmx::TextLineWrapperSettings
• setKnownIssues() : gmx::CommandLineHelpWriter
• setLastNewline() : gmx::test::InteractiveTestHelper
• setLegend() : gmx::AbstractPlotModule
• setLinearAngle() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setLineLength() : gmx::TextLineWrapperSettings
• setLj14Interaction() : gmx::test::anonymous_namespace{pairs.cpp}::ListInput
• setLjc14Interaction() : gmx::test::anonymous_namespace{pairs.cpp}::ListInput
• setLjcnbInteraction() : gmx::test::anonymous_namespace{pairs.cpp}::ListInput
• setLocalAtomOrder() : Nbnxm::GridSet , nonbonded_verlet_t , PairSearch
• setLocalAtomSet() : gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup
• setLocalMMAtomSet() : gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup
• setLocalQMAtomSet() : gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup
• setLogger() : gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup , gmx::QMMMOptions
• setLogPmfSum() : gmx::PointState
• setMaxTime() : gmx::AnalysisDataDisplacementModule
• setMaxValueCount() : gmx::AbstractOptionStorage
• setMaxWarn() : gmx::test::SimulationRunner
• setMinValueCount() : gmx::AbstractOptionStorage
• setMode() : gmx::AnalysisNeighborhood
• setModifiableInputFile() : gmx::test::CommandLineTestBase
• setModuleDisplayName() : gmx::CommandLineHelpContext
• setModuleFlag() : gmx::test::FlagTest
• setModuleOverride() : gmx::CommandLineHelpModule
• setMorse() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setMSDHistogram() : gmx::AnalysisDataDisplacementModule
• setMultipoint() : gmx::AbstractAnalysisData , gmx::AnalysisData
• setName() : gmx::SelectionTreeElement
• setNewState() : gmx::FepStateSetting
• setNumColumnsMax() : Nbnxm::GridSet
• setNumPositionScalingVariables() : gmx::Propagator< integrationStage >
• setNumVelocityScalingVariables() : gmx::Propagator< integrationStage >
• 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::CommandLineHelpModule , gmx::CommandLineModuleManager
• setOutputTempDirectory() : gmx::test::TestFileManager
• setParrinelloRahmanBoxVelocities() : gmx::EnergyData
• setPartialWeightAndCount() : gmx::PointState
• setPbc() : gmx::ListedForcesGpu::Impl , gmx::UpdateConstrainGpu::Impl
• setPBC() : gmx::TrajectoryAnalysisSettings
• setPDihedrals() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setPeriodicBoundaryConditionType() : gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup , gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup
• setPlainOutput() : gmx::AbstractPlotModule
• setPoint() : gmx::AnalysisDataHandle
• setPoints() : gmx::AnalysisDataHandle
• setPolarization() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setPositionScaling() : gmx::MttkPropagatorConnection
• SetPrecision() : gmx::SetPrecision
• setPreviousBlockIndex() : gmx::CorrelationBlockData
• setQMExternalInputFile() : gmx::QMMMOptions
• setQMMMGroupIndices() : gmx::QMMMOptions
• setQuarticAngles() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setQuiet() : gmx::CommandLineModuleManager
• setRadii() : gmx::SurfaceAreaCalculator
• setRbDihedrals() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setReferencePosType() : gmx::SelectionCollection
• setReferenceTemperature() : gmx::ReferenceTemperatureManager
• setReplacement() : gmx::HelpWriterContext
• setRmPBC() : gmx::TrajectoryAnalysisSettings
• setRowCount() : gmx::AbstractAnalysisArrayData
• setScaleFactor() : gmx::DoubleOptionInfo , gmx::FloatOptionInfo , gmx::DoubleOptionStorage , gmx::FloatOptionStorage
• setSearchPathFromEnv() : gmx::DataFileFinder
• setSelectionCollection() : gmx::AnalysisDataPlotSettings
• setSelectionFlag() : gmx::SelectionOptionStorage
• setSelectionOptionValues() : gmx::test::ModuleSelection
• setSettings() : gmx::AbstractPlotModule
• setShowHidden() : gmx::CommandLineHelpContext , gmx::CommandLineHelpModule , gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::OptionsFilter
• setSignal() : gmx::CheckpointHandler , gmx::ResetHandler , gmx::StopHandler
• setSignals() : gmx::SimulationSignaller
• setSimulationTimeStep() : gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup
• setSingleModule() : gmx::CommandLineModuleManager
• SetStartTime() : gmx::SetStartTime
• setStartTime() : gmx::test::SetBothTimeTest , gmx::test::SetStartTimeTest
• setStepData() : gmx::test::anonymous_namespace{energyoutput.cpp}::EnergyOutputTest
• setStoreIsSet() : gmx::AbstractOption
• setSubtitle() : gmx::AbstractPlotModule
• setTargetConstantWeight() : gmx::PointState
• setTargetToZero() : gmx::PointState
• setTestSimulationDatabaseDirectory() : gmx::test::TestFileManager
• setTholePolarization() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• SetTimeStep() : gmx::SetTimeStep
• setTimeStep() : gmx::test::SetBothTimeTest , gmx::test::SetTimeStepTest
• setTimeUnit() : gmx::TimeUnitManager , gmx::AnalysisDataPlotSettings , gmx::TimeUnitBehavior
• setTimeUnitFromEnvironment() : gmx::TimeUnitBehavior
• setTimeUnitStore() : gmx::TimeUnitBehavior
• settings() : gmx::AbstractAverageHistogram , gmx::AnalysisDataSimpleHistogramModule , gmx::AnalysisDataWeightedHistogramModule , gmx::AnalysisDataBinAverageModule , gmx::anonymous_namespace{helpwritercontext.cpp}::IWrapper , gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToString , gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToVector , gmx::TextLineWrapper
• setTitle() : gmx::AbstractPlotModule
• SettleData() : gmx::SettleData
• SettleGpu() : gmx::SettleGpu
• SettleTest() : gmx::test::anonymous_namespace{settle.cpp}::SettleTest
• setTolerance() : gmx::test::anonymous_namespace{splinetable.cpp}::SplineTableTest< T >
• setTopology() : gmx::SelectionCollection , gmx::ITopologyHolderClient , gmx::PositionCalculationCollection , gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
• setTopologyExclusions() : gmx::AnalysisNeighborhood
• setTrajectory() : gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
• setTrimLeadingWhiteSpace() : gmx::TextReader
• setTrimTrailingComment() : gmx::TextReader
• setTrimTrailingWhiteSpace() : gmx::TextReader
• setType() : PreprocessingAtomTypes
• setUlpTol() : gmx::test::SimdBaseTest
• setUlpTolSingleAccuracy() : gmx::test::SimdBaseTest
• setUmbrellaGridpointToGridpoint() : gmx::BiasState , gmx::CoordState
• setup() : gmx::PmeLoadBalanceHelper
• SetUp() : gmx::anonymous_namespace{shake.cpp}::ShakeTest
• setup() : ListedForces , gmx::DomDecHelper , gmx::ISignaller , gmx::NeighborSearchSignaller , gmx::LastStepSignaller , gmx::LoggingSignaller , gmx::TrajectorySignaller , gmx::EnergySignaller , gmx::StatePropagatorData
• setupArrayData() : gmx::test::AnalysisDataTestFixture
• setupDataObject() : gmx::test::AnalysisDataTestFixture
• setupFepThreadedForceBuffer() : FreeEnergyDispatch
• setupGpuShortRangeWork() : nonbonded_verlet_t
• setupGrompp() : gmx::test::BondedInteractionsTest , gmx::test::MimicTest
• setupMdrun() : gmx::test::BondedInteractionsTest
• setupReduction() : gmx::ThreadedForceBuffer< ForceBufferElementType >
• setupRerun() : gmx::test::MimicTest
• SetUpTestSuite() : gmx::test::MdrunTestFixtureBase , gmx::test::anonymous_namespace{pmetest.cpp}::PmeTest
• setUreyBradley() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• setValue() : gmx::KeyValueTreeValueBuilder , gmx::AnalysisDataValue , gmx::AnalysisDataStorageFrame
• setValueCount() : gmx::AbstractOption , gmx::SelectionOptionInfo
• setVector() : gmx::AbstractOption
• SetVelocities() : gmx::SetVelocities
• setVelocityScaling() : gmx::MttkPropagatorConnection
• setVirtualSites() : gmx::VirtualSitesHandler::Impl , gmx::ThreadingInfo , gmx::VirtualSitesHandler
• setWarninp() : gmx::QMMMOptions
• setWaterPolarization() : gmx::test::anonymous_namespace{bonded.cpp}::iListInput
• 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
• shareBiasMultisim() : gmx::AwhParams
• SharedState() : gmx::HelpWriterContext::Impl::SharedState
• shellCompletionWriter() : gmx::CommandLineHelpContext
• shiftForces() : gmx::ForceWithShiftForces , ForceHelperBuffers , gmx::ThreadForceBuffer< ForceBufferElementType >
• shortDescription() : gmx::CommandLineHelpModule , gmx::ICommandLineModule , gmx::anonymous_namespace{cmdlinemodulemanager.cpp}::CMainCommandLineModule , anonymous_namespace{legacymodules.cpp}::ObsoleteToolModule , gmx::test::MockModule
• shouldBackup() : gmx::CommandLineCommonOptionsHolder
• shouldBeQuiet() : gmx::CommandLineCommonOptionsHolder
• shouldContinueComparing() : gmx::test::anonymous_namespace{exactcontinuation.cpp}::ContinuationFramePairManager< FrameReader >
• shouldIgnore() : gmx::test::TestReferenceChecker::Impl
• shouldIgnoreActualModule() : gmx::CommandLineCommonOptionsHolder
• shouldNotifyImmediately() : gmx::internal::AnalysisDataStorageImpl
• shouldShowHelp() : gmx::CommandLineCommonOptionsHolder
• shouldShowHidden() : gmx::CommandLineCommonOptionsHolder
• showHidden() : gmx::CommandLineHelpContext
• shrinkSimplexPointsExceptBest() : gmx::NelderMeadSimplex
• signal() : gmx::ISignaller , gmx::LastStepSignaller , gmx::LoggingSignaller , gmx::NeighborSearchSignaller , gmx::EnergySignaller , gmx::TrajectorySignaller
• signalInterSim() : gmx::SimulationSignaller
• signalSettingStep() : gmx::FepStateSetting
• signsDiffer() : gmx::test::FloatingPointDifference
• Simd4DBool() : gmx::Simd4DBool
• Simd4Double() : gmx::Simd4Double
• Simd4FBool() : gmx::Simd4FBool
• Simd4Float() : gmx::Simd4Float
• SimdArrayRef() : gmx::internal::SimdArrayRef< T >
• SimdBaseTest() : gmx::test::SimdBaseTest
• SimdDBool() : gmx::SimdDBool
• SimdDIBool() : gmx::SimdDIBool
• SimdDInt32() : gmx::SimdDInt32
• SimdDouble() : gmx::SimdDouble
• SimdFBool() : gmx::SimdFBool
• SimdFIBool() : gmx::SimdFIBool
• SimdFInt32() : gmx::SimdFInt32
• SimdFloat() : gmx::SimdFloat
• similarity() : gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityInnerProduct , gmx::DensitySimilarityMeasure , gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityRelativeEntropy , gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityCrossCorrelation
• SimulationAlgorithmSetupError() : gmx::SimulationAlgorithmSetupError
• SimulationContext() : gmx::SimulationContext
• simulationData() : gmx::ModularSimulatorAlgorithmBuilderHelper
• SimulationInputHandle() : gmx::SimulationInputHandle
• SimulationInstabilityError() : gmx::SimulationInstabilityError
• SimulationRunner() : gmx::test::SimulationRunner
• SimulationSignal() : gmx::SimulationSignal
• SimulationSignaller() : gmx::SimulationSignaller
• simulationSignals() : gmx::GlobalCommunicationHelper
• simulationTimeStep() : gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup
• SimulatorConfig() : gmx::SimulatorConfig
• SimulatorEnv() : gmx::SimulatorEnv
• SimulatorStateData() : gmx::SimulatorStateData
• Site() : gmx::Site
• sites() : gmx::IRestraintPotential
• size() : gmx::FixedCapacityVector< typename, size_t > , gmx::KeyValueTreePath , gmx::Range< typename > , gmx::ListOfLists< typename > , PreprocessingAtomTypes , gmx::HashedMap< T > , gmx::ArrayRefWithPadding< typename > , gmx::ArrayRef< typename > , gmx::ThreadForceBuffer< ForceBufferElementType > , gmx::EnumerationArray< EnumType, DataType, ArraySize > , gmx::internal::SimdArrayRef< T > , InteractionsOfType , gmx::test::AnalysisDataTestInputPointSet , PreprocessingBondAtomType , gmx::HostInteractionList , gmx::PaddedVector< T, Allocator >
• skipRemainingPairsForTestPosition() : gmx::AnalysisNeighborhoodPairSearch
• skipUnknown() : gmx::CommandLineParser
• skipUpdates() : gmx::BiasParams
• sliced_extents() : gmx::detail::extents_analyse< R, E0, StaticExtents...> , gmx::extents< StaticExtents > , gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...>
• SolveTestBody() : gmx::test::anonymous_namespace{pmesolvetest.cpp}::SolveTestBody
• sortAtomIds() : InteractionOfType
• spacing() : gmx::GridAxis
• spawnThreads() : gmx::Mdrunner
• SplineAndSpreadTestBody() : gmx::test::anonymous_namespace{pmesplinespreadtest.cpp}::SplineAndSpreadTestBody
• spread() : gmx::GaussianOn1DLattice
• spreadForces() : gmx::VirtualSitesHandler::Impl , gmx::VirtualSitesHandler
• srcAtomBegin() : Nbnxm::Grid
• srcAtomEnd() : Nbnxm::Grid
• ssize() : gmx::FixedCapacityVector< typename, size_t > , gmx::ArrayRef< typename > , gmx::ListOfLists< typename >
• standardDeviation() : gmx::AnalysisDataAverageModule
• standardError() : gmx::TextOutputFile
• standardOutput() : gmx::anonymous_namespace{fileredirector.cpp}::DefaultOutputRedirector , gmx::TextOutputFile , gmx::test::TestFileOutputRedirector , gmx::IFileOutputRedirector
• start() : nbnxn_cycle_t , gmx::AnalysisHistogramSettingsInitializer , gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::SynopsisFormatter , gmx::OptionsAssigner , SearchCycleCounting , gmx::internal::OptionSectionImpl
• startContext() : gmx::MessageStringCollector
• startData() : gmx::AnalysisData
• startDataStorage() : gmx::AnalysisDataStorage
• startFormatting() : gmx::TextTableFormatter::Impl::ColumnData
• startFrame() : gmx::AnalysisDataStorage , gmx::AnalysisDataHandle , gmx::internal::AnalysisDataStorageFrameData , gmx::AnalysisDataStorage
• startFrames() : gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance , gmx::TrajectoryAnalysisModule , gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf , gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa
• startModuleExport() : gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::IHelpExport , gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportReStructuredText , gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportCompletion
• startModuleGroupExport() : gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::IHelpExport , gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportCompletion , gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportReStructuredText
• startOption() : gmx::OptionsAssigner
• startPairSearch() : gmx::AnalysisNeighborhoodSearch
• startParallelDataStorage() : gmx::AnalysisDataStorage
• startReferenceData() : gmx::test::MockAnalysisDataModule::Impl
• startReferenceFrame() : gmx::test::MockAnalysisDataModule::Impl
• startSection() : gmx::RepeatingOptionSectionStorage< T > , gmx::OptionsAssigner , gmx::IOptionSectionStorage , gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::OptionsListFormatter
• startSelfPairSearch() : gmx::AnalysisNeighborhoodSearch
• startSet() : gmx::AbstractOptionStorage
• startSource() : gmx::AbstractOptionStorage
• startupInfoFile() : gmx::CommandLineCommonOptionsHolder
• state() : gmx::Bias , gmx::ExponentialMovingAverage
• StatePropagatorData() : gmx::StatePropagatorData
• static_extent() : gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...> , gmx::detail::extents_analyse< 0 > , gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy > , gmx::detail::extents_analyse< R, E0, StaticExtents...> , gmx::extents< StaticExtents >
• StaticAverageHistogram() : gmx::anonymous_namespace{histogram.cpp}::StaticAverageHistogram
• StaticDataFrameHeaderChecker() : gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataFrameHeaderChecker
• StaticDataPointsChecker() : gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataPointsChecker
• StaticDataPointsStorageChecker() : gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataPointsStorageChecker
• stddev() : gmx::NormalDistribution< RealType >::param_type , gmx::NormalDistribution< RealType > , gmx::TabulatedNormalDistribution< RealType, tableBits > , gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type
• StdioTestHelper() : gmx::test::StdioTestHelper
• step() : gmx::TrajectoryFrame
• stepping() : gmx::CpuInfo
• stop() : SearchCycleCounting , nbnxn_cycle_t
• StopConditionSignal() : gmx::StopConditionSignal
• StopConditionTime() : gmx::StopConditionTime
• StopHandler() : gmx::StopHandler
• stoppingAfterCurrentStep() : gmx::StopHandler
• storageImpl() : gmx::internal::AnalysisDataStorageFrameData
• store() : gmx::OptionTemplate< T, U >
• storeAll() : gmx::internal::AnalysisDataStorageImpl
• storeBuilderData() : gmx::ModularSimulatorAlgorithmBuilderHelper
• storeCount() : gmx::OptionTemplate< T, U >
• storeElement() : gmx::ModularSimulatorAlgorithmBuilderHelper
• storeIsSet() : gmx::OptionTemplate< T, U >
• storeSimulationData() : gmx::ModularSimulatorAlgorithmBuilderHelper
• storeState() : gmx::PointState , gmx::HistogramSize
• storeVector() : gmx::OptionTemplate< T, U > , gmx::RepeatingOptionSection< T >
• stream() : gmx::DeviceStreamManager , DeviceStream
• streamIsValid() : gmx::DeviceStreamManager
• stride() : gmx::layout_right::mapping< Extents > , gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
• StringCompare() : gmx::StringCompare
• StringFormatter() : gmx::StringFormatter
• StringInputStream() : gmx::StringInputStream
• StringKeywordMatchItem() : anonymous_namespace{sm_keywords.cpp}::StringKeywordMatchItem
• StringOption() : gmx::StringOption
• StringOptionInfo() : gmx::StringOptionInfo
• StringOptionStorage() : gmx::StringOptionStorage
• StringTable() : StringTable
• StringTableEntry() : StringTableEntry
• stringValue() : gmx::SelectionParserValue
• subArray() : gmx::ArrayRef< typename >
• subblockStart() : BiasOutputSetup
• subRange() : gmx::RangePartitioning
• subscribe() : gmx::MDModulesNotifier< CallParameter, MDModulesNotifierBase > , gmx::BuildMDModulesNotifier<>::NoCallParameter
• Subscriber() : gmx::test::anonymous_namespace{observablesreducer.cpp}::Subscriber
• subscribeToPreProcessingNotifications() : gmx::MDModules , gmx::RestraintMDModule , gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting , gmx::IMDModule , gmx::anonymous_namespace{qmmm.cpp}::QMMM , gmx::anonymous_namespace{electricfield.cpp}::ElectricField
• subscribeToSimulationSetupNotifications() : gmx::anonymous_namespace{electricfield.cpp}::ElectricField , gmx::MDModules , gmx::IMDModule , gmx::RestraintMDModule , gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting , gmx::anonymous_namespace{qmmm.cpp}::QMMM
• substituteMarkupAndWrapToString() : gmx::HelpWriterContext
• substituteMarkupAndWrapToVector() : gmx::HelpWriterContext
• sumOverBlocksBlockSquareWeight() : gmx::CorrelationBlockData
• sumOverBlocksSquareBlockWeight() : gmx::CorrelationBlockData
• supportLevel() : gmx::CpuInfo , gmx::HardwareTopology
• SurfaceAreaCalculator() : gmx::SurfaceAreaCalculator
• swap() : gmx::ArrayRefWithPadding< typename > , gmx::PaddedVector< T, Allocator > , gmx::MultiDimArray< TContainer, Extents, LayoutPolicy > , gmx::ArrayRef< typename >
• swap_group() : swap_group
• swapOutWorst() : gmx::NelderMeadSimplex
• synchronize() : DeviceStream
• synchronizeOnCoordinatesFromAllPpRanks() : gmx::PmeCoordinateReceiverGpu::Impl
• synchronizeOnCoordinatesFromPpRank() : gmx::PmeCoordinateReceiverGpu::Impl
• syncNodes() : gmx::ImdSession::Impl
• SynopsisFormatter() : gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::SynopsisFormatter