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• sampleCount() : gmx::AnalysisDataAverageModule
• saveEdsamPointer() : gmx::Constraints
• scaleAll() : gmx::AbstractAverageHistogram
• scaleAllByVector() : gmx::AbstractAverageHistogram
• scaleBox() : EwaldBoxZScaler
• scaleOperationOnly() : gmx::TranslateAndScale
• scaleSingle() : gmx::AbstractAverageHistogram
• scheduleCheckOfLocalTopology() : gmx::LocalTopologyChecker
• scopedTransform() : gmx::IKeyValueTreeTransformRules
• seed() : 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::SelectionCollection
• selectionCollection() : gmx::AnalysisDataPlotSettings
• SelectionFileOption() : gmx::SelectionFileOption
• SelectionFileOptionInfo() : gmx::SelectionFileOptionInfo
• SelectionOption() : gmx::SelectionOption
• SelectionOptionBehavior() : gmx::SelectionOptionBehavior
• SelectionOptionInfo() : gmx::SelectionOptionInfo
• SelectionOptionManager() : gmx::SelectionOptionManager
• SelectionPosition() : gmx::SelectionPosition
• selectionText() : gmx::Selection
• SelectionTopologyProperties() : gmx::SelectionTopologyProperties
• selectSingleFromArray() : gmx::AnalysisNeighborhoodPositions
• sendCoordinatesToPmeFromCpu() : gmx::PmePpCommGpu
• sendCoordinatesToPmeFromGpu() : gmx::PmePpCommGpu
• sendFToPpCudaDirect() : gmx::PmeForceSenderGpu
• sendFToPpCudaMpi() : gmx::PmeForceSenderGpu
• serialize() : gmx::WriteCheckpointDataHolder , StringTableEntry
• serializeStringTable() : StringTable
• set() : gmx::FlagsTemplate< FlagType >
• setAcceptBooleanNoPrefix() : gmx::OptionsAssigner
• setAllBlocksSizeOne() : gmx::RangePartitioning
• setAnyValue() : gmx::KeyValueTreeValueBuilder
• setAtomProperties() : nonbonded_verlet_t
• setAtomProperty() : AtomProperties
• SetAtoms() : gmx::SetAtoms
• setAverageDataSets() : gmx::AnalysisDataAverageModule
• SetBox() : gmx::SetBox
• setBugText() : gmx::ICommandLineOptionsModuleSettings
• setColumnCount() : gmx::AbstractAnalysisData , gmx::AnalysisData , gmx::AbstractAnalysisArrayData , gmx::test::AnalysisDataTestInput
• 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
• setFileName() : gmx::AbstractPlotModule
• setFirstColumnIndent() : gmx::TextTableFormatter
• setFirstLineIndent() : gmx::TextLineWrapperSettings
• setFlag() : gmx::AbstractOption , gmx::AbstractOptionStorage , gmx::TrajectoryAnalysisSettings
• setFlags() : 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
• 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::AnalysisDataWeightedHistogramModule , gmx::AbstractAverageHistogram , gmx::AnalysisDataSimpleHistogramModule , 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
• setupFepThreadedForceBuffer() : FreeEnergyDispatch
• setupGpuShortRangeWork() : nonbonded_verlet_t
• setValue() : gmx::AnalysisDataValue , gmx::AnalysisDataStorageFrame , gmx::KeyValueTreeValueBuilder
• 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
• shellCompletionWriter() : gmx::CommandLineHelpContext
• shiftForces() : gmx::ForceWithShiftForces , ForceHelperBuffers
• shortDescription() : gmx::ICommandLineModule
• showHidden() : gmx::CommandLineHelpContext
• signalInterSim() : gmx::SimulationSignaller
• 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
• similarity() : gmx::DensitySimilarityMeasure
• SimulationAlgorithmSetupError() : gmx::SimulationAlgorithmSetupError
• SimulationContext() : gmx::SimulationContext
• SimulationInstabilityError() : gmx::SimulationInstabilityError
• SimulationSignal() : gmx::SimulationSignal
• SimulationSignaller() : gmx::SimulationSignaller
• SimulatorConfig() : gmx::SimulatorConfig
• SimulatorEnv() : gmx::SimulatorEnv
• SimulatorStateData() : gmx::SimulatorStateData
• Site() : gmx::Site
• sites() : gmx::IRestraintPotential
• size() : gmx::ListOfLists< typename > , gmx::HashedMap< T > , gmx::ArrayRefWithPadding< typename > , gmx::PaddedVector< T, Allocator > , gmx::KeyValueTreePath , gmx::test::AnalysisDataTestInputPointSet , InteractionsOfType , gmx::FixedCapacityVector< typename, size_t > , gmx::ArrayRef< typename > , gmx::Range< typename > , PreprocessingBondAtomType , PreprocessingAtomTypes , gmx::EnumerationArray< EnumType, DataType, ArraySize >
• 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...>
• sortAtomIds() : InteractionOfType
• spawnThreads() : gmx::Mdrunner
• spreadForces() : gmx::VirtualSitesHandler
• ssize() : gmx::FixedCapacityVector< typename, size_t > , gmx::ArrayRef< typename > , gmx::ListOfLists< typename >
• standardDeviation() : gmx::AnalysisDataAverageModule
• standardError() : gmx::TextOutputFile
• standardOutput() : gmx::test::TestFileOutputRedirector , gmx::IFileOutputRedirector , gmx::TextOutputFile
• start() : gmx::AnalysisHistogramSettingsInitializer , gmx::OptionsAssigner , nbnxn_cycle_t
• startContext() : gmx::MessageStringCollector
• startData() : gmx::AnalysisData
• startDataStorage() : gmx::AnalysisDataStorage
• startFrame() : gmx::AnalysisDataStorage , gmx::AnalysisDataHandle , gmx::AnalysisDataStorage
• startFrames() : gmx::TrajectoryAnalysisModule
• startOption() : gmx::OptionsAssigner
• startPairSearch() : gmx::AnalysisNeighborhoodSearch
• startParallelDataStorage() : gmx::AnalysisDataStorage
• startSection() : gmx::OptionsAssigner
• startSelfPairSearch() : gmx::AnalysisNeighborhoodSearch
• startSet() : gmx::AbstractOptionStorage
• startSource() : gmx::AbstractOptionStorage
• state() : gmx::ExponentialMovingAverage
• static_extent() : gmx::detail::extents_analyse< R, E0, StaticExtents...> , gmx::detail::extents_analyse< 0 > , gmx::extents< StaticExtents > , gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy > , gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...>
• stddev() : gmx::NormalDistribution< RealType > , gmx::NormalDistribution< RealType >::param_type , gmx::TabulatedNormalDistribution< RealType, tableBits > , gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type
• StdioTestHelper() : gmx::test::StdioTestHelper
• 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 >
• storeIsSet() : gmx::OptionTemplate< T, U >
• 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
• StringOption() : gmx::StringOption
• StringOptionInfo() : gmx::StringOptionInfo
• StringTable() : StringTable
• StringTableEntry() : StringTableEntry
• subArray() : gmx::ArrayRef< typename >
• subRange() : gmx::RangePartitioning
• subscribe() : gmx::MDModulesNotifier< CallParameter, MDModulesNotifierBase >
• subscribeToPreProcessingNotifications() : gmx::IMDModule , gmx::MDModules , gmx::RestraintMDModule
• subscribeToSimulationSetupNotifications() : gmx::MDModules , gmx::IMDModule , gmx::RestraintMDModule
• substituteMarkupAndWrapToString() : gmx::HelpWriterContext
• substituteMarkupAndWrapToVector() : gmx::HelpWriterContext
• supportLevel() : gmx::CpuInfo , gmx::HardwareTopology
• swap() : gmx::PaddedVector< T, Allocator > , gmx::ArrayRefWithPadding< typename > , gmx::ArrayRef< typename > , gmx::MultiDimArray< TContainer, Extents, LayoutPolicy >
• synchronize() : DeviceStream