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- s -
sampleCoordAndPmf() :
gmx::BiasState
sampleCount() :
gmx::AnalysisDataFrameAverager
,
gmx::AnalysisDataAverageModule
samplePmf() :
gmx::PointState
sampleProbabilityWeights() :
gmx::BiasState
sampleUmbrellaGridpoint() :
gmx::CoordState
SansDebye() :
gmx::SansDebye
SasaModuleData() :
gmx::analysismodules::anonymous_namespace{sasa.cpp}::SasaModuleData
saveCheckpointState() :
gmx::ParrinelloRahmanBarostat
,
gmx::PullElement
,
gmx::EnergyData::Element
,
gmx::StatePropagatorData::Element
,
gmx::VelocityScalingTemperatureCoupling
,
gmx::ExpandedEnsembleElement
,
gmx::FirstOrderPressureCoupling
,
gmx::FreeEnergyPerturbationData::Element
,
gmx::ICheckpointHelperClient
,
gmx::MttkData
,
gmx::NoseHooverChainsData
saveEdsamPointer() :
gmx::Constraints
SaxsDebye() :
gmx::SaxsDebye
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::AnalysisDataStorageFrame
,
gmx::AnalysisDataHandle
selected() :
gmx::SelectionPosition
Selection() :
gmx::Selection
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
selfEnergy() :
gmx::CoulombCalculator< KernelCoulombType::RF >
,
gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical >
,
gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated >
SelMethodEvalContext() :
gmx::SelMethodEvalContext
sendCoordinatesToPme() :
gmx::PmePpCommGpu::Impl
sendCoordinatesToPmeFromCpu() :
gmx::PmePpCommGpu
sendCoordinatesToPmeFromGpu() :
gmx::PmePpCommGpu
sendEnergies() :
gmx::MimicCommunicator
sendForces() :
gmx::MimicCommunicator
sendFToPpGpuAwareMpi() :
gmx::PmeForceSenderGpu
,
gmx::PmeForceSenderGpu::Impl
sendFToPpPeerToPeer() :
gmx::PmeForceSenderGpu
,
gmx::PmeForceSenderGpu::Impl
sendInitData() :
gmx::MimicCommunicator
serialize() :
gmx::AwhParams
,
gmx::WriteCheckpointDataHolder
,
StringTableEntry
serializeParticle() :
SimulationParticle
serializeStringTable() :
StringTable
set() :
gmx::LincsGpu
,
gmx::SettleGpu
,
gmx::UpdateConstrainGpu::Impl
,
gmx::FlagsTemplate< FlagType >
set_unit_system() :
gmx::ColvarProxyGromacs
setAbsTol() :
gmx::test::SimdBaseTest
setAcceptBooleanNoPrefix() :
gmx::OptionsAssigner
setAllowedValueCount() :
gmx::SelectionOptionStorage
setAlternateStepPpTaskCompletionEvent() :
gmx::MdGpuGraph::Impl
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
setBinWidth() :
gmx::ComputeDebyeScattering
setBound() :
WorkDivision
SetBox() :
gmx::SetBox
setBreak() :
gmx::analysismodules::anonymous_namespace{dssp.cpp}::SecondaryStructuresData
setBridge() :
gmx::analysismodules::anonymous_namespace{dssp.cpp}::SecondaryStructuresData
setBugText() :
gmx::ICommandLineOptionsModuleSettings
setCalculateAtomArea() :
gmx::SurfaceAreaCalculator
setCalculateSurfaceDots() :
gmx::SurfaceAreaCalculator
setCalculateVolume() :
gmx::SurfaceAreaCalculator
setCellIndices() :
Nbnxm::Grid
setCheckpointHandler() :
gmx::CheckpointHelperBuilder
setColumnCount() :
gmx::AnalysisDataFrameLocalData< ValueType >
,
gmx::AnalysisDataFrameAverager
,
gmx::test::AnalysisDataTestInput
,
gmx::AbstractAnalysisData
,
gmx::AnalysisData
,
gmx::AbstractAnalysisArrayData
setColumnFirstLineOffset() :
gmx::TextTableFormatter
setComm() :
gmx::ColvarsSimulationsParameters
setConstraints() :
gmx::Constraints
,
gmx::SettleData
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::AnalysisDataFrameLocalData< ValueType >
,
gmx::AbstractAnalysisData
,
gmx::AnalysisData
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
setEnergyGroups() :
gmx::EnergyGroupsPerCluster
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
setFileAndLineNumber() :
WarningHandler
setFileName() :
gmx::analysismodules::anonymous_namespace{select.cpp}::IndexFileWriterModule
,
gmx::AbstractPlotModule
setFirstColumnIndent() :
gmx::TextTableFormatter
setFirstLineIndent() :
gmx::TextLineWrapperSettings
setFitGroupIndices() :
gmx::DensityFittingOptions
setFlag() :
gmx::AbstractOptionStorage
,
gmx::AbstractOption
,
gmx::TrajectoryAnalysisSettings
setFlags() :
t_state
,
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
setHelixPosition() :
gmx::analysismodules::anonymous_namespace{dssp.cpp}::SecondaryStructuresData
setHelpText() :
gmx::CommandLineHelpWriter
,
gmx::ICommandLineOptionsModuleSettings
,
gmx::TrajectoryAnalysisSettings
setHistogramSize() :
gmx::HistogramSize
setIndent() :
gmx::TextLineWrapperSettings
setIndex() :
gmx::analysismodules::anonymous_namespace{dssp.cpp}::ResInfo
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
setLocalAtomSetManager() :
gmx::ColvarsSimulationsParameters
setLocalMMAtomSet() :
gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup
setLocalQMAtomSet() :
gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup
setLogger() :
gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup
,
gmx::QMMMOptions
,
gmx::ColvarsOptions
,
gmx::ColvarsSimulationsParameters
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
setParameters() :
gmx::ColvarsOptions
setParrinelloRahmanBoxVelocities() :
gmx::EnergyData
setPartialWeightAndCount() :
gmx::PointState
setPBC() :
gmx::TrajectoryAnalysisSettings
setPbc() :
gmx::ListedForcesGpu::Impl
,
gmx::UpdateConstrainGpu::Impl
setPDihedrals() :
gmx::test::anonymous_namespace{bonded.cpp}::iListInput
setPeriodicBoundaryConditionType() :
gmx::ColvarsSimulationsParameters
,
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::DoubleOptionStorage
,
gmx::FloatOptionStorage
,
gmx::DoubleOptionInfo
,
gmx::FloatOptionInfo
setSearchPathFromEnv() :
gmx::DataFileFinder
setSecondaryStructureType() :
gmx::analysismodules::anonymous_namespace{dssp.cpp}::SecondaryStructuresData
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::ColvarsSimulationsParameters
,
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
setStoreData() :
gmx::EnergyTerm
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::test::SetTimeStepTest
,
gmx::test::SetBothTimeTest
SetTimeStep() :
gmx::SetTimeStep
setTimeUnit() :
gmx::AnalysisDataPlotSettings
,
gmx::TimeUnitManager
,
gmx::TimeUnitBehavior
setTimeUnitFromEnvironment() :
gmx::TimeUnitBehavior
setTimeUnitStore() :
gmx::TimeUnitBehavior
settings() :
gmx::AnalysisDataSimpleHistogramModule
,
gmx::anonymous_namespace{helpwritercontext.cpp}::IWrapper
,
gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToString
,
gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToVector
,
gmx::AbstractAverageHistogram
,
gmx::AnalysisDataWeightedHistogramModule
,
gmx::AnalysisDataBinAverageModule
,
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::PositionCalculationCollection
,
gmx::ColvarsSimulationsParameters
,
gmx::ITopologyHolderClient
,
gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
,
gmx::SelectionCollection
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::ISignaller
,
gmx::LoggingSignaller
SetUp() :
gmx::anonymous_namespace{shake.cpp}::ShakeTest
setup() :
ListedForces
,
gmx::DomDecHelper
,
gmx::PmeLoadBalanceHelper
,
gmx::NeighborSearchSignaller
,
gmx::LastStepSignaller
,
gmx::TrajectorySignaller
,
gmx::EnergySignaller
,
gmx::StatePropagatorData
setupArrayData() :
gmx::test::AnalysisDataTestFixture
setupDataObject() :
gmx::test::AnalysisDataTestFixture
setupFepThreadedForceBuffer() :
FreeEnergyDispatch
setupGpuShortRangeWork() :
nonbonded_verlet_t
setupGrompp() :
gmx::test::MimicTest
,
gmx::test::BondedInteractionsTest
setupMdrun() :
gmx::test::BondedInteractionsTest
setupReduction() :
gmx::ThreadedForceBuffer< ForceBufferElementType >
setupRerun() :
gmx::test::MimicTest
SetUpTestSuite() :
anonymous_namespace{domain_decomposition.cpp}::DomDecSpecialCasesTest
,
gmx::test::MdrunTestFixtureBase
,
gmx::test::anonymous_namespace{pmetest.cpp}::PmeTest
setUreyBradley() :
gmx::test::anonymous_namespace{bonded.cpp}::iListInput
setUsedGraphLastStep() :
gmx::MdGpuGraph::Impl
setValue() :
gmx::AnalysisDataStorageFrame
,
gmx::KeyValueTreeValueBuilder
,
gmx::AnalysisDataValue
setValueCount() :
gmx::AbstractOption
,
gmx::SelectionOptionInfo
setVector() :
gmx::AbstractOption
SetVelocities() :
gmx::SetVelocities
setVelocityScaling() :
gmx::MttkPropagatorConnection
setVirtualSites() :
gmx::VirtualSitesHandler
,
gmx::ThreadingInfo
,
gmx::VirtualSitesHandler::Impl
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() :
anonymous_namespace{legacymodules.cpp}::ObsoleteToolModule
,
gmx::CommandLineHelpModule
,
gmx::ICommandLineModule
,
gmx::anonymous_namespace{cmdlinemodulemanager.cpp}::CMainCommandLineModule
,
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::EnergySignaller
,
gmx::LastStepSignaller
,
gmx::TrajectorySignaller
,
gmx::LoggingSignaller
,
gmx::NeighborSearchSignaller
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
simdMasks() :
nbnxn_atomdata_t
similarity() :
gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityInnerProduct
,
gmx::DensitySimilarityMeasure
,
gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityCrossCorrelation
,
gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityRelativeEntropy
SimulationAlgorithmSetupError() :
gmx::SimulationAlgorithmSetupError
SimulationContext() :
gmx::SimulationContext
simulationData() :
gmx::ModularSimulatorAlgorithmBuilderHelper
SimulationInputHandle() :
gmx::SimulationInputHandle
SimulationInstabilityError() :
gmx::SimulationInstabilityError
SimulationParticle() :
SimulationParticle
SimulationRunner() :
gmx::test::SimulationRunner
SimulationSignal() :
gmx::SimulationSignal
SimulationSignaller() :
gmx::SimulationSignaller
simulationSignals() :
gmx::GlobalCommunicationHelper
simulationTimeStep() :
gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup
,
gmx::ColvarsSimulationsParameters
SimulatorBuilder() :
gmx::SimulatorBuilder
SimulatorConfig() :
gmx::SimulatorConfig
SimulatorEnv() :
gmx::SimulatorEnv
SimulatorStateData() :
gmx::SimulatorStateData
Site() :
gmx::Site
sites() :
gmx::IRestraintPotential
size() :
gmx::HashedMap< T >
,
PreprocessingBondAtomType
,
gmx::HostInteractionList
,
JClusterList
,
PackedJClusterList
,
gmx::internal::SimdArrayRef< T >
,
gmx::KeyValueTreePath
,
gmx::EnumerationArray< EnumType, DataType, ArraySize >
,
gmx::Range< typename >
,
gmx::test::AnalysisDataTestInputPointSet
,
gmx::ListOfLists< typename >
,
InteractionsOfType
,
PreprocessingAtomTypes
,
gmx::ArrayRef< typename >
,
gmx::ThreadForceBuffer< ForceBufferElementType >
,
InteractionList
,
gmx::FixedCapacityVector< typename, size_t >
,
gmx::PaddedVector< T, Allocator >
,
gmx::ArrayRefWithPadding< typename >
,
t_ilist
skipRemainingPairsForTestPosition() :
gmx::AnalysisNeighborhoodPairSearch
skipUnknown() :
gmx::CommandLineParser
skipUpdates() :
gmx::BiasParams
sliced_extents() :
gmx::extents< StaticExtents >
,
gmx::detail::extents_analyse< R, E0, StaticExtents...>
,
gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...>
slopeOfLinearFit() :
gmx::EnergyTerm
solveCoulombYZX() :
PmeSolve
solveLJYZX() :
PmeSolve
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::ListOfLists< typename >
,
gmx::FixedCapacityVector< typename, size_t >
,
gmx::ArrayRef< typename >
standardDeviation() :
gmx::EnergyTerm
,
gmx::AnalysisDataAverageModule
standardError() :
gmx::TextOutputFile
standardOutput() :
gmx::anonymous_namespace{fileredirector.cpp}::DefaultOutputRedirector
,
gmx::test::TestFileOutputRedirector
,
gmx::IFileOutputRedirector
,
gmx::TextOutputFile
start() :
gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::SynopsisFormatter
,
gmx::OptionsAssigner
,
gmx::internal::OptionSectionImpl
,
SearchCycleCounting
,
gmx::AnalysisHistogramSettingsInitializer
,
nbnxn_cycle_t
startContext() :
gmx::MessageStringCollector
startData() :
gmx::AnalysisData
startDataStorage() :
gmx::AnalysisDataStorage
startFormatting() :
gmx::TextTableFormatter::Impl::ColumnData
startFrame() :
gmx::AnalysisDataStorage
,
gmx::internal::AnalysisDataStorageFrameData
,
gmx::AnalysisDataHandle
,
gmx::AnalysisDataStorage
startFrames() :
gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf
,
gmx::TrajectoryAnalysisModule
,
gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa
,
gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance
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}::HelpExportCompletion
,
gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportReStructuredText
,
gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::IHelpExport
startOption() :
gmx::OptionsAssigner
startPairSearch() :
gmx::AnalysisNeighborhoodSearch
startParallelDataStorage() :
gmx::AnalysisDataStorage
startRecord() :
gmx::MdGpuGraph::Impl
startReferenceData() :
gmx::test::MockAnalysisDataModule::Impl
startReferenceFrame() :
gmx::test::MockAnalysisDataModule::Impl
startSection() :
gmx::IOptionSectionStorage
,
gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::OptionsListFormatter
,
gmx::OptionsAssigner
,
gmx::RepeatingOptionSectionStorage< T >
startSelfPairSearch() :
gmx::AnalysisNeighborhoodSearch
startSet() :
gmx::AbstractOptionStorage
startSource() :
gmx::AbstractOptionStorage
startupInfoFile() :
gmx::CommandLineCommonOptionsHolder
state() :
gmx::ExponentialMovingAverage
,
gmx::Bias
StatePropagatorData() :
gmx::StatePropagatorData
static_extent() :
gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
,
gmx::detail::extents_analyse< R, E0, StaticExtents...>
,
gmx::extents< StaticExtents >
,
gmx::detail::extents_analyse< 0 >
,
gmx::detail::extents_analyse< R, dynamic_extent, 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::TabulatedNormalDistribution< RealType, tableBits >
,
gmx::NormalDistribution< RealType >
,
gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type
,
gmx::NormalDistribution< RealType >::param_type
StdioTestHelper() :
gmx::test::StdioTestHelper
step() :
gmx::EnergyAnalysisFrame
,
gmx::TrajectoryFrame
stepBegin() :
gmx::EnergyTerm
stepEnd() :
gmx::EnergyTerm
stepping() :
gmx::CpuInfo
stop() :
nbnxn_cycle_t
,
SearchCycleCounting
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 >
storeData() :
gmx::EnergyTerm
storeElement() :
gmx::ModularSimulatorAlgorithmBuilderHelper
storeIsSet() :
gmx::OptionTemplate< T, U >
storeSimulationData() :
gmx::ModularSimulatorAlgorithmBuilderHelper
storeState() :
gmx::HistogramSize
,
gmx::PointState
storeVector() :
gmx::OptionTemplate< T, U >
,
gmx::RepeatingOptionSection< T >
stream() :
DeviceStream
,
gmx::DeviceStreamManager
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
submit() :
GridConverter< pmeToFft >
subscribe() :
gmx::MDModulesNotifier< CallParameter, MDModulesNotifierBase >
,
gmx::BuildMDModulesNotifier<>::NoCallParameter
Subscriber() :
gmx::test::anonymous_namespace{observablesreducer.cpp}::Subscriber
subscribeToPreProcessingNotifications() :
gmx::RestraintMDModule
,
gmx::anonymous_namespace{colvarsMDModule_stub.cpp}::ColvarsMDModule
,
gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule
,
gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting
,
gmx::anonymous_namespace{qmmm.cpp}::QMMM
,
gmx::MDModules
,
gmx::anonymous_namespace{electricfield.cpp}::ElectricField
,
gmx::IMDModule
subscribeToSimulationSetupNotifications() :
gmx::RestraintMDModule
,
gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting
,
gmx::MDModules
,
gmx::anonymous_namespace{qmmm.cpp}::QMMM
,
gmx::anonymous_namespace{electricfield.cpp}::ElectricField
,
gmx::anonymous_namespace{colvarsMDModule_stub.cpp}::ColvarsMDModule
,
gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule
,
gmx::IMDModule
substituteMarkupAndWrapToString() :
gmx::HelpWriterContext
substituteMarkupAndWrapToVector() :
gmx::HelpWriterContext
sumOverBlocksBlockSquareWeight() :
gmx::CorrelationBlockData
sumOverBlocksSquareBlockWeight() :
gmx::CorrelationBlockData
supportLevel() :
gmx::HardwareTopology
,
gmx::CpuInfo
SurfaceAreaCalculator() :
gmx::SurfaceAreaCalculator
swap() :
gmx::ArrayRef< typename >
,
gmx::PaddedVector< T, Allocator >
,
gmx::ArrayRefWithPadding< typename >
,
gmx::MultiDimArray< TContainer, Extents, LayoutPolicy >
swap_group() :
swap_group
swapOutWorst() :
gmx::NelderMeadSimplex
synchronize() :
DeviceStream
syncNodes() :
gmx::ImdSession::Impl
SynopsisFormatter() :
gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::SynopsisFormatter
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