- s -
- S2ContactModel()
: PLMD::s2cm::S2ContactModel
- SafePtr()
: PLMD::Plumed::SafePtr
- sameShape()
: PLMD::ves::CoeffsBase
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- sampling_radius()
: PLMD::maze::Optimizer
- SASA_HASEL()
: PLMD::sasa::SASA_HASEL
- SASA_LCPO()
: PLMD::sasa::SASA_LCPO
- savePositions()
: PLMD::GREX
- SAXS()
: PLMD::isdb::SAXS
- scaleAllDerivatives()
: PLMD::ReferenceValuePack
- scaleAllValues()
: PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- scaleAllValuesAndDerivatives()
: PLMD::Grid
- scaledToReal()
: PLMD::Pbc
- scaleEnergy()
: PLMD::isdb::EMMI
- scanField()
: PLMD::IFile
- scanFieldList()
: PLMD::IFile
- scanOneHill()
: PLMD::bias::MetaD
, PLMD::bias::PBMetaD
, PLMD::function::FilesHandler
- score()
: PLMD::maze::Optimizer
- score_mean()
: PLMD::maze::Memetic
- score_member()
: PLMD::maze::Memetic
- score_members()
: PLMD::maze::Memetic
- search()
: PLMD::Brent1DRootSearch< FCLASS >
- Sec()
: PLMD::lepton::Operation
- SecondaryStructureRMSD()
: PLMD::secondarystructure::SecondaryStructureRMSD
- select()
: PLMD::ActionSet
- Select()
: PLMD::isdb::Select
, PLMD::lepton::Operation
- selectFrame()
: PLMD::analysis::LandmarkSelectionBase
- selection_roulette()
: PLMD::maze::Memetic
- selectLandmarks()
: PLMD::analysis::FarthestPointSampling
, PLMD::analysis::LandmarkSelectionBase
, PLMD::analysis::LandmarkStaged
, PLMD::analysis::ReselectLandmarks
, PLMD::analysis::SelectRandomFrames
, PLMD::analysis::SelectWithStride
- selectLatest()
: PLMD::ActionSet
- selectNot()
: PLMD::ActionSet
- Selector()
: PLMD::isdb::MetainferenceBase
, PLMD::isdb::Selector
- SelectRandomFrames()
: PLMD::analysis::SelectRandomFrames
- selectWithLabel()
: PLMD::ActionSet
- SelectWithStride()
: PLMD::analysis::SelectWithStride
- serial()
: PLMD::AtomNumber
- serialCalculation()
: PLMD::vesselbase::ActionWithVessel
- set()
: PLMD::HistogramBead
, PLMD::RMSD
, PLMD::SwitchingFunction
, PLMD::TypesafePtr
, PLMD::Value
, PLMD::ves::FermiSwitchingFunction
- set_capacity()
: PLMD::maze::Memetic
- set_cauchy_mean()
: PLMD::maze::Memetic
- set_cauchy_spread()
: PLMD::maze::Memetic
- set_coding_len()
: PLMD::maze::Memetic
- Set_comm()
: PLMD::Communicator
- Set_fcomm()
: PLMD::Communicator
- set_label()
: PLMD::maze::Optimizer
- set_local_search_rate()
: PLMD::maze::Memetic
- set_local_search_type()
: PLMD::maze::Memetic
- set_mating_rate()
: PLMD::maze::Memetic
- set_mutation_rate()
: PLMD::maze::Memetic
- set_n_global_iterations()
: PLMD::maze::Memetic
- set_n_iterations()
: PLMD::maze::Optimizer
- set_n_local_iterations()
: PLMD::maze::Memetic
- set_n_threads_openmp()
: PLMD::maze::Optimizer
- set_nl_cutoff()
: PLMD::maze::Optimizer
- set_nl_stride()
: PLMD::maze::Optimizer
- set_opt()
: PLMD::maze::Optimizer
- set_opt_value()
: PLMD::maze::Optimizer
- set_optimizer_stride()
: PLMD::maze::Optimizer
- set_rank_openmp()
: PLMD::maze::Optimizer
- set_sampling_radius()
: PLMD::maze::Optimizer
- set_stride_openmp()
: PLMD::maze::Optimizer
- set_value()
: PLMD::drr::UIestimator::n_matrix
, PLMD::drr::UIestimator::n_vector< T >
- setActiveValsAndDerivatives()
: PLMD::vesselbase::StoreDataVessel
- setAlign()
: PLMD::RMSD
- setAllCoeffsDescriptions()
: PLMD::ves::CoeffsBase
- setAllCoeffsSetIterationCounters()
: PLMD::ves::Optimizer
- setAllDimensionLabels()
: PLMD::ves::CoeffsBase
- setAllUniformIntegralsToZero()
: PLMD::ves::BasisFunctions
- setAllValuesToZero()
: PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- setAngularMomentum()
: PLMD::crystallization::Steinhardt
- setArgDerivatives()
: PLMD::isdb::EMMI
, PLMD::isdb::MetainferenceBase
- setArgument()
: PLMD::analysis::DataCollectionObject
- setArgumentDerivatives()
: PLMD::ReferenceValuePack
- setArgumentNames()
: PLMD::PDB
- setArgumentValue()
: PLMD::PDB
- setAtom()
: PLMD::multicolvar::AtomValuePack
- setAtomActive()
: PLMD::multicolvar::BridgedMultiColvarFunction
- setAtomDerivatives()
: PLMD::ReferenceValuePack
- setAtomIndex()
: PLMD::multicolvar::AtomValuePack
, PLMD::ReferenceValuePack
- setAtomIndices()
: PLMD::ReferenceAtoms
- setAtomNumbers()
: PLMD::PDB
- setAtomNumbersAndArgumentNames()
: PLMD::analysis::DataCollectionObject
- setAtomPositions()
: PLMD::analysis::DataCollectionObject
, PLMD::PDB
- setAtomsContiguous()
: PLMD::Atoms
- setAtomsDerivatives()
: PLMD::ActionWithVirtualAtom
, PLMD::Colvar
, PLMD::isdb::EMMI
, PLMD::isdb::MetainferenceBase
- setAtomsForCentralAtom()
: PLMD::multicolvar::MultiColvarBase
- setAtomsFromStrands()
: PLMD::secondarystructure::SecondaryStructureRMSD
- setAtomsGatindex()
: PLMD::Atoms
- setAtomsNlocal()
: PLMD::Atoms
- setAveragingAction()
: PLMD::vesselbase::ActionWithAveraging
- setBackupString()
: PLMD::OFile
- setBias()
: PLMD::bias::Bias
- setBiasGridNeeded()
: PLMD::ves::TargetDistribution
- setBiasMaximumToZero()
: PLMD::ves::LinearBasisSetExpansion
- setBiasMinimumToZero()
: PLMD::ves::LinearBasisSetExpansion
- setBiasOutputStride()
: PLMD::ves::Optimizer
- setBiasWithoutCutoffGridNeeded()
: PLMD::ves::TargetDistribution
- setBounds()
: PLMD::gridtools::GridVessel
, PLMD::gridtools::HistogramOnGrid
- setBoundsOnDistances()
: PLMD::DRMSD
, PLMD::SingleDomainRMSD
- setBox()
: PLMD::Atoms
, PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
, PLMD::Pbc
- setBoxDerivatives()
: PLMD::ActionWithVirtualAtom
, PLMD::Colvar
, PLMD::isdb::EMMI
, PLMD::isdb::MetainferenceBase
- setBoxDerivativesNoPbc()
: PLMD::ActionWithVirtualAtom
, PLMD::Colvar
- setBufferStart()
: PLMD::vesselbase::BridgeVessel
, PLMD::vesselbase::Vessel
- setc()
: PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- setCalcData()
: PLMD::isdb::MetainferenceBase
- setCharge()
: PLMD::ActionWithVirtualAtom
, PLMD::Units
- setCharges()
: PLMD::Atoms
- setCoeffDescription()
: PLMD::ves::CoeffsBase
- setCol()
: PLMD::TensorGeneric< n, m >
- setCollectEnergy()
: PLMD::Atoms
- setComponentsIntroduction()
: PLMD::Keywords
- setCubeUnits()
: PLMD::gridtools::GridVessel
- setCurrentBiasMaxValue()
: PLMD::ves::VesBias
- setCurrentStepSize()
: PLMD::ves::Optimizer
- setCurrentStepSizes()
: PLMD::ves::Optimizer
- setCutoff()
: PLMD::LinkCells
- setData()
: PLMD::DataFetchingObject
, PLMD::DataFetchingObjectTyped< T >
, PLMD::KernelFunctions
- setDataElement()
: PLMD::vesselbase::AveragingVessel
- setDataLabel()
: PLMD::ves::CoeffsBase
- setDataSize()
: PLMD::vesselbase::AveragingVessel
- setDerivative()
: PLMD::function::Function
, PLMD::multicolvar::CatomPack
, PLMD::MultiValue
, PLMD::Value
- setDerivatives()
: PLMD::isdb::EMMI
, PLMD::isdb::MetainferenceBase
- setDescription()
: PLMD::ves::BasisFunctions
- setDimension()
: PLMD::ves::TargetDistribution
- setDimensionLabel()
: PLMD::ves::CoeffsBase
- setDirection()
: PLMD::Direction
- setDisplace()
: PLMD::RMSD
- setDomain()
: PLMD::Value
- setDomainDecomposition()
: PLMD::Atoms
- setDynamic()
: PLMD::ves::TargetDistribution
- setEndPlumed()
: PLMD::PlumedMain
- setEnergy()
: PLMD::Atoms
, PLMD::Units
- setExchangeStep()
: PLMD::PlumedMain
- setExtraCV()
: PLMD::ActionAtomistic
, PLMD::Atoms
, PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- setExtraCVForce()
: PLMD::Atoms
, PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- setf()
: PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- setFesGridNeeded()
: PLMD::ves::TargetDistribution
- setFesOutputStride()
: PLMD::ves::Optimizer
- setFesProjOutputStride()
: PLMD::ves::Optimizer
- setFlag()
: PLMD::ExchangePatterns
- setForce()
: PLMD::gridtools::GridVessel
- setForcedNormalization()
: PLMD::ves::TargetDistribution
- setForces()
: PLMD::Atoms
- setForcesOnAtoms()
: PLMD::ActionAtomistic
- setFromVector()
: PLMD::Matrix< T >
- setGradients()
: PLMD::ActionWithVirtualAtom
, PLMD::Value
- setGradientsIfNeeded()
: PLMD::ActionWithValue
, PLMD::ActionWithVirtualAtom
- setGridBins()
: PLMD::ves::LinearBasisSetExpansion
, PLMD::ves::VesBias
- setGridElement()
: PLMD::gridtools::GridVessel
- setGridMax()
: PLMD::ves::VesBias
- setGridMin()
: PLMD::ves::VesBias
- setHardCutoffOnWeight()
: PLMD::vesselbase::StoreDataVessel
- setHeavyFlush()
: PLMD::FileBase
- setIndex()
: PLMD::AtomNumber
, PLMD::multicolvar::AtomValuePack
, PLMD::multicolvar::CatomPack
- setInputData()
: PLMD::CLTool
- setInterval()
: PLMD::ves::BasisFunctions
- setIntervalBounded()
: PLMD::ves::BasisFunctions
- setIntervalNonBounded()
: PLMD::ves::BasisFunctions
- setIntrinsicInterval()
: PLMD::ves::BasisFunctions
- setIterationCounter()
: PLMD::ves::CoeffsBase
, PLMD::ves::Optimizer
- setIterationCounterAndTime()
: PLMD::ves::CoeffsBase
- setKbT()
: PLMD::Atoms
- setKernelType()
: PLMD::HistogramBead
- setLabel()
: PLMD::ves::BasisFunctions
, PLMD::ves::CoeffsBase
- setLabelPrefix()
: PLMD::ves::BasisFunctions
- setLabels()
: PLMD::ves::BasisFunctions
, PLMD::ves::CoeffsBase
- setLastUpdate()
: PLMD::NeighborList
- setLength()
: PLMD::Units
- setLinePrefix()
: PLMD::OFile
- setLinkCellCutoff()
: PLMD::multicolvar::MultiColvarBase
- setLocalDerivative()
: PLMD::vesselbase::StoreDataVessel
- setLowMemOption()
: PLMD::vesselbase::ActionWithVessel
- setm()
: PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- setMass()
: PLMD::ActionWithVirtualAtom
, PLMD::Units
- setMasses()
: PLMD::Atoms
- setMatrixIndexesForTask()
: PLMD::adjmat::AdjacencyMatrixBase
- setMDChargeUnits()
: PLMD::Atoms
- setMDEnergyUnits()
: PLMD::Atoms
- setMDLengthUnits()
: PLMD::Atoms
- setMDMassUnits()
: PLMD::Atoms
- setMDNaturalUnits()
: PLMD::Atoms
- setMDTimeUnits()
: PLMD::Atoms
- setMetaDer()
: PLMD::isdb::MetainferenceBase
- setMinimumOfTargetDistGridToZero()
: PLMD::ves::TargetDistribution
- setMinToZero()
: PLMD::Grid
- setNarg()
: PLMD::isdb::MetainferenceBase
- setNatoms()
: PLMD::Atoms
- setNaturalUnits()
: PLMD::Atoms
- setNelemAndShape()
: PLMD::TypesafePtr
- setNoDerivatives()
: PLMD::gridtools::GridVessel
- setNofR()
: PLMD::ExchangePatterns
- setNonPeriodic()
: PLMD::ves::BasisFunctions
- setNorm()
: PLMD::vesselbase::AveragingVessel
- setNotPeriodic()
: PLMD::ActionWithValue
, PLMD::Value
- setNumberInVolume()
: PLMD::multicolvar::VolumeGradientBase
- setNumberOfAtoms()
: PLMD::multicolvar::AtomValuePack
- setNumberOfBasisFunctions()
: PLMD::ves::BasisFunctions
- setNumericalIntegrationBins()
: PLMD::ves::BasisFunctions
- setNumThreads()
: PLMD::OpenMP
- setOperation()
: PLMD::lepton::ExpressionProgram
- setOption()
: PLMD::Action
- setOrder()
: PLMD::ves::BasisFunctions
- setOutputAction()
: PLMD::vesselbase::BridgeVessel
- setOutputFmt()
: PLMD::GridBase
, PLMD::ves::CoeffsBase
- setOutputForce()
: PLMD::bias::Bias
- setOutputValue()
: PLMD::vesselbase::ValueVessel
- setp()
: PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- setParallel()
: PLMD::ves::LinearBasisSetExpansion
- setParameter()
: PLMD::isdb::MetainferenceBase
- setParameters()
: PLMD::isdb::MetainferenceBase
- setPeriodic()
: PLMD::ActionWithValue
, PLMD::ves::BasisFunctions
- setPosition()
: PLMD::ActionWithVirtualAtom
- setPositions()
: PLMD::Atoms
, PLMD::PDB
- setPositionsCenter()
: PLMD::RMSDCoreData
- setPositionsCenterIsRemoved()
: PLMD::RMSDCoreData
- setRealPrecision()
: PLMD::Atoms
- setReference()
: PLMD::ERMSD
, PLMD::RMSD
- setReferenceArguments()
: PLMD::ReferenceArguments
- setReferenceAtoms()
: PLMD::Direction
, PLMD::DRMSD
, PLMD::MultiDomainRMSD
, PLMD::ReferenceAtoms
, PLMD::SingleDomainRMSD
- setReferenceCenter()
: PLMD::RMSDCoreData
- setReferenceCenterIsRemoved()
: PLMD::RMSDCoreData
- setRemainingToDefault()
: PLMD::CLTool
- setRequestList()
: PLMD::NeighborList
- setRescaledToBias()
: PLMD::BiasRepresentation
- setRestart()
: PLMD::PlumedMain
- setRow()
: PLMD::TensorGeneric< n, m >
- setScore()
: PLMD::isdb::MetainferenceBase
- setSecondaryStructure()
: PLMD::secondarystructure::SecondaryStructureRMSD
- setSeed()
: PLMD::ExchangePatterns
, PLMD::Random
- setSerial()
: PLMD::AtomNumber
, PLMD::ves::LinearBasisSetExpansion
- setStatic()
: PLMD::ves::TargetDistribution
- setStepOfLastBiasGridUpdate()
: PLMD::ves::LinearBasisSetExpansion
- setStepOfLastBiasWithoutCutoffGridUpdate()
: PLMD::ves::LinearBasisSetExpansion
- setStepOfLastFesGridUpdate()
: PLMD::ves::LinearBasisSetExpansion
- setStepSize()
: PLMD::ves::Optimizer
- setStepSizes()
: PLMD::ves::Optimizer
- setStride()
: PLMD::ActionPilot
- setStyle()
: PLMD::Keywords::KeyType
- setSuffix()
: PLMD::PlumedMain
- setTargetDistance()
: PLMD::dimred::DimensionalityReductionBase
, PLMD::dimred::PCA
, PLMD::dimred::SketchMapBase
- setTargetDistAverages()
: PLMD::ves::VesBias
- setTargetDistAveragesToZero()
: PLMD::ves::VesBias
- setTargetDistOutputStride()
: PLMD::ves::Optimizer
- setTargetDistProjOutputStride()
: PLMD::ves::Optimizer
- setTime()
: PLMD::Units
, PLMD::ves::CoeffsBase
- setTimeStep()
: PLMD::Atoms
- setType()
: PLMD::RMSD
, PLMD::ves::BasisFunctions
, PLMD::ves::CoeffsBase
- setUniformIntegral()
: PLMD::ves::BasisFunctions
- setUniformIntegrals()
: PLMD::ves::BasisFunctions
- setUnits()
: PLMD::Atoms
, PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- setup()
: PLMD::pamm::HBPammObject
, PLMD::pamm::PammObject
- setup_targets()
: PLMD::DRMSD
, PLMD::IntermolecularDRMSD
, PLMD::IntramolecularDRMSD
- setupActiveTaskSet()
: PLMD::adjmat::ClusterAnalysisBase
, PLMD::multicolvar::MultiColvarBase
- setupAdditionalGrids()
: PLMD::ves::TargetDistribution
, PLMD::ves::TD_Custom
, PLMD::ves::TD_LinearCombination
, PLMD::ves::TD_ProductCombination
, PLMD::ves::TD_ProductDistribution
, PLMD::ves::TD_Uniform
- setupAtomsFromLinkCells()
: PLMD::multicolvar::AtomValuePack
- setupBasisFunctionsInfo()
: PLMD::ves::CoeffsBase
- setupBF()
: PLMD::ves::BasisFunctions
- setupBiasCutoff()
: PLMD::ves::TargetDistribution
, PLMD::ves::VesBias
- setupBiasFileOutput()
: PLMD::ves::VesBias
, PLMD::ves::VesLinearExpansion
- setupBiasGrid()
: PLMD::ves::LinearBasisSetExpansion
- setupConnector()
: PLMD::adjmat::AdjacencyMatrixBase
, PLMD::adjmat::AlignedMatrixBase
, PLMD::adjmat::ContactMatrix
, PLMD::adjmat::HBondMatrix
, PLMD::adjmat::TopologyMatrix
, PLMD::pamm::HBPammMatrix
- setupConstants()
: PLMD::colvar::EEFSolv
- setupCurrentAtomList()
: PLMD::multicolvar::MultiColvarBase
- setupExponentiallyDecayingAveraging()
: PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- setupFesFileOutput()
: PLMD::ves::VesBias
, PLMD::ves::VesLinearExpansion
- setupFesGrid()
: PLMD::ves::LinearBasisSetExpansion
- setupFesProjFileOutput()
: PLMD::ves::VesBias
, PLMD::ves::VesLinearExpansion
- setupFesProjGrid()
: PLMD::ves::LinearBasisSetExpansion
- setupFibonacciGrid()
: PLMD::gridtools::GridVessel
- setupGeneralGrid()
: PLMD::ves::LinearBasisSetExpansion
- setupGrid()
: PLMD::ves::WaveletGrid
- setupGrids()
: PLMD::ves::TargetDistribution
- setupHASELparam()
: PLMD::sasa::SASA_HASEL
- setupInterval()
: PLMD::ves::BasisFunctions
- setupLabels()
: PLMD::ves::BasisFunctions
, PLMD::ves::BF_Combined
, PLMD::ves::BF_Cosine
, PLMD::ves::BF_Fourier
, PLMD::ves::BF_Gaussians
, PLMD::ves::BF_Powers
, PLMD::ves::BF_Sine
, PLMD::ves::BF_Wavelets
- setupLCPOparam()
: PLMD::sasa::SASA_LCPO
- setupLinkCells()
: PLMD::multicolvar::MultiColvarBase
- setupMatrices()
: PLMD::ves::WaveletGrid
- setupMatrix()
: PLMD::ves::CoeffsMatrix
- setupMaxSurfMap()
: PLMD::sasa::SASA_HASEL
, PLMD::sasa::SASA_LCPO
- setupMPICommunication()
: PLMD::DynamicList< T >
- setupMultiColvarBase()
: PLMD::multicolvar::MultiColvarBase
- setupNonUseSpeciesLinkCells()
: PLMD::multicolvar::MultiColvarBase
- setupOFiles()
: PLMD::ves::Optimizer
- setupOutObservable()
: PLMD::fisst::FISST
- setupOutRestart()
: PLMD::eds::EDS
, PLMD::fisst::FISST
- setupPCAStorage()
: PLMD::ArgumentOnlyDistance
, PLMD::MultiDomainRMSD
, PLMD::OptimalRMSD
, PLMD::ReferenceConfiguration
, PLMD::SimpleRMSD
- setupPeriodicity()
: PLMD::Value
- setupPrintValue()
: PLMD::OFile
- setupRegions()
: PLMD::crystallization::Gradient
, PLMD::multicolvar::VolumeAround
, PLMD::multicolvar::VolumeCavity
, PLMD::multicolvar::VolumeGradientBase
, PLMD::multicolvar::VolumeInCylinder
, PLMD::multicolvar::VolumeInEnvelope
, PLMD::multicolvar::VolumeInSphere
, PLMD::multicolvar::VolumeTetrapore
- setupRMSDObject()
: PLMD::OptimalRMSD
, PLMD::SingleDomainRMSD
- setupTargetDistFileOutput()
: PLMD::ves::VesBias
- setupTargetDistPntr()
: PLMD::ves::OutputBasisFunctions
- setupTargetDistProjFileOutput()
: PLMD::ves::VesBias
- setupTargetDistribution()
: PLMD::ves::LinearBasisSetExpansion
- setupTypeMap()
: PLMD::colvar::EEFSolv
- setupUniformIntegrals()
: PLMD::ves::BasisFunctions
, PLMD::ves::BF_Chebyshev
, PLMD::ves::BF_Combined
, PLMD::ves::BF_Cosine
, PLMD::ves::BF_Fourier
, PLMD::ves::BF_Legendre
, PLMD::ves::BF_Sine
- setupUniformTargetDistribution()
: PLMD::ves::LinearBasisSetExpansion
- setupValueMap()
: PLMD::colvar::EEFSolv
- setValIndex()
: PLMD::ReferenceValuePack
- setValue()
: PLMD::ActionWithValue
, PLMD::Grid
, PLMD::GridBase
, PLMD::multicolvar::AtomValuePack
, PLMD::MultiValue
, PLMD::SparseGrid
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- setValueAndDerivatives()
: PLMD::Grid
, PLMD::GridBase
, PLMD::gridtools::GridVessel
, PLMD::SparseGrid
- setValues()
: PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- setValuesFromDifferentShape()
: PLMD::ves::CoeffsVector
- setVariableLocations()
: PLMD::lepton::CompiledExpression
- setVectorDimensionality()
: PLMD::crystallization::VectorMultiColvar
- setVirial()
: PLMD::Atoms
, PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- sgn()
: PLMD::logmfd::LogMFD
, PLMD::maze::tls
- shapeOfIndices()
: PLMD::ves::CoeffsBase
- share()
: PLMD::Atoms
- shareAll()
: PLMD::Atoms
- shareData()
: PLMD::PlumedMain
- ShortcutVessel()
: PLMD::vesselbase::ShortcutVessel
- Shuffle()
: PLMD::Random
- side_chain_atoms()
: PLMD::isdb::CS2Backbone
- simpleAlignment()
: PLMD::RMSD
- SimpleCubic()
: PLMD::crystallization::SimpleCubic
- SimpleMD()
: PLMD::cltools::SimpleMD
- SimpleRMSD()
: PLMD::SimpleRMSD
- Simulated_Annealing()
: PLMD::maze::Simulated_Annealing
- Sin()
: PLMD::lepton::Operation
- singleDomainRequests()
: PLMD::ReferenceAtoms
- SingleDomainRMSD()
: PLMD::SingleDomainRMSD
- Sinh()
: PLMD::lepton::Operation
- size()
: PLMD::Keywords
, PLMD::NeighborList
, PLMD::PDB
- SketchMap()
: PLMD::dimred::SketchMap
- SketchMapBase()
: PLMD::dimred::SketchMapBase
- SketchMapConjGrad()
: PLMD::dimred::SketchMapConjGrad
- SketchMapPointwise()
: PLMD::dimred::SketchMapPointwise
- SketchMapRead()
: PLMD::dimred::SketchMapRead
- SketchMapSmacof()
: PLMD::dimred::SketchMapSmacof
- SMAC()
: PLMD::crystallization::SMAC
- SMACMatrix()
: PLMD::adjmat::SMACMatrix
- SmacofMDS()
: PLMD::dimred::SmacofMDS
- solve()
: PLMD::maze::Memetic
- Sort()
: PLMD::function::Sort
- sort()
: PLMD::LatticeReduction
- sort_members()
: PLMD::maze::Memetic
- sortActiveList()
: PLMD::DynamicList< T >
, PLMD::MultiValue
- SparseGrid()
: PLMD::SparseGrid
- SpathVessel()
: PLMD::mapping::SpathVessel
- specialSymbol()
: PLMD::MolDataClass
- spline()
: PLMD::ves::BF_CubicBsplines
- Split()
: PLMD::Communicator
- split()
: PLMD::isdb::CS2BackboneDB
- splitInputDerivatives()
: PLMD::multicolvar::MultiColvarBase
- Sprint()
: PLMD::adjmat::Sprint
- Sqrt()
: PLMD::lepton::Operation
- Square()
: PLMD::lepton::Operation
- stack()
: PLMD::Exception
- start()
: PLMD::Stopwatch
, PLMD::Stopwatch::Watch
- start_step_0()
: PLMD::maze::Optimizer
- start_step_stride()
: PLMD::maze::Optimizer
- startPause()
: PLMD::Stopwatch
, PLMD::Stopwatch::Watch
- startStep()
: PLMD::Atoms
- startStop()
: PLMD::Stopwatch
, PLMD::Stopwatch::Watch
- startWith()
: PLMD::Tools
- Stats()
: PLMD::function::Stats
- std()
: PLMD::maze::tls
- Steered_MD()
: PLMD::maze::Steered_MD
- Steinhardt()
: PLMD::crystallization::Steinhardt
- Step()
: PLMD::lepton::Operation
- StepSize()
: PLMD::ves::Optimizer
- stochastic_hill_climbing()
: PLMD::maze::Memetic
- stop()
: PLMD::PlumedMain
, PLMD::Stopwatch
, PLMD::Stopwatch::Watch
, PLMD::Subprocess
- Stopwatch()
: PLMD::Stopwatch
- StoreDataVessel()
: PLMD::vesselbase::StoreDataVessel
- storeDerivatives()
: PLMD::vesselbase::StoreDataVessel
- storedValueIsActive()
: PLMD::multicolvar::MultiColvarBase
, PLMD::vesselbase::StoreDataVessel
- storeThenAverage()
: PLMD::vesselbase::ActionWithAveraging
- storeValues()
: PLMD::vesselbase::StoreDataVessel
- stringToType()
: PLMD::ves::WaveletGrid
- stripLeadingAndTrailingBlanks()
: PLMD::Tools
- style()
: PLMD::Keywords
- Subprocess()
: PLMD::Subprocess
- substituteSimplerExpression()
: PLMD::lepton::ParsedExpression
- Subtract()
: PLMD::lepton::Operation
- subtractFromValues()
: PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- Sum()
: PLMD::Communicator
, PLMD::vesselbase::Sum
- sumCommMPI()
: PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- sumMultiSimCommMPI()
: PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- switchOnPCAOption()
: PLMD::ReferenceValuePack