Here is a list of all documented class members with links to the class documentation for each member:

- s -

• sample() : DdMd::Analyzer , DdMd::AnalyzerManager , DdMd::AutoCorrAnalyzer< Data, Product > , DdMd::AverageAnalyzer , DdMd::ConfigWriter , DdMd::EnergyAnalyzer , DdMd::ExternalEnergyAverage , DdMd::LogEnergy , DdMd::OrderParamNucleation , DdMd::OutputBoxdim , DdMd::OutputEnergy , DdMd::OutputPairEnergies , DdMd::OutputPressure , DdMd::OutputStressTensor , DdMd::OutputTemperature , DdMd::PairEnergyAverage , DdMd::StressAutoCorr , DdMd::StructureFactor , DdMd::StructureFactorGrid , DdMd::SymmTensorAverageAnalyzer , DdMd::TensorAverageAnalyzer , DdMd::TrajectoryWriter , DdMd::VanHove , DdMd::VirialStressTensor , DdMd::VirialStressTensorAverage , McMd::Analyzer , McMd::AnalyzerManager , McMd::AtomMSD , McMd::BennettsMethod , McMd::BlockRadiusGyration , McMd::BondLengthDist , McMd::BoundaryAverage , McMd::ClusterHistogram , McMd::ComMSD , McMd::CompositionProfile , McMd::ConfigWriter , McMd::Crosslinker , McMd::EndtoEnd , McMd::EndtoEndXYZ , McMd::G1MSD , McMd::InterIntraLink , McMd::IntraBondStressAutoCorr< SystemType > , McMd::IntraBondTensorAutoCorr< SystemType > , McMd::IntraPairAutoCorr , McMd::IntraStructureFactor , McMd::IntraStructureFactorGrid , McMd::LammpsDumpWriter , McMd::LinearRouseAutoCorr , McMd::LinkLengthDist , McMd::LinkLifeTime , McMd::LinkLTPos , McMd::LinkMSD , McMd::LogProgress , McMd::McBondEnergyAverage , McMd::McEnergyAnalyzer , McMd::McEnergyAverage , McMd::McEnergyOutput , McMd::McExternalEnergyAverage , McMd::McMuExchange , McMd::McNVTChemicalPotential , McMd::McPairEnergyAverage , McMd::McVirialStressTensorAverage , McMd::MdEnergyAnalyzer , McMd::MdEnergyOutput , McMd::MdKineticEnergyAverage , McMd::MdPairEnergyCoefficients , McMd::MdPotentialEnergyAverage , McMd::MdVirialStressTensorAverage , McMd::NLinkAverage , McMd::PerturbDerivative , McMd::PressureAverage< SystemType > , McMd::RadiusGyration , McMd::RDF , McMd::RingRouseAutoCorr , McMd::SemiGrandDistribution , McMd::SSChainDist , McMd::StressAutoCorr< SystemType > , McMd::StressTensorAverage< SystemType > , McMd::StructureFactor , McMd::StructureFactorGrid , McMd::StructureFactorP , McMd::TrajectoryWriter , McMd::TypeDistribution , McMd::VanHove , McMd::VelProf , Tools::Analyzer , Tools::AnalyzerManager , Tools::AtomMSD , Tools::LogStep , Tools::PairEnergy , Tools::TrajectoryWriter , Util::AutoCorr< Data, Product > , Util::AutoCorrArray< Data, Product > , Util::AutoCorrStage< Data, Product > , Util::Average , Util::AverageStage , Util::Distribution , Util::IntDistribution , Util::MeanSqDispArray< Data > , Util::SymmTensorAverage , Util::TensorAverage
• Samples : DdMd::StructureFactor
• save() : DdMd::Analyzer , DdMd::AnalyzerManager , DdMd::AnglePotentialImpl< Interaction > , DdMd::AtomStorage , DdMd::AutoCorrAnalyzer< Data, Product > , DdMd::AverageAnalyzer , DdMd::BondPotentialImpl< Interaction > , DdMd::Buffer , DdMd::ConfigWriter , DdMd::DdMdGroupTrajectoryWriter , DdMd::DihedralPotentialImpl< Interaction > , DdMd::Domain , DdMd::EnergyAnalyzer , DdMd::ExternalEnergyAverage , DdMd::ExternalPotentialImpl< Interaction > , DdMd::GroupStorage< N > , DdMd::Integrator , DdMd::LogEnergy , DdMd::NphIntegrator , DdMd::NptIntegrator , DdMd::NveIntegrator , DdMd::NvtIntegrator , DdMd::NvtLangevinIntegrator , DdMd::OrderParamNucleation , DdMd::OutputBoxdim , DdMd::OutputEnergy , DdMd::OutputPairEnergies , DdMd::OutputPressure , DdMd::OutputStressTensor , DdMd::OutputTemperature , DdMd::PairEnergyAnalyzer , DdMd::PairEnergyAverage , DdMd::PairPotential , DdMd::PairPotentialImpl< Interaction > , DdMd::Simulation , DdMd::StressAutoCorr , DdMd::StructureFactor , DdMd::StructureFactorGrid , DdMd::SymmTensorAverageAnalyzer , DdMd::TensorAverageAnalyzer , DdMd::TrajectoryWriter , DdMd::VanHove , DdMd::VirialStressTensor , DdMd::VirialStressTensorAverage , McMd::Analyzer , McMd::AnalyzerManager , McMd::AnglePotentialImpl< Interaction > , McMd::AtomDisplaceMove , McMd::AtomMSD , McMd::AverageAnalyzer< SystemType > , McMd::BennettsMethod , McMd::BlockRadiusGyration , McMd::BondLengthDist , McMd::BondPotentialImpl< Interaction > , McMd::BoundaryAverage , McMd::CfbDoubleRebridgeMove , McMd::CfbEndMove , McMd::CfbLinear , McMd::CfbLinearEndMove , McMd::CfbRebridgeBase , McMd::CfbRebridgeMove , McMd::CfbReptateMove , McMd::CfbReptationMove , McMd::CfbRingRebridgeMove , McMd::ClusterHistogram , McMd::Command , McMd::ComMSD , McMd::CompositionProfile , McMd::ConfigWriter , McMd::DihedralPotentialImpl< Interaction > , McMd::DpdMove , McMd::EndSwapMove , McMd::ExternalPotentialImpl< Interaction > , McMd::HarmonicCvBias , McMd::HomopolymerSemiGrandMove , McMd::HomopolymerSG , McMd::HybridMdMove , McMd::HybridNphMdMove , McMd::IntraBondStressAutoCorr< SystemType > , McMd::IntraBondTensorAutoCorr< SystemType > , McMd::IntraPairAutoCorr , McMd::IntraStructureFactor , McMd::IntraStructureFactorGrid , McMd::LammpsDumpWriter , McMd::LinearCvBias , McMd::LinearRouseAutoCorr , McMd::LinearSG , McMd::McEnergyAnalyzer , McMd::McEnergyOutput , McMd::McMove , McMd::McMoveManager , McMd::McMuExchange , McMd::McNVTChemicalPotential , McMd::McPairEnergyAverage , McMd::McPairPotentialImpl< Interaction > , McMd::McSimulation , McMd::McVirialStressTensorAverage , McMd::MdEnergyAnalyzer , McMd::MdEnergyOutput , McMd::MdEwaldPairPotentialImpl< Interaction > , McMd::MdEwaldPotential , McMd::MdKineticEnergyAverage , McMd::MdMove , McMd::MdPairEnergyCoefficients , McMd::MdPairPotentialImpl< Interaction > , McMd::MdPotentialEnergyAverage , McMd::MdSimulation , McMd::MdSpmePotential , McMd::MdVirialStressTensorAverage , McMd::NphIntegrator , McMd::NveVvIntegrator , McMd::NvtDpdVvIntegrator , McMd::NvtLangevinIntegrator , McMd::NvtNhIntegrator , McMd::PairList , McMd::Perturbation , McMd::PerturbDerivative , McMd::PressureAverage< SystemType > , McMd::RadiusGyration , McMd::RDF , McMd::ReplicaMove , McMd::RigidDisplaceMove , McMd::RingOctaRebridgeMove , McMd::RingRouseAutoCorr , McMd::RingTetraRebridgeMove , McMd::SemiGrandDistribution , McMd::Simulation , McMd::StressAutoCorr< SystemType > , McMd::StressTensorAverage< SystemType > , McMd::StructureFactor , McMd::StructureFactorGrid , McMd::StructureFactorP , McMd::StructureFactorPGrid , McMd::TrajectoryWriter , McMd::TypeDistribution , McMd::VanHove , Simp::BoundaryEnsemble , Simp::BoxExternal , Simp::CosineAngle , Simp::CosineDihedral , Simp::CosineSqAngle , Simp::Diblock , Simp::DpdPair , Simp::EnergyEnsemble , Simp::EwaldInteraction , Simp::FeneBond , Simp::GeneralPeriodicExternal , Simp::HarmonicAngle , Simp::HarmonicBond , Simp::HarmonicL0Bond , Simp::Homopolymer , Simp::HomoRing , Simp::LamellarOrderingExternal , Simp::LJPair , Simp::LocalLamellarOrderingExternal , Simp::Multiblock , Simp::MultiHarmonicDihedral , Simp::NucleationExternal , Simp::OrthoBoxExternal , Simp::PeriodicExternal , Simp::Point , Simp::SimplePeriodicExternal , Simp::SlitExternal , Simp::Species , Simp::SphericalTabulatedExternal , Util::AutoCorr< Data, Product > , Util::AutoCorrArray< Data, Product > , Util::AutoCorrelation< Data, Product > , Util::Average , Util::Distribution , Util::FileMaster , Util::IntDistribution , Util::Manager< Data > , Util::MeanSqDispArray< Data > , Util::ParamComponent , Util::ParamComposite , Util::Parameter , Util::RadialDistribution , Util::Random , Util::Serializable , Util::SymmTensorAverage , Util::TensorAverage
• saveConfig() : DdMd::SerializeConfigIo , McMd::System
• saveEnsembles() : DdMd::Simulation , McMd::System
• saveFileMaster() : DdMd::Simulation , McMd::System
• saveFileName() : DdMd::Integrator
• saveInterval() : DdMd::Analyzer , DdMd::Integrator , DdMd::Modifier
• saveLinkMaster() : McMd::System
• saveOptional() : Util::ParamComposite , Util::Parameter
• saveOptionalCArray() : Util::Parameter
• saveOptionalCArray2D() : Util::Parameter
• saveOutputFileName() : DdMd::Analyzer
• saveParameters() : McMd::McSystem , McMd::MdSystem , McMd::System
• savePerturbation() : McMd::System
• savePotentialStyles() : DdMd::Simulation , McMd::System
• saveReplicaMove() : McMd::System
• saveValue() : Util::CArray2DParam< Type > , Util::CArrayParam< Type > , Util::DArrayParam< Type > , Util::DMatrixParam< Type > , Util::DSymmMatrixParam< Type > , Util::FArrayParam< Type, N > , Util::Parameter , Util::ScalarParam< Type >
• ScalarParam() : Util::ScalarParam< Type >
• scanBridge() : McMd::RingOctaRebridgeMove , McMd::RingTetraRebridgeMove
• ScopedPtr() : Util::ScopedPtr< T >
• seed() : Util::MTRand_int32 , Util::Random
• SemiGrandDistribution() : McMd::SemiGrandDistribution
• send() : DdMd::AtomCollector , DdMd::AtomDistributor , DdMd::Buffer , DdMd::GroupCollector< N > , DdMd::GroupDistributor< N > , Util::MemoryOArchive
• sendRecv() : DdMd::Buffer
• sendSize() : DdMd::Buffer
• serialize : DdMd::AtomType , DdMd::Group< N > , McMd::Analyzer , McMd::AtomMSD , McMd::AtomType , McMd::AverageAnalyzer< SystemType > , McMd::BennettsMethod , McMd::BlockRadiusGyration , McMd::BondLengthDist , McMd::BoundaryAverage , McMd::CellList , McMd::ClusterHistogram , McMd::ComMSD , McMd::CompositionProfile , McMd::ConfigWriter , McMd::HomopolymerSemiGrandMove , McMd::IntraBondStressAutoCorr< SystemType > , McMd::IntraBondTensorAutoCorr< SystemType > , McMd::IntraPairAutoCorr , McMd::IntraStructureFactor , McMd::IntraStructureFactorGrid , McMd::LammpsDumpWriter , McMd::LinearRouseAutoCorr , McMd::McEnergyOutput , McMd::McIntraBondStressAutoCorr , McMd::McIntraBondTensorAutoCorr , McMd::McMuExchange , McMd::McNVTChemicalPotential , McMd::McPairEnergyAverage , McMd::McSimulation , McMd::MdEnergyOutput , McMd::MdIntraBondStressAutoCorr , McMd::MdIntraBondTensorAutoCorr , McMd::MdKineticEnergyAverage , McMd::MdPairEnergyCoefficients , McMd::MdPotentialEnergyAverage , McMd::PairSelector , McMd::PerturbDerivative , McMd::PressureAverage< SystemType > , McMd::RadiusGyration , McMd::RDF , McMd::RigidDisplaceMove , McMd::RingRouseAutoCorr , McMd::SemiGrandDistribution , McMd::StressAutoCorr< SystemType > , McMd::StressTensorAverage< SystemType > , McMd::StructureFactor , McMd::StructureFactorGrid , McMd::StructureFactorP , McMd::StructureFactorPGrid , McMd::TrajectoryWriter , McMd::TypeDistribution , McMd::VanHove , Simp::MonoclinicBoundary , Simp::OrthoRegion , Simp::OrthorhombicBoundary , Simp::SpeciesGroup< NAtom > , Tools::Species , Util::AutoCorr< Data, Product > , Util::AutoCorrArray< Data, Product > , Util::AutoCorrStage< Data, Product > , Util::Average , Util::AverageStage , Util::DArray< Data > , Util::Distribution , Util::DMatrix< Data > , Util::DSArray< Data > , Util::FArray< Data, Capacity > , Util::FMatrix< Data, M, N > , Util::FSArray< Data, Capacity > , Util::GArray< Data > , Util::GridArray< Data > , Util::IntDistribution , Util::IntVector , Util::MeanSqDispArray< Data > , Util::MTRand_int32 , Util::ParamComponent , Util::RadialDistribution , Util::Random , Util::Rational , Util::RingBuffer< Data > , Util::SymmTensorAverage , Util::Tensor , Util::TensorAverage , Util::Vector
• SerializeConfigIo() : DdMd::SerializeConfigIo
• serializePrivate() : Util::AutoCorrStage< Data, Product >
• set() : DdMd::AnglePotential , DdMd::AnglePotentialImpl< Interaction > , DdMd::BondPotential , DdMd::BondPotentialImpl< Interaction > , DdMd::DihedralPotential , DdMd::DihedralPotentialImpl< Interaction > , DdMd::ExternalPotential , DdMd::ExternalPotentialImpl< Interaction > , DdMd::Modifier , DdMd::PairPotential , DdMd::PairPotentialImpl< Interaction > , McMd::AnglePotential , McMd::AnglePotentialImpl< Interaction > , McMd::BondPotential , McMd::BondPotentialImpl< Interaction > , McMd::DihedralPotential , McMd::DihedralPotentialImpl< Interaction > , McMd::LinkPotentialImpl< Interaction > , McMd::McPairPotentialImpl< Interaction > , McMd::MdCoulombPotential , McMd::MdEwaldPairPotentialImpl< Interaction > , McMd::MdEwaldPotential , McMd::MdPairPotentialImpl< Interaction > , McMd::MdSpmePotential , McMd::PairPotential , Simp::CompensatedPair< BarePair, LinkPotential > , Simp::CompositeBond< BareBond, BarePair > , Simp::CosineAngle , Simp::CosineDihedral , Simp::CosineSqAngle , Simp::DpdPair , Simp::EwaldInteraction , Simp::FeneBond , Simp::HarmonicAngle , Simp::HarmonicBond , Simp::HarmonicL0Bond , Simp::LJPair , Simp::MultiHarmonicDihedral , Simp::WcaPair , Util::Bit , Util::Setable< T >
• Setable() : Util::Setable< T >
• setActualOrdered() : Util::FlagSet
• setAllowed() : Util::FlagSet
• setAnalyzerManager() : McMd::Simulation
• setAtom() : McMd::Group< NAtom >
• setAtomCapacity() : McMd::CellList
• setAtomContexts() : Tools::ConfigReader
• setAtomId() : DdMd::Group< N > , Simp::SpeciesGroup< NAtom >
• setAtomMasks() : DdMd::ConfigIo
• setAtomPtr() : DdMd::Group< N >
• setAtomType() : Simp::Species
• setAvoidDoubleCounting() : McMd::PairSelector
• setBase() : Util::MpiStructBuilder
• setBlockFactor() : Util::AverageStage
• setBoltzmannVelocities() : DdMd::Simulation , McMd::MdSystem
• setBondPotential() : McMd::Generator
• setBoundary() : DdMd::Domain , Simp::BoxExternal , Simp::GeneralPeriodicExternal , Simp::LamellarOrderingExternal , Simp::LocalLamellarOrderingExternal , Simp::NucleationExternal , Simp::OrthoBoxExternal , Simp::PeriodicExternal , Simp::SimplePeriodicExternal , Simp::SlitExternal , Simp::SphericalTabulatedExternal
• setCapacity() : DdMd::AtomCollector , DdMd::AtomDistributor , DdMd::GroupCollector< N > , DdMd::GroupDistributor< N >
• setCharge() : McMd::AtomType
• setClassName() : Util::ParamComposite
• setColumn() : Util::Tensor
• setCommandFileName() : Util::FileMaster
• setCommandManager() : McMd::Simulation
• setCommonControl() : Util::FileMaster
• setConfigIo() : DdMd::Simulation , McMd::System
• setConfigReader() : Tools::Processor
• setConfigWriter() : Tools::Processor
• setCubic() : Simp::OrthorhombicBoundary
• setCurrent() : Util::ArrayIterator< Data > , Util::ConstArrayIterator< Data > , Util::ConstPArrayIterator< Data > , Util::ListIterator< Data > , Util::PArrayIterator< Data >
• setCursor() : Util::XmlBase
• setDefaultPrecision() : Util::Format
• setDefaultWidth() : Util::Format
• setDimensions() : Util::Grid
• setDirectoryId() : Util::FileMaster
• setEcho() : Util::ParamComponent
• setEnd() : Util::ArrayIterator< Data > , Util::ConstArrayIterator< Data > , Util::ConstPArrayIterator< Data > , Util::PArrayIterator< Data >
• setEnergy() : DdMd::Potential
• setEpsilon() : Simp::CompensatedPair< BarePair, LinkPotential > , Simp::DpdPair , Simp::LJPair
• setEta() : McMd::NphIntegrator
• setExchange() : DdMd::Plan
• setExpectPerturbation() : McMd::System
• setExternalParameter() : Simp::BoxExternal , Simp::GeneralPeriodicExternal , Simp::LamellarOrderingExternal , Simp::LocalLamellarOrderingExternal , Simp::NucleationExternal , Simp::OrthoBoxExternal , Simp::PeriodicExternal , Simp::SimplePeriodicExternal , Simp::SlitExternal
• setFactory() : Util::Manager< Data >
• setFile() : Util::Log
• setFileMaster() : McMd::Analyzer , McMd::System
• setFilePrefix() : UnitTest
• setFirstAngle() : McMd::Molecule
• setFirstAtom() : McMd::Molecule
• setFirstBond() : McMd::Molecule
• setFirstDihedral() : McMd::Molecule
• setFlags() : DdMd::Plan
• setGhost() : DdMd::Plan
• setGridCommunicator() : DdMd::Domain
• setHasAtomContext() : DdMd::Atom
• setHasCharge() : McMd::AtomType
• setId() : DdMd::Atom , DdMd::AtomType , DdMd::Cell , DdMd::Group< N > , McMd::AtomType , McMd::Cluster , McMd::Molecule , McMd::System , Simp::Species , Tools::Cell , Tools::Species
• setIndent() : Util::ParamComponent
• setInputPrefix() : Util::FileMaster
• setIoCommunicator() : McMd::Simulation , Util::Factory< Data > , Util::MpiFileIo
• setIsActive() : McMd::Link , Util::ParamComposite
• setIsGhost() : DdMd::Atom
• setIsGhostCell() : DdMd::Cell
• setIsRequired() : Util::ParamComposite
• setIsSetup() : DdMd::Integrator
• setLastCell() : DdMd::Cell , Tools::Cell
• setList() : Util::Node< Data >
• setMask() : Util::Bit
• setMass() : DdMd::AtomType , McMd::AtomType
• setMethodId() : DdMd::PairPotential
• setMolecule() : McMd::Atom , McMd::ClusterLink
• setMoleculeState() : McMd::HomopolymerSG , McMd::LinearSG , McMd::SpeciesMutator
• setMoleculeStateId() : McMd::SpeciesMutator
• setMonoclinic() : Simp::MonoclinicBoundary
• setMu() : Simp::SpeciesEnsemble
• setMutatorPtr() : Simp::Species
• setName() : DdMd::AtomType , McMd::AtomType
• setNAngle() : McMd::Molecule
• setNAngleType() : DdMd::AnglePotential , DdMd::AnglePotentialImpl< Interaction > , Simp::CosineAngle , Simp::CosineSqAngle , Simp::HarmonicAngle
• setNAtom() : McMd::Molecule
• setNAtomType() : DdMd::ExternalPotential , DdMd::ExternalPotentialImpl< Interaction > , DdMd::PairPotential , DdMd::PairPotentialImpl< Interaction > , Simp::BoxExternal , Simp::CompensatedPair< BarePair, LinkPotential > , Simp::DpdPair , Simp::GeneralPeriodicExternal , Simp::LamellarOrderingExternal , Simp::LJPair , Simp::LocalLamellarOrderingExternal , Simp::NucleationExternal , Simp::OrthoBoxExternal , Simp::PeriodicExternal , Simp::SimplePeriodicExternal , Simp::SlitExternal , Simp::SphericalTabulatedExternal
• setNBond() : McMd::Molecule
• setNBondType() : DdMd::BondPotential , DdMd::BondPotentialImpl< Interaction > , Simp::CompositeBond< BareBond, BarePair > , Simp::FeneBond , Simp::HarmonicBond , Simp::HarmonicL0Bond
• setNDihedral() : McMd::Molecule
• setNDihedralType() : DdMd::DihedralPotential , DdMd::DihedralPotentialImpl< Interaction > , Simp::CosineDihedral , Simp::MultiHarmonicDihedral
• setNEnsemble() : Util::AutoCorrArray< Data, Product > , Util::MeanSqDispArray< Data >
• setNext() : Util::Node< Data >
• setNextCell() : DdMd::Cell , Tools::Cell
• setNorm() : Util::RadialDistribution
• setNSamplePerBlock() : Util::Average , Util::SymmTensorAverage , Util::TensorAverage
• setNull() : Util::ConstPArrayIterator< Data > , Util::PArrayIterator< Data >
• setOffsetArray() : DdMd::Cell , Tools::Cell
• setOptions() : DdMd::Simulation , McMd::McSimulation , McMd::MdSimulation , Tools::Processor
• setOrthorhombic() : Simp::MonoclinicBoundary , Simp::OrthorhombicBoundary
• setOutputIntegral() : Util::RadialDistribution
• setOutputPrefix() : Util::FileMaster
• setPairCutoff() : DdMd::Exchanger
• setPairEnergies() : DdMd::PairPotential
• setPairPotential() : McMd::McSystem
• setParam() : Util::AutoCorr< Data, Product > , Util::AutoCorrArray< Data, Product > , Util::AutoCorrStage< Data, Product > , Util::Distribution , Util::IntDistribution , Util::MeanSqDispArray< Data > , Util::RadialDistribution
• setParameter() : McMd::McEnergyPerturbation , McMd::McExternalPerturbation< Interaction > , McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction > , McMd::McPairPerturbation< Interaction > , McMd::Perturbation
• setParamFileName() : Util::FileMaster
• setParent() : TestRunner , Util::ParamComposite
• setPrecision() : Util::Dbl
• setPressure() : Simp::BoundaryEnsemble
• setPrev() : Util::Node< Data >
• setProbability() : McMd::McMove
• setReverseUpdateFlag() : DdMd::Potential , DdMd::Simulation
• setRNG() : Util::Ar1Process
• setRootPrefix() : Util::FileMaster
• setRow() : Util::Tensor
• setSeed() : Util::Random
• setSigma() : Simp::DpdPair , Simp::LJPair
• setSimulation() : McMd::System
• setSpecies() : McMd::Molecule
• setStress() : DdMd::Potential
• setString() : Util::Label , Util::XmlBase
• setSystem() : McMd::Molecule
• setTemperature() : Simp::EnergyEnsemble
• setTetragonal() : Simp::OrthorhombicBoundary
• setToZero() : Util::Polynomial< T >
• setTrajectoryReader() : Tools::Processor
• setTypeId() : DdMd::Atom , DdMd::Group< N > , McMd::Atom , McMd::Group< NAtom > , Simp::SpeciesGroup< NAtom >
• setup() : DdMd::Analyzer , DdMd::AnalyzerManager , DdMd::AtomCollector , DdMd::AtomDistributor , DdMd::AutoCorrAnalyzer< Data, Product > , DdMd::AverageAnalyzer , DdMd::EnergyAnalyzer , DdMd::GroupCollector< N > , DdMd::GroupDistributor< N > , DdMd::Integrator
• Setup : DdMd::Modifier::Flags
• setup() : DdMd::Modifier , DdMd::ModifierManager , DdMd::NphIntegrator , DdMd::NptIntegrator , DdMd::NveIntegrator , DdMd::NvtIntegrator , DdMd::NvtLangevinIntegrator , DdMd::OutputBoxdim , DdMd::OutputEnergy , DdMd::OutputPressure , DdMd::OutputStressTensor , DdMd::OutputTemperature , DdMd::StressAutoCorr , DdMd::SymmTensorAverageAnalyzer , DdMd::TensorAverageAnalyzer , DdMd::TrajectoryWriter , McMd::Analyzer , McMd::AnalyzerManager , McMd::AtomMSD , McMd::AverageAnalyzer< SystemType > , McMd::BennettsMethod , McMd::BlockRadiusGyration , McMd::BondLengthDist , McMd::BoundaryAverage , McMd::CellList , McMd::CfbRebridgeBase , McMd::ClusterHistogram , McMd::ComMSD , McMd::CompositionProfile , McMd::ConfigWriter , McMd::Crosslinker , McMd::DpdMove , McMd::EndtoEnd , McMd::EndtoEndXYZ , McMd::G1MSD , McMd::InterIntraLink , McMd::IntraBondStressAutoCorr< SystemType > , McMd::IntraBondTensorAutoCorr< SystemType > , McMd::IntraPairAutoCorr , McMd::IntraStructureFactor , McMd::IntraStructureFactorGrid , McMd::LammpsDumpWriter , McMd::LinearRouseAutoCorr , McMd::LinkLengthDist , McMd::LinkLifeTime , McMd::LinkLTPos , McMd::LinkMSD , McMd::McEnergyAnalyzer , McMd::McMove , McMd::McMoveManager , McMd::McMuExchange , McMd::McNVTChemicalPotential , McMd::McPairEnergyAverage , McMd::MdEnergyAnalyzer , McMd::MdIntegrator , McMd::MdKineticEnergyAverage , McMd::MdPotentialEnergyAverage , McMd::NLinkAverage , McMd::NphIntegrator , McMd::NveVvIntegrator , McMd::NvtDpdVvIntegrator , McMd::NvtLangevinIntegrator , McMd::NvtNhIntegrator , McMd::PairList , McMd::PerturbDerivative , McMd::PressureAverage< SystemType > , McMd::RadiusGyration , McMd::RDF , McMd::RingRouseAutoCorr , McMd::SSChainDist , McMd::StressAutoCorr< SystemType > , McMd::StressTensorAverage< SystemType > , McMd::StructureFactor , McMd::StructureFactorGrid , McMd::StructureFactorP , McMd::StructureFactorPGrid , McMd::TrajectoryWriter , McMd::VanHove , McMd::VelProf , Tools::Analyzer , Tools::AnalyzerManager , Tools::AtomMSD , Tools::LogStep , Tools::PairEnergy , Tools::TrajectoryWriter
• setUp() : UnitTest
• setup() : Util::Binomial
• setupAtoms() : DdMd::Integrator
• setupCellList() : McMd::Generator
• setValue() : Util::Dbl , Util::Int , Util::Lng , Util::ScalarParam< Type >
• setVerbose() : UnitTest
• setWeight() : McMd::SpeciesMutator
• setWidth() : Util::Dbl , Util::Int , Util::Lng
• setZeroForces() : McMd::MdSystem
• setZeroVelocities() : McMd::MdSystem
• shift() : DdMd::Domain , Simp::MonoclinicBoundary , Simp::OrthorhombicBoundary , Util::Grid , Util::GridArray< Data > , Util::Polynomial< T >
• shift_ : McMd::BennettsMethod
• shiftAtoms() : McMd::MdSystem
• shiftGen() : Simp::MonoclinicBoundary , Simp::OrthorhombicBoundary
• sigma() : Simp::DpdPair , Simp::LJPair
• sigma_ : Simp::LJPair
• sigmaSq_ : Simp::LJPair
• Signal() : Util::Signal< T > , Util::Signal< void >
• SimplePeriodicExternal() : Simp::SimplePeriodicExternal
• simulate() : McMd::McSimulation , McMd::MdSimulation
• simulation() : DdMd::Analyzer , DdMd::AnalyzerFactory , DdMd::ExternalPotential , DdMd::Modifier , DdMd::ModifierFactory
• Simulation() : DdMd::Simulation
• simulation() : DdMd::SimulationAccess , McMd::ConfigIo , McMd::Generator , McMd::McAnalyzerFactory , McMd::McCommandFactory , McMd::McCommandManager , McMd::McMove , McMd::McMoveFactory , McMd::MdAnalyzerFactory , McMd::MdCommandFactory , McMd::MdCommandManager , McMd::MdIntegrator
• Simulation() : McMd::Simulation
• simulation() : McMd::System , McMd::SystemAnalyzerFactory , McMd::SystemInterface , McMd::TrajectoryReader
• SimulationAccess() : DdMd::SimulationAccess
• sinPhi() : Simp::Torsion
• sinTheta() : Simp::Bend
• size() : DdMd::GroupStorage< N > , DdMd::Mask , McMd::Cluster , McMd::Mask , Tools::AtomStorage , Tools::Species , Tools::TypeMap , Util::ArrayStack< Data > , Util::DSArray< Data > , Util::FArray< Data, Capacity > , Util::FPArray< Data, Capacity > , Util::FSArray< Data, Capacity > , Util::GArray< Data > , Util::Grid , Util::GridArray< Data > , Util::GStack< Data > , Util::List< Data > , Util::Manager< Data > , Util::MemoryCounter , Util::PArray< Data > , Util::RingBuffer< Data > , Util::SSet< Data, Capacity > , Util::SymmetryGroup< Symmetry >
• size_ : McMd::Perturbation , Util::DSArray< Data > , Util::FPArray< Data, Capacity > , Util::FSArray< Data, Capacity > , Util::PArray< Data > , Util::SSet< Data, Capacity >
• skin() : DdMd::PairPotential
• skin_ : DdMd::PairPotential
• skip() : Util::XmlBase
• Sliplinker() : McMd::Sliplinker
• SliplinkerAll() : McMd::SliplinkerAll
• SliplinkerEnd() : McMd::SliplinkerEnd
• SliplinkMcAnalyzerFactory() : McMd::SliplinkMcAnalyzerFactory
• SliplinkMcModule() : McMd::SliplinkMcModule
• SliplinkMcMoveFactory() : McMd::SliplinkMcMoveFactory
• SliplinkMdAnalyzerFactory() : McMd::SliplinkMdAnalyzerFactory
• SliplinkMove() : McMd::SliplinkMove
• SlitExternal() : Simp::SlitExternal
• SmpConfigIo() : McMd::SmpConfigIo
• sourceRank() : DdMd::Domain
• SpecialExternal() : McMd::SpecialExternal
• SpecialFactory() : McMd::SpecialFactory
• SpecialPotential() : McMd::SpecialPotential
• SpecialPotentialFacade() : McMd::SpecialPotentialFacade< PotentialType, FactoryType >
• species() : McMd::Generator , McMd::Molecule , McMd::Simulation
• Species() : Simp::Species
• species() : Tools::Configuration , Tools::Molecule
• Species() : Tools::Species
• SpeciesAngle : Simp::Species
• speciesAngle() : Simp::Species
• speciesAngles_ : Simp::Species
• SpeciesBond : Simp::Species
• speciesBond() : Simp::Species
• speciesBonds_ : Simp::Species
• speciesDihedral() : Simp::Species
• SpeciesDihedral : Simp::Species
• speciesDihedrals_ : Simp::Species
• SpeciesEnsemble() : Simp::SpeciesEnsemble
• speciesFactory() : McMd::Simulation
• SpeciesGroup() : Simp::SpeciesGroup< NAtom >
• speciesId : DdMd::AtomContext , McMd::CfbLinear , Tools::Atom
• speciesId_ : McMd::CfbDoubleRebridgeMove , McMd::CfbEndMove , McMd::CfbRebridgeMove , McMd::CfbRingRebridgeMove , McMd::EndSwapMove , McMd::HomopolymerSemiGrandMove , McMd::IntraStructureFactor , McMd::RingOctaRebridgeMove , McMd::RingTetraRebridgeMove
• SpeciesManager() : McMd::SpeciesManager
• SpeciesMutator() : McMd::SpeciesMutator
• speciesPtr_ : McMd::HomopolymerSemiGrandMove
• SphericalTabulatedExternal() : Simp::SphericalTabulatedExternal
• square() : Util::IntVector , Util::Vector
• SSChainDist() : McMd::SSChainDist
• SSet() : Util::SSet< Data, Capacity >
• stageInterval() : Util::AutoCorrStage< Data, Product > , Util::AverageStage
• stamp() : DdMd::DdTimer
• start() : DdMd::DdTimer , Util::Timer
• stateOccupancy() : McMd::SpeciesMutator
• stateWeight() : McMd::SpeciesMutator
• stdDeviation() : Util::AverageStage
• step() : McMd::MdIntegrator , McMd::NphIntegrator , McMd::NveVvIntegrator , McMd::NvtDpdVvIntegrator , McMd::NvtLangevinIntegrator , McMd::NvtNhIntegrator
• stop() : DdMd::DdTimer , Util::Timer
• storage() : DdMd::AnglePotential , DdMd::BondPotential , DdMd::DihedralPotential , DdMd::ExternalPotential , DdMd::PairPotential
• Str() : Util::Str
• stress() : DdMd::Potential , McMd::MdCoulombPotential
• StressAnalyzer() : DdMd::StressAnalyzer
• StressAutoCorr() : DdMd::StressAutoCorr , McMd::StressAutoCorr< SystemType >
• StressAutoCorrelation() : DdMd::StressAutoCorrelation
• StressCalculator() : McMd::StressCalculator
• StressTensorAverage() : McMd::StressTensorAverage< SystemType >
• string() : Util::Label , Util::XmlBase
• StructureFactor() : DdMd::StructureFactor , McMd::StructureFactor
• structureFactorDelta_ : McMd::IntraStructureFactor
• StructureFactorGrid() : DdMd::StructureFactorGrid , McMd::StructureFactorGrid
• StructureFactorP() : McMd::StructureFactorP
• StructureFactorPGrid() : McMd::StructureFactorPGrid
• structureFactors_ : DdMd::StructureFactor , McMd::IntraStructureFactor , McMd::StructureFactor , McMd::StructureFactorP
• subscribeMoleculeSetChange() : McMd::System
• subtract() : Util::IntVector , Util::Tensor , Util::Vector
• symmetrize() : Util::Tensor
• SymmetryGroup() : Util::SymmetryGroup< Symmetry >
• SymmTensorAverage() : Util::SymmTensorAverage
• SymmTensorAverageAnalyzer() : DdMd::SymmTensorAverageAnalyzer
• system() : McMd::ConfigIo , McMd::Generator , McMd::LinearPerturbation< SystemType > , McMd::McAnalyzerFactory , McMd::McCommandFactory , McMd::McCommandManager , McMd::McMoveFactory , McMd::McSimulation , McMd::MdAnalyzerFactory , McMd::MdCommandFactory , McMd::MdCommandManager , McMd::MdIntegrator , McMd::MdSimulation , McMd::Molecule , McMd::ReplicaMove
• System() : McMd::System
• system() : McMd::SystemAnalyzer< SystemType > , McMd::SystemInterface , McMd::SystemMove , McMd::TrajectoryReader
• SystemAnalyzer() : McMd::SystemAnalyzer< SystemType >
• SystemAnalyzerFactory() : McMd::SystemAnalyzerFactory
• SystemInterface() : McMd::SystemInterface
• SystemMove() : McMd::SystemMove