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• Random() : PLMD::Random
• RandomExchanges() : PLMD::generic::RandomExchanges
• randomize_velocities() : PLMD::cltools::SimpleMD
• RandU01() : PLMD::Random
• RDC() : PLMD::colvar::RDC
• read() : PLMD::ArgumentOnlyDistance , PLMD::Direction , PLMD::DotProductDistance , PLMD::DRMSD , PLMD::FakeFrame
• Read() : PLMD::generic::Read
• read() : PLMD::IntermolecularDRMSD , PLMD::IntramolecularDRMSD , PLMD::KernelFunctions , PLMD::MultiDomainRMSD , PLMD::OptimalRMSD , PLMD::PDB , PLMD::ReferenceConfiguration , PLMD::SimpleRMSD , PLMD::TargetDist
• read_cs() : PLMD::colvar::CS2Backbone
• read_input() : PLMD::cltools::SimpleMD
• read_natoms() : PLMD::cltools::SimpleMD
• read_positions() : PLMD::cltools::SimpleMD
• readArgument() : PLMD::vesselbase::ActionWithInputVessel
• readArgumentsFromPDB() : PLMD::ReferenceArguments
• readAtoms() : PLMD::multicolvar::MultiColvar
• readAtomsFromPDB() : PLMD::Action , PLMD::ActionAtomistic , PLMD::ReferenceAtoms
• readAtomsLikeKeyword() : PLMD::multicolvar::MultiColvar
• readBackboneAtoms() : PLMD::secondarystructure::SecondaryStructureRMSD
• readBinary() : PLMD::Atoms
• readBounds() : PLMD::DRMSD
• readBunch() : PLMD::function::FilesHandler
• readChunkOfGaussians() : PLMD::bias::MetaD , PLMD::bias::PBMetaD
• readCommandLineArgs() : PLMD::CLTool
• readDataFromFile() : PLMD::analysis::Analysis
• readFrame() : PLMD::MultiReferenceBase
• readFromFilepointer() : PLMD::PDB
• readFromPoint() : PLMD::BiasRepresentation
• readGaussians() : PLMD::bias::MetaD , PLMD::bias::PBMetaD
• readGroupKeywords() : PLMD::multicolvar::MultiColvarBase
• readInput() : PLMD::CLTool
• readInputFile() : PLMD::CLTool , PLMD::PlumedMain
• readInputLine() : PLMD::PlumedMain
• readInputWords() : PLMD::PlumedMain
• readMaxThreeSpeciesMatrix() : PLMD::adjmat::AdjacencyMatrixBase
• readMaxTwoSpeciesMatrix() : PLMD::adjmat::AdjacencyMatrixBase
• readOrientationConnector() : PLMD::adjmat::AlignedMatrixBase , PLMD::adjmat::ContactAlignedMatrix , PLMD::adjmat::SMACMatrix
• readReference() : PLMD::SingleDomainRMSD
• readRestOfFrame() : PLMD::MultiReferenceBase , PLMD::PointWiseMapping
• ReadStateFull() : PLMD::Random
• readThreeGroups() : PLMD::multicolvar::MultiColvarBase
• readTwoGroups() : PLMD::multicolvar::MultiColvarBase
• readVesselKeywords() : PLMD::vesselbase::ActionWithVessel
• realToScaled() : PLMD::Pbc
• recalculateMatrixElement() : PLMD::adjmat::AdjacencyMatrixBase
• recalculateStoredQuantity() : PLMD::adjmat::AdjacencyMatrixVessel , PLMD::vesselbase::StoreDataVessel
• Recv() : PLMD::Communicator
• reduce() : PLMD::LatticeReduction
• reduce2() : PLMD::LatticeReduction
• reduceFast() : PLMD::LatticeReduction
• reduceSlow() : PLMD::LatticeReduction
• ReferenceArguments() : PLMD::ReferenceArguments
• ReferenceAtoms() : PLMD::ReferenceAtoms
• ReferenceConfiguration() : PLMD::ReferenceConfiguration
• ReferenceConfigurationOptions() : PLMD::ReferenceConfigurationOptions
• ReferenceValuePack() : PLMD::ReferenceValuePack
• registerKeywords() : PLMD::Action , PLMD::ActionAtomistic , PLMD::ActionPilot , PLMD::ActionSetup , PLMD::ActionWithArguments , PLMD::ActionWithValue , PLMD::ActionWithVirtualAtom , PLMD::adjmat::ActionWithInputMatrix , PLMD::adjmat::AdjacencyMatrixBase , PLMD::adjmat::AdjacencyMatrixVessel , PLMD::adjmat::AlignedMatrixBase , PLMD::adjmat::ClusterAnalysisBase , PLMD::adjmat::ClusterDiameter , PLMD::adjmat::ClusterDistribution , PLMD::adjmat::ClusteringBase , PLMD::adjmat::ClusterProperties , PLMD::adjmat::ClusterSize , PLMD::adjmat::ClusterWithSurface , PLMD::adjmat::ContactAlignedMatrix , PLMD::adjmat::ContactMatrix , PLMD::adjmat::DFSClustering , PLMD::adjmat::HBondMatrix , PLMD::adjmat::MatrixColumnSums , PLMD::adjmat::MatrixRowSums , PLMD::adjmat::OutputCluster , PLMD::adjmat::SMACMatrix , PLMD::adjmat::Sprint , PLMD::analysis::Analysis , PLMD::analysis::AnalysisWithLandmarks , PLMD::analysis::Average , PLMD::analysis::AverageVessel , PLMD::analysis::ClassicalMultiDimensionalScaling , PLMD::analysis::Committor , PLMD::analysis::Histogram , PLMD::analysis::PCA , PLMD::bias::ABMD , PLMD::bias::Bias , PLMD::bias::BiasValue , PLMD::bias::ExtendedLagrangian , PLMD::bias::External , PLMD::bias::LWalls , PLMD::bias::MetaD , PLMD::bias::Metainference , PLMD::bias::MovingRestraint , PLMD::bias::PBMetaD , PLMD::bias::Restraint , PLMD::bias::ReweightBase , PLMD::bias::ReweightBias , PLMD::bias::ReweightMetad , PLMD::bias::ReweightTemperature , PLMD::bias::UWalls , PLMD::CLTool , PLMD::cltools::CLToolSumHills , PLMD::cltools::Driver< real > , PLMD::cltools::GenTemplate , PLMD::cltools::Info , PLMD::cltools::kt , PLMD::cltools::Manual , PLMD::cltools::SimpleMD , PLMD::colvar::Angle , PLMD::colvar::Cell , PLMD::colvar::ColvarFake , PLMD::colvar::Constant , PLMD::colvar::ContactMap , PLMD::colvar::Coordination , PLMD::colvar::CoordinationBase , PLMD::colvar::CS2Backbone , PLMD::colvar::DHEnergy , PLMD::colvar::Dipole , PLMD::colvar::Distance , PLMD::colvar::DRMSD , PLMD::colvar::Energy , PLMD::colvar::ERMSD , PLMD::colvar::FretEfficiency , PLMD::colvar::Gyration , PLMD::colvar::JCoupling , PLMD::colvar::MultiRMSD , PLMD::colvar::NOE , PLMD::colvar::PathMSD , PLMD::colvar::PathMSDBase , PLMD::colvar::PCARMSD , PLMD::colvar::Position , PLMD::colvar::PRE , PLMD::colvar::PropertyMap , PLMD::colvar::Puckering , PLMD::colvar::RDC , PLMD::Colvar , PLMD::colvar::RMSD , PLMD::colvar::Template , PLMD::colvar::Torsion , PLMD::colvar::Volume , PLMD::crystallization::CubicHarmonicBase , PLMD::crystallization::Fccubic , PLMD::crystallization::Gradient , PLMD::crystallization::GradientVessel , PLMD::crystallization::InterMolecularTorsions , PLMD::crystallization::LocalSteinhardt< T > , PLMD::crystallization::MoleculeOrientation , PLMD::crystallization::MoleculePlane , PLMD::crystallization::OrientationSphere , PLMD::crystallization::Q3 , PLMD::crystallization::Q4 , PLMD::crystallization::Q6 , PLMD::crystallization::SimpleCubic , PLMD::crystallization::SMAC , PLMD::crystallization::Steinhardt , PLMD::crystallization::Tetrahedral , PLMD::crystallization::VectorMean , PLMD::crystallization::VectorMultiColvar , PLMD::crystallization::VectorSum , PLMD::function::Combine , PLMD::function::Ensemble , PLMD::function::FuncPathMSD , PLMD::function::FuncSumHills , PLMD::function::Function , PLMD::function::LocalEnsemble , PLMD::function::Matheval , PLMD::function::Piecewise , PLMD::function::Sort , PLMD::function::Stats , PLMD::function::Target , PLMD::generic::Debug , PLMD::generic::DumpAtoms , PLMD::generic::DumpDerivatives , PLMD::generic::DumpForces , PLMD::generic::DumpMassCharge , PLMD::generic::DumpProjections , PLMD::generic::EffectiveEnergyDrift , PLMD::generic::FitToTemplate , PLMD::generic::Flush , PLMD::generic::Group , PLMD::generic::Include , PLMD::generic::Print , PLMD::generic::RandomExchanges , PLMD::generic::Read , PLMD::generic::ResetCell , PLMD::generic::Time , PLMD::generic::UpdateIf , PLMD::generic::WholeMolecules , PLMD::generic::WrapAround , PLMD::gridtools::ActionWithGrid , PLMD::gridtools::ActionWithInputGrid , PLMD::gridtools::AverageOnGrid , PLMD::gridtools::ContourFindingBase , PLMD::gridtools::ConvertToFES , PLMD::gridtools::DumpCube , PLMD::gridtools::DumpGrid , PLMD::gridtools::FindContour , PLMD::gridtools::FindContourSurface , PLMD::gridtools::FindSphericalContour , PLMD::gridtools::FourierTransform , PLMD::gridtools::GridPrintingBase , PLMD::gridtools::GridVessel , PLMD::gridtools::HistogramOnGrid , PLMD::gridtools::InterpolateGrid , PLMD::HistogramBead , PLMD::manyrestraints::ManyRestraintsBase , PLMD::manyrestraints::UWalls , PLMD::mapping::Mapping , PLMD::mapping::Path , PLMD::mapping::PathBase , PLMD::mapping::PCAVars , PLMD::mapping::PropertyMap , PLMD::mapping::SpathVessel , PLMD::mapping::ZpathVessel , PLMD::multicolvar::ActionVolume , PLMD::multicolvar::AlphaBeta , PLMD::multicolvar::Angles , PLMD::multicolvar::Bridge , PLMD::multicolvar::BridgedMultiColvarFunction , PLMD::multicolvar::CenterOfMultiColvar , PLMD::multicolvar::CoordinationNumbers , PLMD::multicolvar::Density , PLMD::multicolvar::DihedralCorrelation , PLMD::multicolvar::DistanceFromContour , PLMD::multicolvar::Distances , PLMD::multicolvar::DumpMultiColvar , PLMD::multicolvar::FilterBetween , PLMD::multicolvar::FilterLess , PLMD::multicolvar::FilterMore , PLMD::multicolvar::InPlaneDistances , PLMD::multicolvar::LocalAverage , PLMD::multicolvar::MultiColvar , PLMD::multicolvar::MultiColvarBase , PLMD::multicolvar::MultiColvarDensity , PLMD::multicolvar::MultiColvarFilter , PLMD::multicolvar::MultiColvarFunction , PLMD::multicolvar::NumberOfLinks , PLMD::multicolvar::Torsions , PLMD::multicolvar::VolumeAround , PLMD::multicolvar::VolumeCavity , PLMD::multicolvar::VolumeGradientBase , PLMD::multicolvar::VolumeInCylinder , PLMD::multicolvar::VolumeInSphere , PLMD::multicolvar::VolumeTetrapore , PLMD::multicolvar::XDistances , PLMD::multicolvar::XYDistances , PLMD::secondarystructure::AlphaRMSD , PLMD::secondarystructure::AntibetaRMSD , PLMD::secondarystructure::ParabetaRMSD , PLMD::secondarystructure::SecondaryStructureRMSD , PLMD::setup::Load , PLMD::setup::Restart , PLMD::setup::Units , PLMD::SetupMolInfo , PLMD::SwitchingFunction , PLMD::vatom::Center , PLMD::vatom::COM , PLMD::vatom::FixedAtom , PLMD::vatom::Ghost , PLMD::vesselbase::ActionWithAveraging , PLMD::vesselbase::ActionWithInputVessel , PLMD::vesselbase::ActionWithVessel , PLMD::vesselbase::AltMin , PLMD::vesselbase::AveragingVessel , PLMD::vesselbase::Between , PLMD::vesselbase::FunctionVessel , PLMD::vesselbase::Highest , PLMD::vesselbase::Histogram , PLMD::vesselbase::LessThan , PLMD::vesselbase::Lowest , PLMD::vesselbase::Max , PLMD::vesselbase::Mean , PLMD::vesselbase::Min , PLMD::vesselbase::Moments , PLMD::vesselbase::MoreThan , PLMD::vesselbase::OrderingVessel , PLMD::vesselbase::ShortcutVessel , PLMD::vesselbase::StoreDataVessel , PLMD::vesselbase::Sum , PLMD::vesselbase::ValueVessel , PLMD::vesselbase::Vessel
• remove() : PLMD::ActionRegister , PLMD::analysis::LandmarkRegister , PLMD::Atoms , PLMD::CLToolRegister , PLMD::Keywords , PLMD::MetricRegister , PLMD::vesselbase::VesselRegister
• remove_problematic() : PLMD::colvar::CS2Backbone
• removeCenter() : PLMD::RMSD
• removeDuplicates() : PLMD::Tools
• removeGroup() : PLMD::Atoms
• removeVirtualAtom() : PLMD::Atoms
• requestArguments() : PLMD::ActionWithArguments
• requestAtoms() : PLMD::ActionAtomistic , PLMD::ActionWithVirtualAtom , PLMD::Colvar , PLMD::multicolvar::VolumeGradientBase
• rescaleForces() : PLMD::MDAtomsBase , PLMD::MDAtomsTyped< T >
• reserve() : PLMD::Keywords
• reserved() : PLMD::Keywords
• reserveFlag() : PLMD::Keywords
• reserveKeyword() : PLMD::crystallization::GradientVessel , PLMD::crystallization::VectorMean , PLMD::crystallization::VectorSum , PLMD::mapping::SpathVessel , PLMD::mapping::ZpathVessel , PLMD::vesselbase::AltMin , PLMD::vesselbase::Between , PLMD::vesselbase::Highest , PLMD::vesselbase::Histogram , PLMD::vesselbase::LessThan , PLMD::vesselbase::Lowest , PLMD::vesselbase::Max , PLMD::vesselbase::Mean , PLMD::vesselbase::Min , PLMD::vesselbase::Moments , PLMD::vesselbase::MoreThan , PLMD::vesselbase::Sum
• reset() : PLMD::IFile , PLMD::Stopwatch::Time , PLMD::vesselbase::AveragingVessel
• reset_style() : PLMD::Keywords
• resetActive() : PLMD::PlumedMain
• ResetCell() : PLMD::generic::ResetCell
• resize() : PLMD::analysis::AverageVessel , PLMD::crystallization::GradientVessel , PLMD::crystallization::VectorMean , PLMD::crystallization::VectorSum , PLMD::gridtools::GridVessel , PLMD::Matrix< T > , PLMD::multicolvar::CatomPack , PLMD::MultiValue , PLMD::ReferenceValuePack , PLMD::vesselbase::BridgeVessel , PLMD::vesselbase::FunctionVessel , PLMD::vesselbase::Moments , PLMD::vesselbase::OrderingVessel , PLMD::vesselbase::ShortcutVessel , PLMD::vesselbase::StoreDataVessel , PLMD::vesselbase::Vessel
• resizeBookeepingArray() : PLMD::multicolvar::MultiColvarBase
• resizeBuffer() : PLMD::vesselbase::Vessel
• resizeDerivatives() : PLMD::Value
• resizeFunctions() : PLMD::vesselbase::ActionWithVessel
• resizeRestOfFrame() : PLMD::MultiReferenceBase , PLMD::PointWiseMapping
• resizeTemporyMultiValues() : PLMD::vesselbase::StoreDataVessel
• resizeVectors() : PLMD::Atoms
• rest_of_description() : PLMD::analysis::LandmarkSelectionBase
• Restart() : PLMD::setup::Restart
• Restraint() : PLMD::bias::Restraint
• retrieveActiveList() : PLMD::DynamicList< T >
• retrieveAdjacencyLists() : PLMD::adjmat::AdjacencyMatrixVessel
• retrieveAtoms() : PLMD::ActionAtomistic , PLMD::multicolvar::MultiColvarBase
• retrieveAtomsInCluster() : PLMD::adjmat::ClusterAnalysisBase , PLMD::adjmat::ClusteringBase , PLMD::adjmat::ClusterWithSurface
• retrieveCentralAtomPos() : PLMD::multicolvar::BridgedMultiColvarFunction
• retrieveConnectionValue() : PLMD::adjmat::ActionWithInputMatrix
• retrieveDerivatives() : PLMD::adjmat::AdjacencyMatrixVessel , PLMD::vesselbase::StoreDataVessel
• retrieveDomain() : PLMD::crystallization::InterMolecularTorsions , PLMD::multicolvar::Torsions , PLMD::vesselbase::ActionWithVessel
• retrieveEdgeList() : PLMD::adjmat::AdjacencyMatrixVessel
• retrieveMatrix() : PLMD::adjmat::AdjacencyMatrixVessel
• retrieveNeighboringAtoms() : PLMD::LinkCells
• retrieveSequentialValue() : PLMD::vesselbase::StoreDataVessel
• retrieveTypeDimensions() : PLMD::adjmat::AdjacencyMatrixBase
• retrieveValueWithIndex() : PLMD::vesselbase::StoreDataVessel
• retrieveWeightWithIndex() : PLMD::vesselbase::StoreDataVessel
• ReweightBase() : PLMD::bias::ReweightBase
• ReweightBias() : PLMD::bias::ReweightBias
• ReweightMetad() : PLMD::bias::ReweightMetad
• ReweightTemperature() : PLMD::bias::ReweightTemperature
• rewind() : PLMD::OFile
• RingInfo() : PLMD::colvar::CS2Backbone::RingInfo
• RMSD() : PLMD::colvar::RMSD , PLMD::RMSD
• RMSDBase() : PLMD::RMSDBase
• RMSDCoreData() : PLMD::RMSDCoreData
• RootFindingBase() : PLMD::RootFindingBase< FCLASS >
• Row() : PLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row
• run() : PLMD::analysis::ClassicalScaling , PLMD::CLToolMain
• runAllTasks() : PLMD::vesselbase::ActionWithVessel
• runAnalysis() : PLMD::analysis::Analysis
• runFinalJobs() : PLMD::Action , PLMD::analysis::Analysis , PLMD::gridtools::ConvertToFES , PLMD::gridtools::GridPrintingBase
• runJobsAtEndOfCalculation() : PLMD::PlumedMain