Here is a list of all class members with links to the classes they belong to:

- r -

• r : PLMD::Communicator::Request
• RADIUS : PLMD::colvar::Gyration
• radius : PLMD::molfile::molfile_atom_t
• random : PLMD::bias::ABMD
• RANDOM : PLMD::ExchangePatterns
• random : PLMD::ExchangePatterns
• Random() : PLMD::Random
• RandomExchanges() : PLMD::generic::RandomExchanges
• randomize_velocities() : PLMD::cltools::SimpleMD
• RandU01() : PLMD::Random
• rank : PLMD::DynamicList< T >
• rational : PLMD::SwitchingFunction
• RDC() : PLMD::RDC
• read() : PLMD::DRMSD , PLMD::EuclideanDistance , PLMD::FakeFrame
• Read() : PLMD::generic::Read
• read : PLMD::IFile::Field , PLMD::KernelFunctions , PLMD::MultiDomainRMSD , PLMD::NormalizedEuclideanDistance , PLMD::OptimalRMSD , PLMD::PDB , PLMD::ReferenceConfiguration , PLMD::SimpleRMSD , PLMD::TargetDist
• read_angles : PLMD::molfile::molfile_plugin_t
• read_backbone : PLMD::SetupMolInfo
• read_bonds : PLMD::molfile::molfile_plugin_t
• read_input() : PLMD::cltools::SimpleMD
• read_molecule_metadata : PLMD::molfile::molfile_plugin_t
• read_natoms() : PLMD::cltools::SimpleMD
• read_next_timestep : PLMD::molfile::molfile_plugin_t
• read_positions() : PLMD::cltools::SimpleMD
• read_qm_metadata : PLMD::molfile::molfile_plugin_t
• read_qm_rundata : PLMD::molfile::molfile_plugin_t
• read_qm_timestep_metadata : PLMD::molfile::molfile_plugin_t
• read_rawgraphics : PLMD::molfile::molfile_plugin_t
• read_structure : PLMD::molfile::molfile_plugin_t
• read_timestep : PLMD::molfile::molfile_plugin_t
• read_timestep_metadata : PLMD::molfile::molfile_plugin_t
• read_volumetric_data : PLMD::molfile::molfile_plugin_t
• read_volumetric_metadata : PLMD::molfile::molfile_plugin_t
• 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
• readBunch() : PLMD::function::FilesHandler
• readChunkOfGaussians() : PLMD::bias::MetaD
• readCommandLineArgs() : PLMD::CLTool
• readDataFromFile() : PLMD::analysis::Analysis
• readFrame() : PLMD::MultiReferenceBase
• readFromFilepointer() : PLMD::PDB
• readFromPoint() : PLMD::BiasRepresentation
• readGaussians() : PLMD::bias::MetaD
• readGroupsKeyword() : PLMD::multicolvar::MultiColvar
• readInput() : PLMD::CLTool
• readInputFile() : PLMD::CLTool , PLMD::PlumedMain
• readInputWords() : PLMD::PlumedMain
• readReference() : PLMD::SingleDomainRMSD
• readRestOfFrame() : PLMD::MultiReferenceBase , PLMD::PointWiseMapping
• readSpeciesKeyword() : PLMD::multicolvar::MultiColvar
• ReadStateFull() : PLMD::Random
• readThreeGroups() : PLMD::multicolvar::MultiColvar
• readTwoGroups() : PLMD::multicolvar::MultiColvar
• readvals : PLMD::generic::Read
• readVesselKeywords() : PLMD::vesselbase::ActionWithVessel
• realToScaled() : PLMD::Pbc
• receive() : PLMD::IMD
• recompute() : PLMD::crystallization::StoreVectorsVessel , PLMD::multicolvar::AdjacencyMatrixVessel , PLMD::vesselbase::StoreDataVessel
• Recv() : PLMD::Communicator
• reduce() : PLMD::LatticeReduction
• reduce2() : PLMD::LatticeReduction
• reduced : PLMD::NeighborList , PLMD::Pbc
• reduceFast() : PLMD::LatticeReduction
• reduceSlow() : PLMD::LatticeReduction
• reference : PLMD::colvar::ContactMap , PLMD::colvar::PathMSDBase , PLMD::RMSD
• reference_args : PLMD::ReferenceArguments
• reference_atoms : PLMD::ReferenceAtoms
• ReferenceArguments() : PLMD::ReferenceArguments
• ReferenceAtoms() : PLMD::ReferenceAtoms
• ReferenceConfiguration() : PLMD::ReferenceConfiguration , PLMD::ReferenceConfigurationOptions
• ReferenceConfigurationOptions() : PLMD::ReferenceConfigurationOptions
• references : PLMD::secondarystructure::SecondaryStructureRMSD
• registerKeywords() : PLMD::Action , PLMD::ActionAtomistic , PLMD::ActionPilot , PLMD::ActionSetup , PLMD::ActionWithArguments , PLMD::ActionWithValue , PLMD::ActionWithVirtualAtom , PLMD::analysis::Analysis , PLMD::analysis::AnalysisWithLandmarks , PLMD::analysis::ClassicalMultiDimensionalScaling , PLMD::analysis::Committor , PLMD::analysis::Histogram , PLMD::bias::ABMD , PLMD::bias::Bias , PLMD::bias::BiasValue , PLMD::bias::External , PLMD::bias::LWalls , PLMD::bias::MetaD , PLMD::bias::MovingRestraint , PLMD::bias::Restraint , 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::DHEnergy , PLMD::colvar::Dipole , PLMD::colvar::Distance , PLMD::colvar::DRMSD , PLMD::colvar::Energy , PLMD::colvar::Gyration , PLMD::colvar::MultiRMSD , PLMD::colvar::NOE , PLMD::colvar::PathMSD , PLMD::colvar::PathMSDBase , PLMD::colvar::Position , PLMD::colvar::PropertyMap , PLMD::Colvar , PLMD::colvar::RMSD , PLMD::colvar::Template , PLMD::colvar::Torsion , PLMD::colvar::Volume , PLMD::crystallization::Fccubic , PLMD::crystallization::LocalSteinhardt< T > , PLMD::crystallization::MoleculeOrientation , PLMD::crystallization::OrientationSphere , PLMD::crystallization::Q3 , PLMD::crystallization::Q4 , PLMD::crystallization::Q6 , PLMD::crystallization::SimpleCubic , PLMD::crystallization::Steinhardt , PLMD::crystallization::StoreVectorsVessel , PLMD::crystallization::Tetrahedral , PLMD::crystallization::VectorMean , PLMD::crystallization::VectorMultiColvar , PLMD::function::Combine , PLMD::function::Ensemble , PLMD::function::FuncPathMSD , PLMD::function::FuncSumHills , PLMD::function::Function , PLMD::function::Matheval , PLMD::function::Piecewise , PLMD::function::Sort , PLMD::function::Target , PLMD::generic::Debug , PLMD::generic::DumpAtoms , PLMD::generic::DumpDerivatives , PLMD::generic::DumpForces , PLMD::generic::DumpProjections , PLMD::generic::FitToTemplate , PLMD::generic::Flush , PLMD::generic::Group , PLMD::generic::Include , PLMD::generic::Print , PLMD::generic::RandomExchanges , PLMD::generic::Read , PLMD::generic::Time , PLMD::generic::WholeMolecules , PLMD::HistogramBead , PLMD::IMD , PLMD::manyrestraints::ManyRestraintsBase , PLMD::manyrestraints::UWalls , PLMD::mapping::Mapping , PLMD::mapping::Path , PLMD::mapping::PathBase , PLMD::mapping::PropertyMap , PLMD::mapping::SpathVessel , PLMD::mapping::ZpathVessel , PLMD::multicolvar::ActionVolume , PLMD::multicolvar::AdjacencyMatrixAction , PLMD::multicolvar::AdjacencyMatrixVessel , PLMD::multicolvar::AlphaBeta , PLMD::multicolvar::Angles , PLMD::multicolvar::Bridge , PLMD::multicolvar::CoordinationNumbers , PLMD::multicolvar::Density , PLMD::multicolvar::DHEnergy , PLMD::multicolvar::DihedralCorrelation , PLMD::multicolvar::Distances , PLMD::multicolvar::DumpMultiColvar , PLMD::multicolvar::LocalAverage , PLMD::multicolvar::MultiColvar , PLMD::multicolvar::MultiColvarBase , PLMD::multicolvar::MultiColvarFunction , PLMD::multicolvar::NumberOfLinks , PLMD::multicolvar::Sprint , PLMD::multicolvar::StoreColvarVessel , PLMD::multicolvar::Torsions , PLMD::multicolvar::VolumeAround , PLMD::multicolvar::XDistances , PLMD::RDC , 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::Ghost , PLMD::vesselbase::ActionWithInputVessel , PLMD::vesselbase::ActionWithVessel , PLMD::vesselbase::Between , PLMD::vesselbase::FunctionVessel , PLMD::vesselbase::Histogram , PLMD::vesselbase::LessThan , PLMD::vesselbase::Max , PLMD::vesselbase::Mean , PLMD::vesselbase::Min , PLMD::vesselbase::Moments , PLMD::vesselbase::MoreThan , PLMD::vesselbase::ShortcutVessel , PLMD::vesselbase::StoreDataVessel , PLMD::vesselbase::StoreValueAndWeightVessel , PLMD::vesselbase::StoreValueVessel , PLMD::vesselbase::Sum , PLMD::vesselbase::Vessel
• remark : PLMD::PDB
• remarklen : PLMD::molfile::molfile_metadata_t
• remarks : PLMD::molfile::molfile_metadata_t
• remove() : PLMD::ActionRegister , PLMD::analysis::LandmarkRegister , PLMD::Atoms , PLMD::CLToolRegister , PLMD::Keywords , PLMD::MetricRegister , PLMD::vesselbase::VesselRegister
• removeDuplicates() : PLMD::Tools
• removeGroup() : PLMD::Atoms
• removeVirtualAtom() : PLMD::Atoms
• requestArguments() : PLMD::ActionWithArguments
• requestAtoms() : PLMD::ActionAtomistic , PLMD::ActionWithVirtualAtom , PLMD::Colvar , PLMD::multicolvar::ActionVolume
• requestlist_ : PLMD::NeighborList
• rescaledToBias : PLMD::BiasRepresentation
• rescaleForces() : PLMD::MDAtomsBase , PLMD::MDAtomsTyped< T >
• reserve() : PLMD::Keywords
• reserved() : PLMD::Keywords
• reserved_keys : PLMD::Keywords
• reserveFlag() : PLMD::Keywords
• reserveKeyword() : PLMD::crystallization::VectorMean , PLMD::mapping::SpathVessel , PLMD::mapping::ZpathVessel , PLMD::multicolvar::DHEnergy , PLMD::vesselbase::Between , PLMD::vesselbase::Histogram , PLMD::vesselbase::LessThan , PLMD::vesselbase::Max , PLMD::vesselbase::Mean , PLMD::vesselbase::Min , PLMD::vesselbase::Moments , PLMD::vesselbase::MoreThan , PLMD::vesselbase::Sum
• reset() : PLMD::IFile , PLMD::Stopwatch::Time
• reset_style() : PLMD::Keywords
• resetActive() : PLMD::PlumedMain
• resetOutputForces() : PLMD::bias::Bias
• resid : PLMD::molfile::md_atom , PLMD::molfile::molfile_atom_t
• residue : PLMD::PDB
• residueNames : PLMD::generic::DumpAtoms
• residuenames : PLMD::PDB
• residueNumbers : PLMD::generic::DumpAtoms
• resize() : PLMD::crystallization::VectorMean , PLMD::Matrix< T > , PLMD::vesselbase::BridgeVessel , PLMD::vesselbase::FunctionVessel , PLMD::vesselbase::Moments , PLMD::vesselbase::ShortcutVessel , PLMD::vesselbase::StoreDataVessel , PLMD::vesselbase::Vessel
• resizeBuffer() : PLMD::vesselbase::Vessel
• resizeDerivatives() : PLMD::Value
• resizeDynamicArrays() : PLMD::multicolvar::MultiColvarFunction
• resizeFunctions() : PLMD::vesselbase::ActionWithVessel
• resizeLocalArrays() : PLMD::multicolvar::MultiColvarBase
• resizeRestOfFrame() : PLMD::MultiReferenceBase , PLMD::PointWiseMapping
• resizeVectors() : PLMD::Atoms
• resname : PLMD::molfile::md_atom , PLMD::molfile::molfile_atom_t
• rest_of_description() : PLMD::analysis::LandmarkSelectionBase
• restart : PLMD::PlumedMain
• Restart() : PLMD::setup::Restart
• Restraint() : PLMD::bias::Restraint
• retrieveActiveList() : PLMD::DynamicList< T >
• retrieveAtomicDerivatives() : PLMD::ReferenceAtoms
• retrieveAtoms() : PLMD::ActionAtomistic
• retrieveCentralAtomPos() : PLMD::multicolvar::MultiColvarBase
• retrieveDomain() : PLMD::multicolvar::Torsions , PLMD::vesselbase::ActionWithVessel
• retrieveMatrix() : PLMD::multicolvar::AdjacencyMatrixAction
• retrieveNeighboringAtoms() : PLMD::LinkCells
• retrieveNorm() : PLMD::analysis::Analysis
• reusing_data : PLMD::analysis::Analysis
• rev : PLMD::molfile::md_file
• rewind() : PLMD::OFile
• rfile : PLMD::analysis::Analysis
• rg_type : PLMD::colvar::Gyration
• rmsd : PLMD::colvar::MultiRMSD , PLMD::colvar::RMSD
• RMSD() : PLMD::colvar::RMSD , PLMD::RMSD
• RMSDBase() : PLMD::RMSDBase
• RNMX : PLMD::Random
• rotate : PLMD::generic::Print
• rotateArguments : PLMD::generic::Print
• rotateCountdown : PLMD::generic::Print
• rotateLast : PLMD::generic::Print
• rotmat0on1 : PLMD::Kearsley
• rotmat1on0 : PLMD::Kearsley
• Row() : PLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row
• rtemp : PLMD::analysis::Analysis
• run() : PLMD::analysis::ClassicalScaling , PLMD::CLToolMain , PLMD::molfile::molfile_qm_t
• runAllTasks() : PLMD::vesselbase::ActionWithVessel
• runAnalysis() : PLMD::analysis::Analysis
• runFinalJobs() : PLMD::Action , PLMD::analysis::Analysis
• runJobsAtEndOfCalculation() : PLMD::PlumedMain
• running : PLMD::Stopwatch::Watch
• runtitle : PLMD::molfile::molfile_qm_sysinfo_t
• runtype : PLMD::molfile::molfile_qm_sysinfo_t
• rw : PLMD::Matrix< T >