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

- r -

• r : PLMD::Communicator::Request , PLMD::generic::CreateMask
• R0 : PLMD::membranefusion::fusionPoreExpansionP
• r00 : PLMD::piv::PIV
• R0_ : PLMD::isdb::FretEfficiency
• r0_ : PLMD::ves::FermiSwitchingFunction
• r_eff_ : PLMD::s2cm::S2ContactModel
• r_globalshift_ : PLMD::s2cm::S2ContactModel
• R_HIS : PLMD::isdb::CS2Backbone::RingInfo
• r_min_ : PLMD::maze::Random_Acceleration_MD
• R_PHE : PLMD::isdb::CS2Backbone::RingInfo
• R_TRP1 : PLMD::isdb::CS2Backbone::RingInfo
• R_TRP2 : PLMD::isdb::CS2Backbone::RingInfo
• R_TYR : PLMD::isdb::CS2Backbone::RingInfo
• RadialTetra() : PLMD::symfunc::RadialTetra
• RADIUS : PLMD::colvar::Gyration
• radius : PLMD::molfile::molfile_atom_t
• rand : PLMD::bias::ExtendedLagrangian
• rand_ : PLMD::eds::EDS , PLMD::fisst::FISST
• RandInt() : PLMD::Random
• random : PLMD::bias::ABMD , PLMD::ExchangePatterns
• RANDOM : PLMD::ExchangePatterns
• random : PLMD::generic::CreateMask , PLMD::isdb::Metainference , PLMD::isdb::MetainferenceBase
• Random() : PLMD::Random
• random_ : PLMD::isdb::EMMI
• Random_Acceleration_MD() : PLMD::maze::Random_Acceleration_MD
• random_fwd : PLMD::ExchangePatterns
• random_restart_hill_climbing() : PLMD::maze::Memetic
• Random_Walk() : PLMD::maze::Random_Walk
• RandomExchanges() : PLMD::generic::RandomExchanges
• randomize() : PLMD::maze::rnd
• randomize_velocities() : PLMD::cltools::SimpleMD
• randomizeValuesGaussian() : PLMD::ves::CoeffsMatrix , PLMD::ves::CoeffsVector
• RandU01() : PLMD::Random
• rank_ : PLMD::isdb::EMMI , PLMD::isdb::Shadow , PLMD::maze::Optimizer , PLMD::opes::OPESexpanded , PLMD::opes::OPESmetad< mode > , PLMD::ves::VesDeltaF
• rational() : PLMD::switchContainers::rational< isFast, nis2m >
• rbegin() : PLMD::gch::small_vector< T, InlineCapacity, Allocator >
• rct_ : PLMD::opes::OPESexpanded
• rct_ustride_ : PLMD::bias::MetaD
• rcut2 : PLMD::contour::DistanceFromContourBase
• RCYL : PLMD::funnel::Funnel , PLMD::membranefusion::fusionPoreNucleationP
• RCYLMEM : PLMD::membranefusion::memFusionP
• RDC() : PLMD::isdb::RDC
• RDF() : PLMD::gridtools::RDF
• read() : PLMD::function::Bessel , PLMD::function::Between , PLMD::function::Combine , PLMD::function::Custom , PLMD::function::FunctionTemplateBase , PLMD::function::Highest , PLMD::function::LessThan , PLMD::function::Moments , PLMD::function::MoreThan , PLMD::function::Piecewise , PLMD::function::Sort , PLMD::function::Sum
• Read() : PLMD::generic::Read
• read() : PLMD::gridtools::EvaluateGridFunction , PLMD::IFile::Field , PLMD::KernelFunctions , PLMD::PDB , PLMD::refdist::Difference , PLMD::symfunc::CylindricalHarmonic , PLMD::symfunc::Fccubic , PLMD::symfunc::SphericalHarmonic , PLMD::TargetDist
• read_angles : PLMD::molfile::molfile_plugin_t
• read_backbone : PLMD::GenericMolInfo
• read_bias() : PLMD::isdb::Rescale
• read_bonds : PLMD::molfile::molfile_plugin_t
• read_exp_errors() : PLMD::isdb::EMMI
• read_exp_overlaps() : PLMD::isdb::EMMI
• read_input() : PLMD::cltools::PesMD , PLMD::cltools::SimpleMD
• read_inputfiles() : PLMD::drr::UIestimator::UIestimator
• read_molecule_metadata : PLMD::molfile::molfile_plugin_t
• read_natoms() : PLMD::cltools::SimpleMD
• read_next_timestep : PLMD::molfile::molfile_plugin_t
• read_one_group : PLMD::adjmat::AdjacencyMatrixBase
• 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_status() : PLMD::isdb::EMMI
• read_structure : PLMD::molfile::molfile_plugin_t
• read_timestep : PLMD::molfile::molfile_plugin_t
• read_timestep_metadata : PLMD::molfile::molfile_plugin_t
• read_timestep_pagealign_size : PLMD::molfile::molfile_plugin_t
• read_volumetric_data : PLMD::molfile::molfile_plugin_t
• read_volumetric_data_ex : PLMD::molfile::molfile_plugin_t
• read_volumetric_metadata : PLMD::molfile::molfile_plugin_t
• readAtomsFromPDB() : PLMD::Action , PLMD::ActionAtomistic
• readBackboneAtoms() : PLMD::secondarystructure::SecondaryStructureRMSD
• readBinary() : PLMD::ActionForInterface , PLMD::ActionToPutData , PLMD::DomainDecomposition , PLMD::PbcAction , PLMD::PlumedMain , PLMD::Value
• readBunch() : PLMD::function::FilesHandler
• readCoeffsFromFiles() : PLMD::ves::Optimizer , PLMD::ves::VesBias
• readCommandLineArgs() : PLMD::CLTool
• readDataFromFile() : PLMD::ves::CoeffsVector
• readDeltaG() : PLMD::sasa::SASA_HASEL , PLMD::sasa::SASA_LCPO
• readFromFile() : PLMD::ves::CoeffsVector
• readFromFilepointer() : PLMD::PDB
• readFromPoint() : PLMD::BiasRepresentation
• readGaussians() : PLMD::bias::MetaD , PLMD::bias::PBMetaD
• ReadGridInSetup() : PLMD::gridtools::ReadGridInSetup
• readHeaderFromFile() : PLMD::ves::CoeffsVector
• readInput() : PLMD::CLTool
• readInputFile() : PLMD::CLTool , PLMD::PlumedMain
• readInputFrames() : PLMD::mapping::Path
• readInputLine() : PLMD::ActionShortcut , PLMD::PlumedMain
• readInputLines() : PLMD::PlumedMain
• readinputs() : PLMD::sizeshape::position_linear_proj , PLMD::sizeshape::position_maha_dist
• readInputWords() : PLMD::PlumedMain
• readInRestart() : PLMD::eds::EDS , PLMD::fisst::FISST
• readInRestartTargetDistGrid() : PLMD::ves::TargetDistribution
• readInRestartTargetDistribution() : PLMD::ves::LinearBasisSetExpansion
• ReadLagrangians() : PLMD::bias::MaxEnt
• readLCPOparam() : PLMD::isdb::SAXS , PLMD::sasa::SASA_LCPO
• readMaxSurf() : PLMD::sasa::SASA_HASEL , PLMD::sasa::SASA_LCPO
• readOneSetFromFile() : PLMD::ves::CoeffsVector
• readPDB() : PLMD::sasa::SASA_HASEL , PLMD::sasa::SASA_LCPO
• readPropertyInformation() : PLMD::mapping::Path
• readSASAparam() : PLMD::sasa::SASA_HASEL
• readShortcutKeywords() : PLMD::ActionShortcut , PLMD::multicolvar::MultiColvarShortcuts
• readShortcutWords() : PLMD::secondarystructure::SecondaryStructureRMSD
• ReadStateFull() : PLMD::Random
• readTemperingSpecs() : PLMD::bias::MetaD
• readvals : PLMD::generic::Read
• real_output : PLMD::fourier::FourierTransform
• reallyBuildArgumentStore() : PLMD::ActionWithVector
• realToScaled() : PLMD::Pbc
• recalculateSmacofWeights() : PLMD::dimred::ArrangePoints
• Reciprocal() : PLMD::lepton::Operation
• RECIPROCAL : PLMD::lepton::Operation
• recursive_merge_ : PLMD::opes::OPESmetad< mode >
• Recv() : PLMD::Communicator
• reduce() : PLMD::LatticeReduction
• reduce2() : PLMD::LatticeReduction
• reduce_tasks : PLMD::ActionWithVector
• reduced : PLMD::NeighborList , PLMD::Pbc
• reduceFast() : PLMD::LatticeReduction
• reduceSlow() : PLMD::LatticeReduction
• ref : PLMD::switchContainers::nativeqSwitch
• ref_f_name : PLMD::sizeshape::position_linear_proj , PLMD::sizeshape::position_maha_dist
• ref_file : PLMD::piv::PIV
• ref_str : PLMD::sizeshape::position_linear_proj , PLMD::sizeshape::position_maha_dist
• refargs : PLMD::mapping::PathProjectionCalculator
• refatoms : PLMD::generic::WrapAround
• reference : PLMD::colvar::ContactMap , PLMD::colvar::PathMSDBase , PLMD::function::FuncPathGeneral , PLMD::gch::small_vector< T, InlineCapacity, Allocator > , PLMD::gch::small_vector_iterator< Pointer, DifferenceType > , PLMD::GenericMolInfo , PLMD::RMSD , PLMD::RMSDCoreData
• reference_center : PLMD::RMSD
• reference_center_is_calculated : PLMD::RMSD
• reference_center_is_removed : PLMD::RMSD
• reference_mat : PLMD::ERMSD
• referenceCounter : PLMD::PlumedMain
• refs : PLMD::generic::WholeMolecules
• Register() : PLMD::Register
• registerInputFileKeywords() : PLMD::mapping::Path
• registerKeywords() : PLMD::Action , PLMD::ActionAnyorder , PLMD::ActionAtomistic , PLMD::ActionForInterface , PLMD::ActionPilot , PLMD::ActionSetup , PLMD::ActionShortcut , PLMD::ActionToGetData , PLMD::ActionToPutData , PLMD::ActionWithArguments , PLMD::ActionWithMatrix , PLMD::ActionWithValue , PLMD::ActionWithVector , PLMD::ActionWithVirtualAtom , PLMD::adjmat::AdjacencyMatrixBase , PLMD::adjmat::Bridge , PLMD::adjmat::BridgeMatrix , PLMD::adjmat::ContactMatrix , PLMD::adjmat::ContactMatrixShortcut , PLMD::adjmat::DistanceMatrix , PLMD::adjmat::HbondMatrix , PLMD::adjmat::Neighbors , PLMD::adjmat::TopologyMatrix , PLMD::adjmat::TorsionsMatrix , PLMD::bias::ABMD , PLMD::bias::Bias , PLMD::bias::BiasValue , PLMD::bias::ExtendedLagrangian , PLMD::bias::External , PLMD::bias::LWalls , PLMD::bias::MaxEnt , PLMD::bias::MetaD , PLMD::bias::MovingRestraint , PLMD::bias::PBMetaD , PLMD::bias::Restraint , PLMD::bias::RestraintShortcut , PLMD::bias::ReweightBase , PLMD::bias::ReweightBias , PLMD::bias::ReweightMetad , PLMD::bias::ReweightTemperaturePressure , PLMD::bias::UWalls , PLMD::bias::Walls , PLMD::CLTool , PLMD::cltools::CLToolSumHills , PLMD::cltools::Completion , PLMD::cltools::Driver< real > , PLMD::cltools::GenExample , PLMD::cltools::GenJson , PLMD::cltools::GenTemplate , PLMD::cltools::Info , PLMD::cltools::kt , PLMD::cltools::Manual , PLMD::cltools::PdbRenumber , PLMD::cltools::PesMD , PLMD::cltools::ShowGraph , PLMD::cltools::SimpleMD , PLMD::cltools::SwitchingPlotter , PLMD::clusters::ClusterDiameter , PLMD::clusters::ClusterDistribution , PLMD::clusters::ClusterDistributionShortcut , PLMD::clusters::ClusteringBase , PLMD::clusters::ClusterNatoms , PLMD::clusters::ClusterProperties , PLMD::clusters::ClusterWeights , PLMD::clusters::ClusterWithSurface , PLMD::clusters::DFSClustering , PLMD::clusters::OutputCluster , PLMD::colvar::Angle , PLMD::colvar::Cell , PLMD::colvar::ColvarFake , PLMD::colvar::ColvarShortcut< T > , PLMD::colvar::ContactMap , PLMD::colvar::Coordination , PLMD::colvar::CoordinationBase , PLMD::colvar::DHEnergy , PLMD::colvar::DihedralCorrelation , PLMD::colvar::Dimer , PLMD::colvar::Dipole , PLMD::colvar::Distance , PLMD::colvar::DRMSD , PLMD::colvar::EEFSolv , PLMD::colvar::Energy , PLMD::colvar::ERMSD , PLMD::colvar::ExtraCV , PLMD::colvar::GHBFIX , PLMD::colvar::Gyration , PLMD::colvar::GyrationShortcut , PLMD::colvar::MultiColvarTemplate< T > , PLMD::colvar::MultiRMSD , PLMD::colvar::PathMSD , PLMD::colvar::PathMSDBase , PLMD::colvar::PCARMSD , PLMD::colvar::Plane , PLMD::colvar::Position , PLMD::colvar::ProjectionOnAxis , PLMD::colvar::PropertyMap , PLMD::colvar::Puckering , PLMD::Colvar , PLMD::colvar::RMSD , PLMD::colvar::RMSDShortcut , PLMD::colvar::RMSDVector , PLMD::colvar::SelectMassCharge , PLMD::colvar::Template , PLMD::colvar::Torsion , PLMD::colvar::Volume , PLMD::contour::ContourFindingBase , PLMD::contour::DistanceFromContour , PLMD::contour::DistanceFromContourBase , PLMD::contour::DistanceFromSphericalContour , PLMD::contour::DumpContour , PLMD::contour::FindContour , PLMD::contour::FindContourSurface , PLMD::contour::FindSphericalContour , PLMD::crystdistrib::BopsShortcut , PLMD::crystdistrib::DopsShortcut , PLMD::crystdistrib::Quaternion , PLMD::crystdistrib::QuaternionBondProductMatrix , PLMD::crystdistrib::QuaternionProductMatrix , PLMD::crystdistrib::RopsShortcut , PLMD::dimred::ArrangePoints , PLMD::dimred::ClassicalMultiDimensionalScaling , PLMD::dimred::PCA , PLMD::dimred::ProjectPoints , PLMD::dimred::SketchMap , PLMD::dimred::SketchMapProjection , PLMD::DomainDecomposition , PLMD::eds::EDS , PLMD::envsim::EnvironmentSimilarity , PLMD::fisst::FISST , PLMD::fourier::FourierTransform , PLMD::function::annfunc::ANN , PLMD::function::Bessel , PLMD::function::Between , PLMD::function::Combine , PLMD::function::Custom , PLMD::function::Ensemble , PLMD::function::FuncPathGeneral , PLMD::function::FuncPathMSD , PLMD::function::FuncSumHills , PLMD::function::Function , PLMD::function::FunctionOfMatrix< T > , PLMD::function::FunctionOfScalar< T > , PLMD::function::FunctionOfVector< T > , PLMD::function::FunctionShortcut< T > , PLMD::function::FunctionTemplateBase , PLMD::function::Highest , PLMD::function::LessThan , PLMD::function::LocalEnsemble , PLMD::function::Moments , PLMD::function::MoreThan , PLMD::function::Piecewise , PLMD::function::Product , PLMD::function::Sort , PLMD::function::Stats , PLMD::function::Sum , PLMD::funnel::Funnel , PLMD::funnel::FUNNEL_PS , PLMD::generic::Accumulate , PLMD::generic::Average , PLMD::generic::Collect , PLMD::generic::Committor , PLMD::generic::Constant , PLMD::generic::CreateMask , PLMD::generic::Debug , PLMD::generic::DumpAtoms , PLMD::generic::DumpDerivatives , PLMD::generic::DumpForces , PLMD::generic::DumpMassCharge , PLMD::generic::DumpPDB , PLMD::generic::DumpProjections , PLMD::generic::DumpVector , PLMD::generic::EffectiveEnergyDrift , PLMD::generic::EndPlumed , PLMD::generic::FitToTemplate , PLMD::generic::Flush , PLMD::generic::GatherReplicas , PLMD::generic::Include , PLMD::generic::MassChargeInput , PLMD::generic::Ones , PLMD::generic::PDB2Constant , PLMD::generic::Plumed , PLMD::generic::Print , PLMD::generic::PrintNDX , PLMD::generic::RandomExchanges , PLMD::generic::Read , PLMD::generic::ResetCell , PLMD::generic::Time , PLMD::generic::UpdateIf , PLMD::generic::WholeMolecules , PLMD::generic::WrapAround , PLMD::GenericMolInfo , PLMD::gridtools::ActionWithGrid , PLMD::gridtools::ConvertToFES , PLMD::gridtools::DumpGrid , PLMD::gridtools::EvaluateFunctionOnGrid , PLMD::gridtools::EvaluateGridFunction , PLMD::gridtools::FindGridOptimum , PLMD::gridtools::FunctionOfGrid< T > , PLMD::gridtools::Gradient , PLMD::gridtools::Histogram , PLMD::gridtools::InterpolateGrid , PLMD::gridtools::KDE , PLMD::gridtools::KLEntropy , PLMD::gridtools::MultiColvarDensity , PLMD::gridtools::PairEntropies , PLMD::gridtools::PairEntropy , PLMD::gridtools::RDF , PLMD::gridtools::ReadGridInSetup , PLMD::Group , PLMD::HistogramBead , PLMD::isdb::Caliber , PLMD::isdb::CS2Backbone , PLMD::isdb::EMMI , PLMD::isdb::FretEfficiency , PLMD::isdb::JCoupling , PLMD::isdb::Metainference , PLMD::isdb::MetainferenceBase , PLMD::isdb::NOE , PLMD::isdb::PRE , PLMD::isdb::RDC , PLMD::isdb::Rescale , PLMD::isdb::SAXS , PLMD::isdb::Select , PLMD::isdb::Selector , PLMD::isdb::Shadow , PLMD::landmarks::CollectFrames , PLMD::landmarks::FarthestPointSampling , PLMD::landmarks::LandmarkSelection , PLMD::landmarks::LogSumExp , PLMD::logmfd::LogMFD , PLMD::mapping::AdaptivePath , PLMD::mapping::GeometricPath , PLMD::mapping::GeometricPathShortcut , PLMD::mapping::Path , PLMD::mapping::PathDisplacements , PLMD::mapping::PathProjectionCalculator , PLMD::mapping::PathReparameterization , PLMD::mapping::PathTools , PLMD::mapping::PCAVars , PLMD::matrixtools::CovarianceMatrix , PLMD::matrixtools::Determinant , PLMD::matrixtools::DiagonalizeMatrix , PLMD::matrixtools::InvertMatrix , PLMD::matrixtools::MatrixOperationBase , PLMD::matrixtools::MatrixTimesMatrix , PLMD::matrixtools::MatrixTimesVector , PLMD::matrixtools::OuterProduct , PLMD::matrixtools::TransposeMatrix , PLMD::matrixtools::Voronoi , PLMD::maze::Loss , PLMD::maze::Memetic , PLMD::maze::Optimizer , PLMD::maze::OptimizerBias , PLMD::maze::Random_Acceleration_MD , PLMD::maze::Random_Walk , PLMD::maze::Simulated_Annealing , PLMD::maze::Steered_MD , PLMD::membranefusion::fusionPoreExpansionP , PLMD::membranefusion::fusionPoreNucleationP , PLMD::membranefusion::memFusionP , PLMD::metatensor::MetatensorPlumedAction , PLMD::multicolvar::AlphaBeta , PLMD::multicolvar::Angles , PLMD::multicolvar::CoordAngles , PLMD::multicolvar::Dihcor , PLMD::multicolvar::Distances , PLMD::multicolvar::DumpMultiColvar , PLMD::multicolvar::InPlaneDistances , PLMD::multicolvar::MFilterLess , PLMD::multicolvar::MFilterMore , PLMD::multicolvar::PlaneShortcut , PLMD::multicolvar::Torsions , PLMD::multicolvar::UWalls , PLMD::multicolvar::XAngle , PLMD::multicolvar::XYTorsions , PLMD::opes::ECVcustom , PLMD::opes::ECVlinear , PLMD::opes::ECVmultiThermal , PLMD::opes::ECVmultiThermalBaric , PLMD::opes::ECVumbrellasFile , PLMD::opes::ECVumbrellasLine , PLMD::opes::ExpansionCVs , PLMD::opes::OPESexpanded , PLMD::opes::OPESmetad< mode > , PLMD::pamm::HBPammMatrix , PLMD::pamm::HBPammShortcut , PLMD::pamm::PAMM , PLMD::PbcAction , PLMD::piv::PIV , PLMD::refdist::Difference , PLMD::refdist::Displacement , PLMD::refdist::EuclideanDistance , PLMD::refdist::Kernel , PLMD::refdist::MahalanobisDistance , PLMD::refdist::MatrixProductDiagonal , PLMD::refdist::NormalizedEuclideanDistance , PLMD::s2cm::S2ContactModel , PLMD::sasa::SASA_HASEL , PLMD::sasa::SASA_LCPO , PLMD::secondarystructure::AlphaRMSD , PLMD::secondarystructure::AntibetaRMSD , PLMD::secondarystructure::ParabetaRMSD , PLMD::secondarystructure::SecondaryStructureRMSD , PLMD::setup::Load , PLMD::setup::Restart , PLMD::setup::Units , PLMD::sizeshape::position_linear_proj , PLMD::sizeshape::position_maha_dist , PLMD::sprint::Sprint , PLMD::SwitchingFunction , PLMD::symfunc::AngularTetra , PLMD::symfunc::AtomicSMAC , PLMD::symfunc::CoordinationNumbers , PLMD::symfunc::CoordShellVectorFunction , PLMD::symfunc::CylindricalHarmonic , PLMD::symfunc::Fccubic , PLMD::symfunc::HexacticParameter , PLMD::symfunc::LocalAverage , PLMD::symfunc::LocalCrystallinity , PLMD::symfunc::LocalSteinhardt , PLMD::symfunc::RadialTetra , PLMD::symfunc::SMAC , PLMD::symfunc::SphericalHarmonic , PLMD::symfunc::Steinhardt , PLMD::symfunc::ThreeBodyGFunctions , PLMD::valtools::Concatenate , PLMD::valtools::Flatten , PLMD::valtools::SelectComponents , PLMD::valtools::SelectWithMask , PLMD::valtools::VStack , PLMD::vatom::ArgsToVatom , PLMD::vatom::Center , PLMD::vatom::CenterShortcut , PLMD::vatom::FixedAtom , PLMD::vatom::Ghost , PLMD::ves::BasisFunctions , PLMD::ves::BF_Chebyshev , PLMD::ves::BF_Combined , PLMD::ves::BF_Cosine , PLMD::ves::BF_CubicBsplines , PLMD::ves::BF_Custom , PLMD::ves::BF_Fourier , PLMD::ves::BF_Gaussians , PLMD::ves::BF_Legendre , PLMD::ves::BF_Powers , PLMD::ves::BF_Sine , PLMD::ves::BF_Wavelets , PLMD::ves::FermiSwitchingFunction , PLMD::ves::LinearBasisSetExpansion , PLMD::ves::MD_LinearExpansionPES , PLMD::ves::Opt_Adam , PLMD::ves::Opt_BachAveragedSGD , PLMD::ves::Opt_Dummy , PLMD::ves::Opt_RobbinsMonroSGD , PLMD::ves::Optimizer , PLMD::ves::OutputBasisFunctions , PLMD::ves::OutputFesBias , PLMD::ves::OutputTargetDistribution , PLMD::ves::TargetDistribution , PLMD::ves::TD_Chi , PLMD::ves::TD_ChiSquared , PLMD::ves::TD_Custom , PLMD::ves::TD_Exponential , PLMD::ves::TD_ExponentiallyModifiedGaussian , PLMD::ves::TD_Gaussian , PLMD::ves::TD_GeneralizedExtremeValue , PLMD::ves::TD_GeneralizedNormal , PLMD::ves::TD_Grid , PLMD::ves::TD_LinearCombination , PLMD::ves::TD_Multicanonical , PLMD::ves::TD_MultithermalMultibaric , PLMD::ves::TD_ProductCombination , PLMD::ves::TD_ProductDistribution , PLMD::ves::TD_Uniform , PLMD::ves::TD_VonMises , PLMD::ves::TD_WellTempered , PLMD::ves::VesBias , PLMD::ves::VesDeltaF , PLMD::ves::VesLinearExpansion , PLMD::volumes::ActionVolume , PLMD::volumes::Density , PLMD::volumes::VolumeAround , PLMD::volumes::VolumeCavity , PLMD::volumes::VolumeInCylinder , PLMD::volumes::VolumeInEnvelope , PLMD::volumes::VolumeInSphere , PLMD::volumes::VolumeShortcut< v > , PLMD::volumes::VolumeTetrapore , PLMD::wham::Wham , PLMD::wham::WhamHistogram , PLMD::wham::WhamWeights
• registerTemperingKeywords() : PLMD::bias::MetaD
• registrationLock() : PLMD::Register
• RegistrationLock() : PLMD::Register::RegistrationLock
• regulariser : PLMD::pamm::HBPammMatrix
• reinitializeIndices() : PLMD::ves::CoeffsBase
• release() : PLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::stack_temporary
• remarklen : PLMD::molfile::molfile_metadata_t
• remarks : PLMD::molfile::molfile_metadata_t
• remove() : PLMD::Keywords , PLMD::RegisterBase< Content >
• removeCenter() : PLMD::RMSD
• removeComponent() : PLMD::Keywords
• removeDuplicates() : PLMD::Tools
• removeOutputComponent() : PLMD::Keywords
• removeStretch() : PLMD::switchContainers::baseSwitch
• renameNodeVariables() : PLMD::lepton::ParsedExpression
• renameVariables() : PLMD::lepton::ParsedExpression
• rend() : PLMD::gch::small_vector< T, InlineCapacity, Allocator >
• reparameterizePart() : PLMD::mapping::PathReparameterization
• replaceLabelString() : PLMD::ves::CoeffsBase
• replica_ : PLMD::isdb::Caliber , PLMD::isdb::EMMI , PLMD::isdb::Metainference , PLMD::isdb::MetainferenceBase , PLMD::isdb::Rescale
• replica_averaging() : PLMD::isdb::Caliber , PLMD::isdb::Metainference , PLMD::isdb::MetainferenceBase
• replica_index : PLMD::Action
• report() : PLMD::CheckInRange
• request_capacity() : PLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >
• requestArguments() : PLMD::ActionWithArguments
• requestAtoms() : PLMD::ActionAtomistic , PLMD::ActionWithVirtualAtom , PLMD::Colvar , PLMD::volumes::ActionVolume
• requestExtraDependencies() : PLMD::ActionWithArguments
• requestlist_ : PLMD::NeighborList
• res_kind : PLMD::isdb::CS2Backbone::ChemicalShift
• res_name : PLMD::isdb::CS2Backbone::ChemicalShift
• res_num : PLMD::isdb::CS2Backbone::ChemicalShift , PLMD::isdb::CS2Backbone
• res_type_curr : PLMD::isdb::CS2Backbone::ChemicalShift
• res_type_next : PLMD::isdb::CS2Backbone::ChemicalShift
• res_type_prev : PLMD::isdb::CS2Backbone::ChemicalShift
• Rescale() : PLMD::isdb::Rescale
• rescale_force() : PLMD::DataPassingObject , PLMD::DataPassingObjectTyped< T >
• rescaledToBias : PLMD::BiasRepresentation
• rescaleForces() : PLMD::ActionToPutData
• reserve() : PLMD::gch::small_vector< T, InlineCapacity, Allocator > , PLMD::Keywords
• reserved() : PLMD::Keywords
• reserved_keys : PLMD::Keywords
• reserveFlag() : PLMD::Keywords
• reset() : PLMD::ActionForInterface , PLMD::DomainDecomposition , PLMD::IFile , PLMD::metatensor::vesin::cpu::GrowableNeighborList
• reset_data() : PLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >
• reset_period_ : PLMD::fisst::FISST
• reset_statistics() : PLMD::eds::EDS
• reset_style() : PLMD::Keywords
• resetable : PLMD::ActionToPutData
• resetActive() : PLMD::PlumedMain
• resetAveraging() : PLMD::ves::CoeffsMatrix , PLMD::ves::CoeffsVector
• resetAveragingCounter() : PLMD::ves::CoeffsMatrix , PLMD::ves::CoeffsVector
• resetBiasFileOutput() : PLMD::ves::VesBias , PLMD::ves::VesLinearExpansion
• ResetCell() : PLMD::generic::ResetCell
• resetFesFileOutput() : PLMD::ves::VesBias , PLMD::ves::VesLinearExpansion
• resetFesProjFileOutput() : PLMD::ves::VesBias
• resetForStepStart() : PLMD::ActionForInterface , PLMD::ActionToPutData , PLMD::DomainDecomposition
• resetInputs() : PLMD::PlumedMain
• resetOutputFmt() : PLMD::ves::CoeffsBase
• resetStepOfLastBiasGridUpdate() : PLMD::ves::LinearBasisSetExpansion
• resetStepOfLastBiasWithoutCutoffGridUpdate() : PLMD::ves::LinearBasisSetExpansion
• resetStepOfLastFesGridUpdate() : PLMD::ves::LinearBasisSetExpansion
• resetStoredTimestep() : PLMD::Action
• resetTargetDistFileOutput() : PLMD::ves::VesBias
• resetTargetDistProjFileOutput() : PLMD::ves::VesBias
• resetToDefaultOutputFmt() : PLMD::GridBase
• reshapeMatrixStore() : PLMD::Value
• resid : PLMD::molfile::md_atom , PLMD::molfile::molfile_atom_t
• residue : PLMD::PDB
• residue_atom : PLMD::isdb::SAXS
• residueNames : PLMD::generic::DumpAtoms
• residuenames : PLMD::PDB
• residueNumbers : PLMD::generic::DumpAtoms
• resize() : PLMD::gch::small_vector< T, InlineCapacity, Allocator > , PLMD::Matrix< T > , PLMD::MultiValue
• resize_with() : PLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >
• resizeCoeffs() : PLMD::ves::CoeffsVector
• resizeDerivatives() : PLMD::Value
• resizeIndices() : PLMD::ves::CoeffsBase
• resizeTemporyVector() : PLMD::MultiValue
• resname : PLMD::molfile::md_atom , PLMD::molfile::molfile_atom_t
• resolution : PLMD::isdb::SAXS
• resolution_function() : PLMD::isdb::SAXS
• restart : PLMD::Action , PLMD::drr::UIestimator::UIestimator , PLMD::PlumedMain
• Restart() : PLMD::setup::Restart
• restartTargetDistribution() : PLMD::ves::LinearBasisSetExpansion
• restartTargetDistributions() : PLMD::ves::VesBias , PLMD::ves::VesLinearExpansion
• Restraint() : PLMD::bias::Restraint
• RestraintShortcut() : PLMD::bias::RestraintShortcut
• rethrow() : PLMD::Plumed
• retrieve_only_rotation : PLMD::RMSDCoreData
• retrieveAdjacencyLists() : PLMD::clusters::ClusteringBase
• retrieveArgumentsAndHeight() : PLMD::gridtools::KDE
• retrieveAtoms() : PLMD::ActionAtomistic , PLMD::ActionWithVector
• retrieveAtomsInCells() : PLMD::LinkCells
• retrieveEdgeList() : PLMD::Value
• retrieveFullMatrix() : PLMD::matrixtools::MatrixOperationBase
• retrieveNeighboringAtoms() : PLMD::LinkCells
• retrieveNeighbours() : PLMD::adjmat::AdjacencyMatrixBase
• return_distances : PLMD::metatensor::vesin::VesinOptions
• return_shifts : PLMD::metatensor::vesin::VesinOptions
• return_vectors : PLMD::metatensor::vesin::VesinOptions
• rev : PLMD::molfile::md_file
• reverse_iterator : PLMD::gch::small_vector< T, InlineCapacity, Allocator >
• reweight : PLMD::bias::MaxEnt
• reweight_factor_ : PLMD::bias::MetaD
• ReweightBase() : PLMD::bias::ReweightBase
• ReweightBias() : PLMD::bias::ReweightBias
• ReweightMetad() : PLMD::bias::ReweightMetad
• ReweightTemperaturePressure() : PLMD::bias::ReweightTemperaturePressure
• rewind() : PLMD::OFile
• rg_type : PLMD::colvar::Gyration
• rgb3f : PLMD::molfile::molfile_volumetric_readwrite_t
• rgb3u : PLMD::molfile::molfile_volumetric_readwrite_t
• rho : PLMD::isdb::SAXS
• rho_corr : PLMD::isdb::SAXS
• RightParen : PLMD::lepton::ParseToken
• Rij : PLMD::isdb::SAXS
• ringInfo : PLMD::isdb::CS2Backbone
• RingInfo() : PLMD::isdb::CS2Backbone::RingInfo
• RMAX : PLMD::membranefusion::fusionPoreExpansionP
• rmsd : PLMD::colvar::PCARMSD
• RMSD() : PLMD::colvar::RMSD
• rmsd : PLMD::generic::FitToTemplate
• RMSD() : PLMD::RMSD
• rmsd_ : PLMD::isdb::Shadow
• rmsd_objects : PLMD::mapping::PathProjectionCalculator
• RMSDCoreData() : PLMD::RMSDCoreData
• rmsdPosClose : PLMD::colvar::PathMSDBase
• RMSDShortcut() : PLMD::colvar::RMSDShortcut
• RMSDVector() : PLMD::colvar::RMSDVector
• RNMX : PLMD::Random
• role : PLMD::ActionForInterface
• root : PLMD::generic::Plumed
• root5 : PLMD::gridtools::GridCoordinatesObject
• root_ : PLMD::Tree
• RootFindingBase() : PLMD::RootFindingBase< FCLASS >
• rootNode : PLMD::lepton::ParsedExpression
• RopsShortcut() : PLMD::crystdistrib::RopsShortcut
• rotate : PLMD::generic::Print
• rotateArguments : PLMD::generic::Print
• rotateCountdown : PLMD::generic::Print
• rotateLast : PLMD::generic::Print
• rotation : PLMD::generic::FitToTemplate , PLMD::generic::ResetCell , PLMD::RMSDCoreData , PLMD::sizeshape::position_linear_proj , PLMD::sizeshape::position_maha_dist
• rotationPosClose : PLMD::colvar::PathMSDBase
• rotationRefClose : PLMD::colvar::PathMSDBase
• round() : PLMD::drr::UIestimator::n_matrix
• Row() : PLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row
• row_starts : PLMD::valtools::Concatenate
• rowstart : PLMD::dimred::ProjectPoints
• rPIV : PLMD::piv::PIV
• rpress_ : PLMD::bias::ReweightTemperaturePressure
• rr00 : PLMD::RMSDCoreData
• rr11 : PLMD::RMSDCoreData
• rs : PLMD::sasa::SASA_HASEL , PLMD::sasa::SASA_LCPO
• rtemp_ : PLMD::bias::ReweightTemperaturePressure
• rtwo : PLMD::isdb::PRE
• rtype : PLMD::isdb::CS2Backbone::RingInfo
• run() : PLMD::CLToolMain , PLMD::molfile::molfile_qm_t
• runAllTasks() : PLMD::ActionWithVector
• runEndOfRowJobs() : PLMD::ActionWithMatrix , PLMD::adjmat::AdjacencyMatrixBase , PLMD::adjmat::Neighbors , PLMD::adjmat::TorsionsMatrix , PLMD::crystdistrib::QuaternionBondProductMatrix , PLMD::crystdistrib::QuaternionProductMatrix , PLMD::function::FunctionOfMatrix< T > , PLMD::matrixtools::MatrixTimesMatrix , PLMD::matrixtools::MatrixTimesVector , PLMD::matrixtools::OuterProduct , PLMD::matrixtools::Voronoi , PLMD::valtools::VStack
• runFinalJobs() : PLMD::Action
• runInSerial() : PLMD::ActionWithVector
• runJobsAtEndOfCalculation() : PLMD::PlumedMain
• running : PLMD::Stopwatch::Watch
• runSingleTaskCalculation() : PLMD::function::FunctionOfVector< T >
• runTask() : PLMD::ActionWithMatrix , PLMD::ActionWithVector
• runtimeptr : PLMD::lepton::CompiledExpression
• runtitle : PLMD::molfile::molfile_qm_sysinfo_t
• runtype : PLMD::molfile::molfile_qm_sysinfo_t
• rw : PLMD::Matrix< T >