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::ExchangePatterns
- Random() : PLMD::Random
- random : PLMD::bias::ABMD, PLMD::ExchangePatterns, PLMD::generic::CreateMask, PLMD::isdb::Metainference, PLMD::isdb::MetainferenceBase
- 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::ArgumentBookeepingHolder
- rank_ : PLMD::isdb::EMMI, PLMD::isdb::Shadow, PLMD::maze::Optimizer, PLMD::opes::OPESexpanded, PLMD::opes::OPESmetad< mode >, PLMD::ves::VesDeltaF
- ranks : PLMD::ArgumentsBookkeeping, PLMD::ParallelActionsInput
- ranks_size : PLMD::ParallelActionsInput
- rbegin() : PLMD::gch::small_vector< T, InlineCapacity, Allocator >
- rct_ : PLMD::opes::OPESexpanded
- rct_ustride_ : PLMD::bias::MetaD
- rCub : PLMD::UniformSphericalVector
- 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::generic::Read
- read() : PLMD::contour::ContourFindingObject< T >, PLMD::contour::FindContourSurfaceObject, PLMD::contour::FindSphericalContourObject, PLMD::fileTraj, PLMD::function::Bessel, PLMD::function::Between, PLMD::function::Combine, PLMD::function::Custom, PLMD::function::Highest, PLMD::function::LessThan, PLMD::function::Moments, PLMD::function::MoreThan, PLMD::function::Piecewise, PLMD::function::Sort, PLMD::gridtools::DiscreteKernel, PLMD::gridtools::EvaluateGridFunction, PLMD::gridtools::HistogramBeadKernel, PLMD::gridtools::KDEHelper< K, P, G >, PLMD::gridtools::MarginalInput, PLMD::gridtools::RegularKernel< K >, PLMD::gridtools::SumOfKernels< K, P >, PLMD::gridtools::UniversalVonMisses, 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_data_file() : PLMD::isdb::BAIES
- 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< 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_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_volumetric_data : PLMD::molfile::molfile_plugin_t
- read_volumetric_metadata : PLMD::molfile::molfile_plugin_t
- readAndRemove() : PLMD::TokenizedLine
- readAndRemoveFlag() : PLMD::TokenizedLine
- readAndRemoveVector() : PLMD::TokenizedLine
- readAtoms() : PLMD::fileParser, PLMD::TrajectoryParser
- readAtomsFromPDB() : PLMD::Action, PLMD::ActionAtomistic
- readBackboneAtoms() : PLMD::secondarystructure::SecondaryStructureBase< T >
- readBandwidth() : PLMD::gridtools::KDEGridTools< K, P >
- readBandwidthAndHeight() : PLMD::gridtools::KDEGridTools< K, P >, PLMD::gridtools::SphericalKDEGridTools
- readBandwidthKeyword() : PLMD::gridtools::KDEGridTools< K, P >
- 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, PLMD::cltools::CLTool
- readDataFromFile() : PLMD::ves::CoeffsVector
- readDeltaG() : PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO
- readFrame() : PLMD::TrajectoryParser
- readFromFile() : PLMD::ves::CoeffsVector
- readFromFilepointer() : PLMD::PDB
- readFromPoint() : PLMD::BiasRepresentation
- readGaussians() : PLMD::bias::MetaD, PLMD::bias::PBMetaD
- ReadGridInSetup() : PLMD::gridtools::ReadGridInSetup
- readGridParameters() : PLMD::gridtools::KDEGridTools< K, P >, PLMD::gridtools::SphericalKDEGridTools
- readHeader() : PLMD::fileParser, PLMD::TrajectoryParser
- readHeaderFromFile() : PLMD::ves::CoeffsVector
- readHeightKeyword() : PLMD::gridtools::KDEGridTools< K, P >
- readInput() : PLMD::CLTool, PLMD::cltools::CLTool
- readInputFile() : PLMD::CLTool, PLMD::cltools::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
- readKernelParameters() : PLMD::gridtools::KDEHelper< K, P, G >
- 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::SecondaryStructureBase< T >
- ReadStateFull() : PLMD::Random
- readTemperingSpecs() : PLMD::bias::MetaD
- readvals : PLMD::generic::Read
- real_output : PLMD::fourier::FourierTransform
- realToScaled() : PLMD::Pbc
- recalculateSmacofWeights() : PLMD::dimred::ArrangePoints
- RECIPROCAL : PLMD::lepton::Operation
- Reciprocal() : PLMD::lepton::Operation::Reciprocal
- recursive_merge_ : PLMD::opes::OPESmetad< mode >
- Recv() : PLMD::Communicator
- reduce() : PLMD::LatticeReduction
- reduce2() : PLMD::LatticeReduction
- reduced : PLMD::NeighborList, PLMD::Pbc
- reduceFast() : PLMD::LatticeReduction
- reduceSlow() : PLMD::LatticeReduction
- ref : PLMD::switchContainers::Data
- 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
- RefderHelper() : PLMD::volumes::VolumeOutput::RefderHelper
- refders : PLMD::volumes::VolumeOutput
- 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, PLMD::View2D< T, N, M >, PLMD::View< T, N >
- reference_center : PLMD::RMSD
- reference_center_is_calculated : PLMD::RMSD
- reference_center_is_removed : PLMD::RMSD
- reference_mat : PLMD::ERMSD
- referenceCounter : PLMD::PlumedMain
- refpos : PLMD::volumes::VolumeInput
- 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< T >, PLMD::adjmat::Bridge, PLMD::adjmat::BridgeMatrix, PLMD::adjmat::ContactMatrix, PLMD::adjmat::ContactMatrixShortcut, PLMD::adjmat::DistanceMatrix, PLMD::adjmat::HbondMatrix, PLMD::adjmat::Neighbors< T >, PLMD::adjmat::NeighborsShortcut, 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::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::Colvar, 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::ContourFindingObject< T >, PLMD::contour::DistanceFromContour, PLMD::contour::DistanceFromContourBase, PLMD::contour::DistanceFromSphericalContour, PLMD::contour::DumpContour, PLMD::contour::FindContour, PLMD::contour::FindContourSurface, PLMD::contour::FindContourSurfaceObject, PLMD::contour::FindSphericalContour, PLMD::contour::FindSphericalContourObject, 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::FunctionWithSingleArgument< T >, 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::SortWithSingleArgument, 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::DiscreteKernel, PLMD::gridtools::DumpGrid, PLMD::gridtools::EvaluateFunctionOnGrid, PLMD::gridtools::EvaluateGridFunction, PLMD::gridtools::FindGridOptimum, PLMD::gridtools::FunctionOfGrid< T >, PLMD::gridtools::GetGridVolumeElement, PLMD::gridtools::Gradient, PLMD::gridtools::Histogram, PLMD::gridtools::HistogramBeadKernel, PLMD::gridtools::IntegrateGrid, PLMD::gridtools::InterpolateGrid, PLMD::gridtools::KDE< K, P, G >, PLMD::gridtools::KDEGridTools< K, P >, PLMD::gridtools::KDEHelper< K, P, G >, PLMD::gridtools::KDEShortcut, PLMD::gridtools::KLEntropy, PLMD::gridtools::Marginal, PLMD::gridtools::MarginalInput, PLMD::gridtools::MultiColvarDensity, PLMD::gridtools::PairEntropy, PLMD::gridtools::RDF, PLMD::gridtools::ReadGridInSetup, PLMD::gridtools::RegularKernel< K >, PLMD::gridtools::SphericalKDEGridTools, PLMD::gridtools::SumOfKernels< K, P >, PLMD::gridtools::UniversalVonMisses, PLMD::Group, PLMD::HistogramBead, PLMD::isdb::BAIES, 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::liquid_crystal::FerroNematicOrder, PLMD::liquid_crystal::NematicOrder, 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::Dissimilarities, PLMD::matrixtools::InvertMatrix, PLMD::matrixtools::MatrixOperationBase, PLMD::matrixtools::MatrixProduct, PLMD::matrixtools::MatrixTimesMatrix< T >, PLMD::matrixtools::MatrixTimesVector, PLMD::matrixtools::MatrixTimesVectorBase< T >, PLMD::matrixtools::OuterProduct, PLMD::matrixtools::OuterProductBase< T >, PLMD::matrixtools::OutputProductFunc, PLMD::matrixtools::OutputProductMax, PLMD::matrixtools::OutputProductMin, 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::metatomic::MetatomicPlumedAction, 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::ParallelTaskManager< T >, 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::Colvar, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, PLMD::secondarystructure::AlphaRMSD, PLMD::secondarystructure::AntibetaRMSD, PLMD::secondarystructure::ParabetaRMSD, PLMD::secondarystructure::SecondaryStructureBase< T >, 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::SwitchingFunctionAccelerable, 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::TrajectoryParser, PLMD::valtools::Concatenate, PLMD::valtools::Flatten, PLMD::valtools::SelectComponents, PLMD::valtools::SelectWithMask, PLMD::valtools::VStack, PLMD::vatom::ActionWithVirtualAtom, 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< T >, 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
- registerLocalKeywords() : PLMD::matrixtools::MatrixTimesVectorBase< T >
- registerTemperingKeywords() : PLMD::bias::MetaD
- RegistrationLock() : PLMD::Register::RegistrationLock
- registrationLock() : PLMD::Register
- 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
- removeDuplicates() : PLMD::Tools
- removeFromACCDevice() : PLMD::colvar::MultiColvarInput, PLMD::crystdistrib::QuatBondProdMatInput, PLMD::HistogramBead, PLMD::Matrix< T >::openAccVectorHelper< Y >, PLMD::Matrix< T >, PLMD::ParallelActionsInput, PLMD::Pbc, PLMD::RequiredMatrixElements, PLMD::secondarystructure::flexibleMemory< T >, PLMD::secondarystructure::SecondaryStructureDRMSDInput, PLMD::switchContainers::Data, PLMD::SwitchingFunctionAccelerable, PLMD::TensorTyped< T, n, m >
- removeOutputComponent() : PLMD::Keywords
- removeStretch() : PLMD::switchContainers::leptonSwitch
- renameNodeVariables() : PLMD::lepton::ParsedExpression
- renameVariables() : PLMD::lepton::ParsedExpression
- rend() : PLMD::gch::small_vector< T, InlineCapacity, Allocator >
- reparameterizePart() : PLMD::mapping::PathReparameterization
- replaceaction : PLMD::Keywords
- replaceLabelString() : PLMD::ves::CoeffsBase
- replica() : PLMD::TokenizedLine
- 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
- replicaToken : PLMD::Tools
- repliedTrajectory() : PLMD::repliedTrajectory
- report() : PLMD::CheckInRange
- request_capacity() : PLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >
- requestArguments() : PLMD::ActionWithArguments
- requestAtoms() : PLMD::ActionAtomistic, PLMD::ActionWithVirtualAtom, PLMD::colvar::Colvar, PLMD::Colvar, PLMD::sasa::Colvar, PLMD::vatom::ActionWithVirtualAtom
- requestExtraDependencies() : PLMD::ActionWithArguments
- requestlist_ : PLMD::NeighborList
- RequiredMatrixElementsUpdater() : PLMD::RequiredMatrixElementsUpdater
- 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::metatomic::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
- resetCollection() : PLMD::LinkCells
- 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
- reshapeConstantValue() : PLMD::Value
- 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::RequiredMatrixElements
- resize_with() : PLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >
- resizeCoeffs() : PLMD::ves::CoeffsVector
- resizeDerivatives() : PLMD::Value
- resizeIndices() : PLMD::ves::CoeffsBase
- resname : PLMD::molfile::md_atom, PLMD::molfile::molfile_atom_t
- resolution : PLMD::isdb::SAXS
- resolution_function() : PLMD::isdb::SAXS
- Restart() : PLMD::setup::Restart
- restart : PLMD::Action, PLMD::drr::UIestimator::UIestimator, PLMD::PlumedMain
- restartTargetDistribution() : PLMD::ves::LinearBasisSetExpansion
- restartTargetDistributions() : PLMD::ves::VesBias, PLMD::ves::VesLinearExpansion
- Restraint() : PLMD::bias::Restraint
- RestraintShortcut() : PLMD::bias::RestraintShortcut
- retrieve_only_rotation : PLMD::RMSDCoreData
- retrieveAdjacencyLists() : PLMD::clusters::ClusteringBase
- retrieveAtoms() : PLMD::ActionAtomistic
- retrieveAtomsInCells() : PLMD::LinkCells
- retrieveEdgeList() : PLMD::Value
- retrieveFullMatrix() : PLMD::matrixtools::MatrixOperationBase
- retrieveNeighboringAtoms() : PLMD::LinkCells
- return_distances : PLMD::metatomic::vesin::VesinOptions
- return_shifts : PLMD::metatomic::vesin::VesinOptions
- return_vectors : PLMD::metatomic::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::fileParser, PLMD::fileTraj, PLMD::OFile, PLMD::TrajectoryParser
- rg_type : PLMD::colvar::Gyration
- rho : PLMD::isdb::SAXS
- rho_corr : PLMD::isdb::SAXS
- RightParen : PLMD::lepton::ParseToken
- Rij : PLMD::isdb::SAXS
- RingInfo() : PLMD::isdb::CS2Backbone::RingInfo
- ringInfo : PLMD::isdb::CS2Backbone
- RMAX : PLMD::membranefusion::fusionPoreExpansionP
- RMSD() : PLMD::colvar::RMSD, PLMD::RMSD
- rmsd : PLMD::colvar::PCARMSD, PLMD::generic::FitToTemplate
- 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
- root_indexes_ : 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 : PLMD::MatrixSquareBracketsAccess< T, C, I, J >::Const_row, PLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row
- row_starts : PLMD::valtools::Concatenate
- rowlen : PLMD::matrixtools::MatrixForceIndexInput, PLMD::matrixtools::MatrixTimesVectorInput, PLMD::matrixtools::MatrixTimesVectorOutput
- 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::ParallelTaskManager< T >
- runFinalJobs() : PLMD::Action
- runInSerial() : PLMD::ParallelTaskManager< T >
- runJobsAtEndOfCalculation() : PLMD::PlumedMain
- running : PLMD::Stopwatch::Watch
- runtimeptr : PLMD::lepton::CompiledExpression
- runtitle : PLMD::molfile::molfile_qm_sysinfo_t
- runtype : PLMD::molfile::molfile_qm_sysinfo_t
- rw : PLMD::Matrix< T >
- rX : PLMD::repliedTrajectory
- rY : PLMD::repliedTrajectory
- rZ : PLMD::repliedTrajectory