- r -
- Random()
: PLMD::Random
- RandomExchanges()
: PLMD::generic::RandomExchanges
- randomize_velocities()
: PLMD::cltools::SimpleMD
- RandU01()
: PLMD::Random
- RDC()
: PLMD::RDC
- read()
: PLMD::DRMSD
, PLMD::EuclideanDistance
, PLMD::FakeFrame
- Read()
: PLMD::generic::Read
- read()
: PLMD::KernelFunctions
, PLMD::MultiDomainRMSD
, PLMD::NormalizedEuclideanDistance
, PLMD::OptimalRMSD
, PLMD::PDB
, PLMD::ReferenceConfiguration
, PLMD::SimpleRMSD
, PLMD::TargetDist
- 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
- 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
- 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
- reduceFast()
: PLMD::LatticeReduction
- reduceSlow()
: PLMD::LatticeReduction
- ReferenceArguments()
: PLMD::ReferenceArguments
- ReferenceAtoms()
: PLMD::ReferenceAtoms
- ReferenceConfiguration()
: PLMD::ReferenceConfiguration
- ReferenceConfigurationOptions()
: PLMD::ReferenceConfigurationOptions
- 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
- 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
- rescaleForces()
: PLMD::MDAtomsBase
, PLMD::MDAtomsTyped< T >
- reserve()
: PLMD::Keywords
- reserved()
: 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
- 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
- rest_of_description()
: PLMD::analysis::LandmarkSelectionBase
- 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
- rewind()
: PLMD::OFile
- RMSD()
: PLMD::colvar::RMSD
, PLMD::RMSD
- RMSDBase()
: PLMD::RMSDBase
- 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
- runJobsAtEndOfCalculation()
: PLMD::PlumedMain