A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X

A: ABMD (PLMD::bias); Operation::Abs (PLMD::lepton); Accelerator (PLMD); GridBase::AcceleratorBase (PLMD); GridBase::AcceleratorHandler (PLMD); Accumulate (PLMD::generic); Operation::Acos (PLMD::lepton); Action (PLMD); ActionAnyorder (PLMD); ActionAtomistic (PLMD); ActionForInterface (PLMD); ActionOptions (PLMD); ActionPilot (PLMD); ActionRegister (PLMD); ActionRegisterPointers (PLMD); ActionRegistration (PLMD); ActionSet (PLMD); ActionSetup (PLMD); ActionShortcut (PLMD); ActionToGetData (PLMD); ActionToPutData (PLMD); ActionVolume (PLMD::volumes); ActionWithArguments (PLMD); ActionWithGrid (PLMD::gridtools); ActionWithMatrix (PLMD); ActionWithValue (PLMD); ActionWithVector (PLMD); ActionWithVirtualAtom (PLMD); ActionWithVirtualAtom (PLMD::vatom); AdaptivePath (PLMD::mapping); Operation::Add (PLMD::lepton); Operation::AddConstant (PLMD::lepton); AdjacencyMatrixBase (PLMD::adjmat); AdjacencyMatrixData (PLMD::adjmat); AdjacencyMatrixInput (PLMD::adjmat); small_vector_base::allocations_are_movable (PLMD::gch::detail); small_vector_base::allocations_are_swappable (PLMD::gch::detail); allocator_inliner (PLMD::gch::detail); allocator_inliner< Allocator, false > (PLMD::gch::detail); allocator_inliner< Allocator, true > (PLMD::gch::detail); allocator_interface (PLMD::gch::detail); AlphaBeta (PLMD::multicolvar); AlphaRMSD (PLMD::secondarystructure); Angle (PLMD); Angle (PLMD::colvar); AngleMulti (PLMD::colvar); Angles (PLMD::multicolvar); AngleShortcut (PLMD::colvar); AngularTetra (PLMD::symfunc); annfunc::ANN (PLMD); ANN (PLMD::function::annfunc); AntibetaRMSD (PLMD::secondarystructure); ArgsToVatom (PLMD::vatom); ArgumentBookeepingHolder (PLMD); ArgumentsBookkeeping (PLMD); ArrangePoints (PLMD::dimred); Operation::Asin (PLMD::lepton); AsmJitRuntimePtr (PLMD::lepton); Exception::Assertion (PLMD); Operation::Atan (PLMD::lepton); Operation::Atan2 (PLMD::lepton); AtomDistribution (PLMD); AtomicSMAC (PLMD::symfunc); AtomNumber (PLMD); Average (PLMD::generic)

B: BAIES (PLMD::isdb); baseSwitch (PLMD::switchContainers); BasisFunctions (PLMD::ves); beadkde (PLMD::gridtools); Bessel (PLMD::function); BesselShortcut (PLMD::function); Between (PLMD::function); BetweenShortcut (PLMD::function); 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); Bias (PLMD::bias); BiasRepresentation (PLMD); BiasValue (PLMD::bias); BiasWeight (PLMD); BitmaskEnum (PLMD::enum_traits); BitmaskEnum< Keywords::argType > (PLMD::enum_traits); BitmaskEnum< Keywords::componentType > (PLMD::enum_traits); bmap (PLMD::adjmat); BopsShortcut (PLMD::crystdistrib); BoundingBox (PLMD::metatomic::vesin); Brent1DRootSearch (PLMD); Bridge (PLMD::adjmat); BridgeMatrix (PLMD::adjmat); small_vector_base::bypass_tag (PLMD::gch::detail)

C: Caliber (PLMD::isdb); Operation::Ceil (PLMD::lepton); Cell (PLMD::colvar); CellList::Cell (PLMD::metatomic::vesin::cpu); LinkCells::CellCollection (PLMD); CellList (PLMD::metatomic::vesin::cpu); CellShift (PLMD::metatomic::vesin); Center (PLMD::vatom); CenterShortcut (PLMD::vatom); CheckInRange (PLMD); CS2Backbone::ChemicalShift (PLMD::isdb); Citations (PLMD); ClassicalMultiDimensionalScaling (PLMD::dimred); CLTool (PLMD); CLTool (PLMD::cltools); CLToolMain (PLMD); CLToolOptions (PLMD); CLToolRegister (PLMD); CLToolRegisterPointers (PLMD); CLToolSumHills (PLMD::cltools); ClusterDiameter (PLMD::clusters); ClusterDistribution (PLMD::clusters); ClusterDistributionShortcut (PLMD::clusters); ClusteringBase (PLMD::clusters); ClusterNatoms (PLMD::clusters); ClusterProperties (PLMD::clusters); ClusterWeights (PLMD::clusters); ClusterWithSurface (PLMD::clusters); cmap (PLMD::adjmat); CoeffsBase (PLMD::ves); CoeffsMatrix (PLMD::ves); CoeffsVector (PLMD::ves); Collect (PLMD::generic); CollectFrames (PLMD::landmarks); colv (PLMD::secondarystructure); Colvar (PLMD); Colvar (PLMD::colvar); Colvar (PLMD::sasa); ColvarFake (PLMD::colvar); ColvarInput (PLMD::colvar); ColvarOutput (PLMD); ColvarShortcut (PLMD::colvar); Combine (PLMD::function); CombineShortcut (PLMD::function); Committor (PLMD::generic); Communicator (PLMD); CompiledExpression (PLMD::lepton); Completion (PLMD::cltools); Combine::component (PLMD::function); Keywords::component (PLMD); Concatenate (PLMD::valtools); ConjugateGradient (PLMD); MatrixSquareBracketsAccess::Const_row (PLMD); Constant (PLMD::generic); Operation::Constant (PLMD::lepton); Communicator::ConstData (PLMD); ContactMap (PLMD::colvar); ContactMatrix (PLMD::adjmat); ContactMatrixShortcut (PLMD::adjmat); RegisterBase::ContentAndFullPath (PLMD); ContourFindingObject (PLMD::contour); convergence (PLMD::opes); ConvertToFES (PLMD::gridtools); CoordAngles (PLMD::multicolvar); Coordination (PLMD::colvar); CoordinationBase (PLMD::colvar); CoordinationNumbers (PLMD::symfunc); CoordShellVectorFunction (PLMD::symfunc); Operation::Cos (PLMD::lepton); Operation::Cosh (PLMD::lepton); cosinusSwitch (PLMD::switchContainers); Operation::Cot (PLMD::lepton); CovarianceMatrix (PLMD::matrixtools); CreateMask (PLMD::generic); Tools::CriticalSectionWithKey (PLMD); CS2Backbone (PLMD::isdb); CS2BackboneDB (PLMD::isdb); Operation::Csc (PLMD::lepton); Operation::Cube (PLMD::lepton); cubicSwitch (PLMD::switchContainers); Custom (PLMD::function); Operation::Custom (PLMD::lepton); CustomFunction (PLMD::lepton); CustomShortcut (PLMD::function); CyHarmShortcut (PLMD::symfunc); CylindricalHarmonic (PLMD::symfunc)

D: Communicator::Data (PLMD); Data (PLMD::switchContainers); DataPassingObject (PLMD); DataPassingObjectTyped (PLMD); DataPassingTools (PLMD); DataPassingToolsTyped (PLMD); Debug (PLMD::generic); default_buffer_size (PLMD::gch); tls::delete_ptr (PLMD::maze); Operation::Delta (PLMD::lepton); Density (PLMD::volumes); PlumedMain::DeprecatedAtoms (PLMD); ColvarOutput::DerivHelper (PLMD); Determinant (PLMD::matrixtools); DFSClustering (PLMD::clusters); DHEnergy (PLMD::colvar); DiagonalizeMatrix (PLMD::matrixtools); DiagonalKernelParams (PLMD::gridtools); Difference (PLMD::refdist); DifferenceShortcut (PLMD::refdist); Dihcor (PLMD::multicolvar); DihedralCorrelation (PLMD::colvar); DihedralCorrelationMulti (PLMD::colvar); DihedralCorrelationShortcut (PLMD::colvar); Dimer (PLMD::colvar); Dipole (PLMD::colvar); DipoleMulti (PLMD::colvar); DipoleShortcut (PLMD::colvar); Tools::DirectoryChanger (PLMD); discretekde (PLMD::gridtools); DiscreteKernel (PLMD::gridtools); Displacement (PLMD::refdist); Dissimilarities (PLMD::matrixtools); dissims (PLMD::matrixtools); Distance (PLMD::colvar); Distance (PLMD::setup); DistanceFromContour (PLMD::contour); DistanceFromContourBase (PLMD::contour); DistanceFromSphericalContour (PLMD::contour); DistanceMatrix (PLMD::adjmat); DistanceMulti (PLMD::colvar); Distances (PLMD::multicolvar); DistanceShortcut (PLMD::colvar); Operation::Divide (PLMD::lepton); DLLoader (PLMD); dmap (PLMD::adjmat); DomainDecomposition::DomainComms (PLMD); ::DomainDecomposition (PLMD); DomainDecomposition (PLMD); DopsShortcut (PLMD::crystdistrib); Driver (PLMD::cltools); DRMSD (PLMD::colvar); DumpAtoms (PLMD::generic); DumpContour (PLMD::contour); DumpDerivatives (PLMD::generic); DumpForces (PLMD::generic); DumpGrid (PLMD::gridtools); DumpMassCharge (PLMD::generic); DumpMultiColvar (PLMD::multicolvar); DumpPDB (PLMD::generic); DumpProjections (PLMD::generic); DumpVector (PLMD::generic); DynamicReferenceRestraining (PLMD::drr)

E: ECVcustom (PLMD::opes); ECVlinear (PLMD::opes); ECVmultiThermal (PLMD::opes); ECVmultiThermalBaric (PLMD::opes); ECVumbrellasFile (PLMD::opes); ECVumbrellasLine (PLMD::opes); EDS (PLMD::eds); EEFSolv (PLMD::colvar); EffectiveEnergyDrift (PLMD::generic); EMMI (PLMD::isdb); EMMIVOX (PLMD::isdb); EndPlumed (PLMD::generic); Energy (PLMD::colvar); Ensemble (PLMD::function); DLLoader::EnsureGlobalDLOpen (PLMD); EnvironmentSimilarity (PLMD::envsim); Operation::Erf (PLMD::lepton); Operation::Erfc (PLMD::lepton); ERMSD (PLMD::colvar); ERMSD (PLMD); EuclideanDistance (PLMD::refdist); EvaluateFunctionOnGrid (PLMD::gridtools); EvaluateGridFunction (PLMD::gridtools); Exception (PLMD); Exception (PLMD::lepton); ExceptionDebug (PLMD); ExceptionError (PLMD); ExceptionRegisterError (PLMD); ExceptionTypeError (PLMD); ExchangePatterns (PLMD); Operation::Exp (PLMD::lepton); ExpansionCVs (PLMD::opes); exploration (PLMD::opes); exponentialSwitch (PLMD::switchContainers); ExpressionProgram (PLMD::lepton); ExpressionTreeNode (PLMD::lepton); ExtendedLagrangian (PLMD::bias); External (PLMD::bias); ExtraCV (PLMD::colvar)

F: F1dim (PLMD); FarthestPointSampling (PLMD::landmarks); fastgaussianSwitch (PLMD::switchContainers); Tools::FastStringUnorderedMap (PLMD); Fccubic (PLMD::symfunc); FccubicShortcut (PLMD::symfunc); FermiSwitchingFunction (PLMD::ves); FerroNematicOrder (PLMD::liquid_crystal); FesWeight (PLMD::ves); IFile::Field (PLMD); OFile::Field (PLMD); FileBase::FieldBase (PLMD); FileBase (PLMD); fileDeleter (PLMD); fileParser (PLMD); FilesHandler (PLMD::function); fileTraj (PLMD); FindContour (PLMD::contour); FindContourSurface (PLMD::contour); FindContourSurfaceObject (PLMD::contour); FindGridOptimum (PLMD::gridtools); FindSphericalContour (PLMD::contour); FindSphericalContourObject (PLMD::contour); fio_iovec (PLMD::molfile); FISST (PLMD::fisst); FitToTemplate (PLMD::generic); FixedAtom (PLMD::vatom); fixedRational (PLMD::switchContainers); flatfkde (PLMD::gridtools); flatkde (PLMD::gridtools); Flatten (PLMD::valtools); FlexibleBin (PLMD); flexibleMemory (PLMD::secondarystructure); Operation::Floor (PLMD::lepton); Flush (PLMD::generic); ForceIndexHolder (PLMD); ForceInput (PLMD); ForceOutput (PLMD); ForwardDecl (PLMD); FourierTransform (PLMD::fourier); FretEfficiency (PLMD::isdb); fromToDataHelper (PLMD::OpenACC); leptonSwitch::funcAndDeriv (PLMD::switchContainers); FuncPathGeneral (PLMD::function); FuncPathMSD (PLMD::function); FuncSumHills (PLMD::function); Function (PLMD::function); FunctionData (PLMD::function); FunctionOfGrid (PLMD::gridtools); FunctionOfMatrix (PLMD::function); FunctionOfScalar (PLMD::function); FunctionOfVector (PLMD::function); FunctionOptions (PLMD::function); FunctionOutput (PLMD::function); FunctionShortcut (PLMD::function); FunctionWithSingleArgument (PLMD::function); Funnel (PLMD::funnel); FUNNEL_PS (PLMD::funnel); fusionPoreExpansionP (PLMD::membranefusion); fusionPoreNucleationP (PLMD::membranefusion)

H: Stopwatch::Handler (PLMD); Subprocess::Handler (PLMD); Tools::CriticalSectionWithKey::Handler (PLMD); allocator_interface::has_alloc_construct (PLMD::gch::detail); allocator_interface::has_alloc_construct_check (PLMD::gch::detail); allocator_interface::has_alloc_construct_check< void_t< decltype(std::declval< A & >().construct(std::declval< V * >(), std::declval< Args >()...))>, A, V, Args... > (PLMD::gch::detail); allocator_interface::has_alloc_construct_impl (PLMD::gch::detail); allocator_interface::has_alloc_construct_impl< typename std::enable_if< is_complete< V >::value >::type, A, V, Args... > (PLMD::gch::detail); allocator_interface::has_alloc_destroy (PLMD::gch::detail); allocator_interface::has_alloc_destroy< A, V, typename std::enable_if< is_complete< V >::value >::type > (PLMD::gch::detail); allocator_interface::has_alloc_destroy_impl (PLMD::gch::detail); allocator_interface::has_alloc_destroy_impl< void_t< decltype(std::declval< A & >().destroy(std::declval< V * >()))>, A, V > (PLMD::gch::detail); allocator_interface::has_ptr_traits_to_address (PLMD::gch::detail); allocator_interface::has_ptr_traits_to_address< P, void_t< decltype(std::pointer_traits< P >::to_address(std::declval< P >()))> > (PLMD::gch::detail); has_size_and_data (PLMD::mergeVectorTools); has_size_and_data< T, std::void_t< decltype(std::declval< T >().size()), decltype(std::declval< T >().data())> > (PLMD::mergeVectorTools); HbondMatrix (PLMD::adjmat); HBPammMatrix (PLMD::pamm); HBPammShortcut (PLMD::pamm); hbpmap (PLMD::pamm); HexacticParameter (PLMD::symfunc); Highest (PLMD::function); HighestShortcut (PLMD::function); Histogram (PLMD::gridtools); HistogramBead (PLMD); HistogramBeadKernel (PLMD::gridtools); hmap (PLMD::adjmat)

I: RegisterBase::ID (PLMD); IFile (PLMD); PathMSDBase::ImagePath (PLMD::colvar); PathMSDBase::imgOrderByDist (PLMD::colvar); PathMSDBase::imgOrderBySimilarity (PLMD::colvar); Include (PLMD::generic); Info (PLMD::cltools); inline_storage (PLMD::gch::detail); InPlaneDistances (PLMD::multicolvar); InputVectors (PLMD::matrixtools); IntegrateGrid (PLMD::gridtools); InterpolateGrid (PLMD::gridtools); Interpolator (PLMD::gridtools); InvertMatrix (PLMD::matrixtools); default_buffer_size::is_complete (PLMD::gch); allocator_interface::is_complete (PLMD::gch::detail); default_buffer_size::is_complete< U, decltype(static_cast< void >(sizeof(U)))> (PLMD::gch); allocator_interface::is_complete< U, decltype(static_cast< void >(sizeof(U)))> (PLMD::gch::detail); allocator_interface::is_contiguous_iterator (PLMD::gch::detail); allocator_interface::is_convertible_pointer (PLMD::gch::detail); small_vector_base::is_emplace_constructible (PLMD::gch::detail); small_vector_base::is_emplace_constructible_impl (PLMD::gch::detail); small_vector_base::is_emplace_constructible_impl< void_t< typename std::enable_if< is_complete< V >::value >::type, decltype(std::declval< AI & >().construct(std::declval< V * >(), std::declval< Args >()...))>, AI, V, Args... > (PLMD::gch::detail); small_vector_base::is_eraseable (PLMD::gch::detail); small_vector_base::is_eraseable< AI, void_t< decltype(std::declval< AI & >().destroy(std::declval< value_ty * >()))> > (PLMD::gch::detail); small_vector_base::is_explicitly_copy_insertable (PLMD::gch::detail); small_vector_base::is_explicitly_move_insertable (PLMD::gch::detail); small_vector_base::is_explicitly_nothrow_copy_insertable (PLMD::gch::detail); small_vector_base::is_explicitly_nothrow_move_insertable (PLMD::gch::detail); allocator_interface::is_memcpyable (PLMD::gch::detail); allocator_interface::is_memcpyable< QualifiedFrom, QualifiedTo, typename std::enable_if< is_complete< QualifiedFrom >::value >::type > (PLMD::gch::detail); allocator_interface::is_memcpyable_integral (PLMD::gch::detail); allocator_interface::is_memcpyable_integral< From, To, typename std::enable_if< is_complete< From >::value >::type > (PLMD::gch::detail); allocator_interface::is_memcpyable_iterator (PLMD::gch::detail); allocator_interface::is_memcpyable_iterator< std::move_iterator< InputIt > > (PLMD::gch::detail); small_vector_base::is_nothrow_emplace_constructible (PLMD::gch::detail); is_nothrow_swappable (PLMD::gch::detail::small_vector_adl); is_nothrow_swappable< T, decltype(swap(std::declval< T & >(), std::declval< T & >()))> (PLMD::gch::detail::small_vector_adl); allocator_interface::is_small_vector_iterator (PLMD::gch::detail); allocator_interface::is_small_vector_iterator< small_vector_iterator< Ts... > > (PLMD::gch::detail); allocator_interface::is_trivially_constructible (PLMD::gch::detail); allocator_interface::is_trivially_constructible_impl (PLMD::gch::detail); allocator_interface::is_trivially_constructible_impl< typename std::enable_if< is_complete< V >::value >::type, V, Args... > (PLMD::gch::detail); allocator_interface::is_trivially_destructible (PLMD::gch::detail); allocator_interface::is_trivially_destructible< V, typename std::enable_if< is_complete< V >::value >::type > (PLMD::gch::detail); allocator_interface::is_uninitialized_memcpyable (PLMD::gch::detail); allocator_interface::is_uninitialized_memcpyable< To, From > (PLMD::gch::detail); allocator_interface::is_uninitialized_memcpyable_impl (PLMD::gch::detail); allocator_interface::is_uninitialized_memcpyable_iterator (PLMD::gch::detail); allocator_interface::is_uninitialized_memcpyable_iterator< std::move_iterator< U >, V > (PLMD::gch::detail)

J: JCoupling (PLMD::isdb)

M: MahalanobisDistance (PLMD::refdist); Manual (PLMD::cltools); Marginal (PLMD::gridtools); MarginalInput (PLMD::gridtools); MarginalWeight (PLMD::ves); MassChargeInput (PLMD::generic); Matrix (PLMD); Matrix (PLMD::metatomic::vesin); MatrixBetween (PLMD::function); MatrixCombine (PLMD::function); MatrixCustom (PLMD::function); MatrixCyHarm (PLMD::symfunc); MatrixElementOutput (PLMD); MatrixFccubic (PLMD::symfunc); MatrixForceIndexInput (PLMD::matrixtools); MatrixLessThan (PLMD::function); MatrixMoreThan (PLMD::function); MatrixOperationBase (PLMD::matrixtools); MatrixOutput (PLMD::adjmat); MatrixProduct (PLMD::matrixtools); MatrixProductDiagonal (PLMD::refdist); MatrixProductDiagonalInput (PLMD::refdist); MatrixSpHarm (PLMD::symfunc); MatrixSquareBracketsAccess (PLMD); MatrixTimesMatrix (PLMD::matrixtools); MatrixTimesMatrixInput (PLMD::matrixtools); MatrixTimesVector (PLMD::matrixtools); MatrixTimesVectorBase (PLMD::matrixtools); MatrixTimesVectorData (PLMD::matrixtools); MatrixTimesVectorInput (PLMD::matrixtools); MatrixTimesVectorOutput (PLMD::matrixtools); MatrixTimesVectorProper (PLMD::matrixtools); MatrixTimesVectorRowSums (PLMD::matrixtools); Operation::Max (PLMD::lepton); MaxEnt (PLMD::bias); md_atom (PLMD::molfile); md_box (PLMD::molfile); md_file (PLMD::molfile); md_header (PLMD::molfile); MD_LinearExpansionPES (PLMD::ves); md_ts (PLMD::molfile); Member (PLMD::maze); Memetic (PLMD::maze); memFusionP (PLMD::membranefusion); MetaD (PLMD::bias); Metainference (PLMD::isdb); MetainferenceBase (PLMD::isdb); MetatomicPlumedAction (PLMD::metatomic); MFilterLess (PLMD::multicolvar); MFilterMore (PLMD::multicolvar); Operation::Min (PLMD::lepton); Minimise1DBrent (PLMD); MinimiseBase (PLMD); MolDataClass (PLMD); molfile_atom_t (PLMD::molfile); molfile_graphics_t (PLMD::molfile); molfile_metadata_t (PLMD::molfile); molfile_plugin_t (PLMD::molfile); molfile_qm_basis_t (PLMD::molfile); molfile_qm_hessian_t (PLMD::molfile); molfile_qm_metadata_t (PLMD::molfile); molfile_qm_sysinfo_t (PLMD::molfile); molfile_qm_t (PLMD::molfile); molfile_qm_timestep_metadata (PLMD::molfile); molfile_qm_timestep_t (PLMD::molfile); molfile_qm_wavefunction_t (PLMD::molfile); molfile_timestep_metadata (PLMD::molfile); molfile_timestep_t (PLMD::molfile); molfile_volumetric_t (PLMD::molfile); MolInfo (PLMD::generic); Moments (PLMD::function); MomentsShortcut (PLMD::function); MoreThan (PLMD::function); MoreThanShortcut (PLMD::function); MovingRestraint (PLMD::bias); MPI_Comm (PLMD); MPI_Datatype (PLMD); MPI_Request (PLMD); MPI_Status (PLMD); mtimes (PLMD::matrixtools); MultiColvarDensity (PLMD::gridtools); MultiColvarInput (PLMD::colvar); MultiColvarShortcuts (PLMD::multicolvar); MultiColvarTemplate (PLMD::colvar); Operation::Multiply (PLMD::lepton); Operation::MultiplyConstant (PLMD::lepton); MultiRMSD (PLMD::colvar); allocator_interface::must_use_alloc_construct (PLMD::gch::detail); allocator_interface::must_use_alloc_destroy (PLMD::gch::detail); mycp (PLMD::matrixtools); mycr (PLMD::matrixtools)

O: OFile (PLMD); ohinp (PLMD::adjmat); olinp (PLMD::adjmat); OneargHighest (PLMD::function); OneHighInput (PLMD::adjmat); OneLowInput (PLMD::adjmat); Ones (PLMD::generic); Matrix::openAccVectorHelper (PLMD); OpenMPVars (PLMD::OpenMP); Operation (PLMD::lepton); OPESexpanded (PLMD::opes); OPESmetad (PLMD::opes); OPESmetad_c (PLMD::opes); OPESmetad_e (PLMD::opes); opfunc (PLMD::matrixtools); opmax (PLMD::matrixtools); opmin (PLMD::matrixtools); Opt_Adam (PLMD::ves); Opt_BachAveragedSGD (PLMD::ves); Opt_Dummy (PLMD::ves); Opt_RobbinsMonroSGD (PLMD::ves); Optimizer (PLMD::maze); Optimizer (PLMD::ves); OptimizerBias (PLMD::maze); FuncPathMSD::ordering (PLMD::function); OuterProduct (PLMD::matrixtools); OuterProductBase (PLMD::matrixtools); OuterProductInput (PLMD::matrixtools); OutputBasisFunctions (PLMD::ves); OutputCluster (PLMD::clusters); OutputFesBias (PLMD::ves); OutputProductFunc (PLMD::matrixtools); OutputProductMax (PLMD::matrixtools); OutputProductMin (PLMD::matrixtools); OutputTargetDistribution (PLMD::ves)

P: SecondaryStructureDRMSDInput::pairDistance (PLMD::secondarystructure); PairEntropy (PLMD::gridtools); FuncPathGeneral::pairordering (PLMD::function); FuncPathMSD::pairordering (PLMD::function); PAMM (PLMD::pamm); ParabetaRMSD (PLMD::secondarystructure); ParallelActionsInput (PLMD); ParallelActionsOutput (PLMD); ParallelTaskManager (PLMD); ParsedExpression (PLMD::lepton); Parser (PLMD::lepton); ParseToken (PLMD::lepton); Path (PLMD::mapping); PathDisplacements (PLMD::mapping); PathMSD (PLMD::colvar); PathMSDBase (PLMD::colvar); PathProjectionCalculator (PLMD::mapping); PathReparameterization (PLMD::mapping); PathTools (PLMD::mapping); Pbc (PLMD); PbcAction (PLMD); PBMetaD (PLMD::bias); PCA (PLMD::dimred); PCARMSD (PLMD::colvar); PCAVars (PLMD::mapping); PDB (PLMD); PDB2Constant (PLMD::generic); PdbRenumber (PLMD::cltools); PesMD (PLMD::cltools); Piecewise (PLMD::function); PiecewiseShortcut (PLMD::function); PIV (PLMD::piv); PlaceholderFunction (PLMD::lepton); Plane (PLMD::colvar); PlaneMulti (PLMD::colvar); PlaneShortcut (PLMD::colvar); PlaneShortcut (PLMD::multicolvar); Plumed (PLMD::generic); plumed; plumed_error; plumed_error_filesystem_path; PlumedMain::plumed_error_handler (PLMD); plumed_function_holder; plumed_nothrow_handler; plumed_nothrow_handler_x; plumed_plumedmain_function_holder_x; plumed_safeptr; plumed_safeptr_x; plumed_symbol_table_type_x; PlumedHandle (PLMD); PlumedMain (PLMD); CellList::Point (PLMD::metatomic::vesin::cpu); Position (PLMD::colvar); position_linear_proj (PLMD::sizeshape); position_maha_dist (PLMD::sizeshape); PositionMulti (PLMD::colvar); PositionShortcut (PLMD::colvar); Operation::Power (PLMD::lepton); Operation::PowerConstant (PLMD::lepton); PRE (PLMD::isdb); TokenizedLine::presentAndFound (PLMD); Print (PLMD::generic); PrintNDX (PLMD::generic); ProbWeight (PLMD); Product (PLMD::function); ProjectionOnAxis (PLMD::colvar); ProjectPoints (PLMD::dimred); ProjectPointsInput (PLMD::dimred); PropertyMap (PLMD::colvar); Puckering (PLMD::colvar); pytorch::PytorchModel (PLMD)

Q: qpop (PLMD::crystdistrib); QuatBondProdMatInput (PLMD::crystdistrib); Quaternion (PLMD::crystdistrib); QuaternionBondProductMatrix (PLMD::crystdistrib); QuaternionMulti (PLMD::crystdistrib); QuaternionProductMatrix (PLMD::crystdistrib); QuaternionShortcut (PLMD::crystdistrib)

R: RadialTetra (PLMD::symfunc); Random (PLMD); Random_Acceleration_MD (PLMD::maze); Random_Walk (PLMD::maze); RandomExchanges (PLMD::generic); rational (PLMD::switchContainers); RDC (PLMD::isdb); RDF (PLMD::gridtools); Read (PLMD::generic); ReadGridInSetup (PLMD::gridtools); Operation::Reciprocal (PLMD::lepton); VolumeOutput::RefderHelper (PLMD::volumes); Register (PLMD); RegisterBase (PLMD); Register::RegistrationLock (PLMD); RegularKernel (PLMD::gridtools); small_vector_base::relocate_with_move (PLMD::gch::detail); repliedTrajectory (PLMD); Communicator::Request (PLMD); RequiredMatrixElements (PLMD); RequiredMatrixElementsUpdater (PLMD); Rescale (PLMD::isdb); ResetCell (PLMD::generic); Restart (PLMD::setup); Restraint (PLMD::bias); RestraintShortcut (PLMD::bias); ReweightBase (PLMD::bias); ReweightBias (PLMD::bias); ReweightMetad (PLMD::bias); ReweightTemperaturePressure (PLMD::bias); CS2Backbone::RingInfo (PLMD::isdb); RMSD (PLMD::colvar); RMSD (PLMD); RMSDCoreData (PLMD); RMSDShortcut (PLMD::colvar); RMSDVector (PLMD::colvar); RMSDVectorData (PLMD::colvar); rnd (PLMD::maze); RootFindingBase (PLMD); RopsShortcut (PLMD::crystdistrib); MatrixSquareBracketsAccess::Row (PLMD)

S: S2ContactModel (PLMD::s2cm); SASA_HASEL (PLMD::sasa); SASA_LCPO (PLMD::sasa); SAXS (PLMD::isdb); ScalarBessel (PLMD::function); ScalarBetween (PLMD::function); ScalarCombine (PLMD::function); ScalarCustom (PLMD::function); ScalarDifference (PLMD::refdist); ScalarEvalGrid (PLMD::gridtools); ScalarHighest (PLMD::function); ScalarLessThan (PLMD::function); ScalarMoments (PLMD::function); ScalarMoreThan (PLMD::function); ScalarPiecewise (PLMD::function); ScalarSort (PLMD::function); Operation::Sec (PLMD::lepton); SecondaryStructureBase (PLMD::secondarystructure); SecondaryStructureDRMSDInput (PLMD::secondarystructure); SecondaryStructureRMSDInput (PLMD::secondarystructure); Select (PLMD::isdb); Operation::Select (PLMD::lepton); SelectComponents (PLMD::valtools); SelectMassCharge (PLMD::colvar); Selector (PLMD::isdb); SelectWithMask (PLMD::valtools); Shadow (PLMD::isdb); PIV::SharedData (PLMD::piv); ShowGraph (PLMD::cltools); SimpleMD (PLMD::cltools); Simulated_Annealing (PLMD::maze); Operation::Sin (PLMD::lepton); SingleargMoments (PLMD::function); Operation::Sinh (PLMD::lepton); TypesafePtr::SizeLike (PLMD); WithCmd::SizeLike (PLMD); SketchMap (PLMD::dimred); SketchMapProjection (PLMD::dimred); SMAC (PLMD::symfunc); SMACOF (PLMD::dimred); small_vector (PLMD::gch); small_vector_base (PLMD::gch::detail); small_vector_data (PLMD::gch::detail); small_vector_data< Pointer, SizeT, T, 0 > (PLMD::gch::detail); small_vector_data_base (PLMD::gch::detail); small_vector_iterator (PLMD::gch); smapSwitch (PLMD::switchContainers); Sort (PLMD::function); SortShortcut (PLMD::function); SortWithSingleArgument (PLMD::function); SparseGrid (PLMD); SpHarmShortcut (PLMD::symfunc); SphericalHarmonic (PLMD::symfunc); sphericalkde (PLMD::gridtools); SphericalKDEGridTools (PLMD::gridtools); SAXS::SplineCoeffs (PLMD::isdb); Sprint (PLMD::sprint); Operation::Sqrt (PLMD::lepton); Operation::Square (PLMD::lepton); small_vector_base::stack_temporary (PLMD::gch::detail); Stats (PLMD::function); Communicator::Status (PLMD); Steered_MD (PLMD::maze); Steinhardt (PLMD::symfunc); Operation::Step (PLMD::lepton); Stopwatch (PLMD); small_vector_base::strong_exception_policy (PLMD::gch::detail); Subprocess (PLMD); SubprocessPid (PLMD); Operation::Subtract (PLMD::lepton); Sum (PLMD::function); SumOfKernels (PLMD::gridtools); Switch (PLMD::switchContainers); SwitchingFunction (PLMD); SwitchingFunctionAccelerable (PLMD); SwitchingPlotter (PLMD::cltools); SwitchInterface (PLMD::switchContainers); SwitchInterface_lepton (PLMD::switchContainers)

T: t_trnheader (PLMD::xdrfile); Operation::Tan (PLMD::lepton); Operation::Tanh (PLMD::lepton); tanhSwitch (PLMD::switchContainers); TargetDist (PLMD); TargetDistModifer (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); MetaD::TemperingSpecs (PLMD::bias); Template (PLMD::colvar); TensorGenericAux (PLMD); TensorTyped (PLMD); theLine (PLMD); ThreeBodyGFunctions (PLMD::symfunc); ThreeBodyGFunctionsInput (PLMD::symfunc); Exception::Throw (PLMD); tiledSimpleCubic (PLMD); Time (PLMD::generic); tls (PLMD::maze); tmap (PLMD::adjmat); TokenizedLine (PLMD); Tools (PLMD); TopologyMatrix (PLMD::adjmat); Torsion (PLMD::colvar); Torsion (PLMD); TorsionMulti (PLMD::colvar); Torsions (PLMD::multicolvar); TorsionShortcut (PLMD::colvar); TorsionsMatrix (PLMD::adjmat); TorsionsMatrixInput (PLMD::adjmat); TrajectoryParser (PLMD); TransposeMatrix (PLMD::matrixtools); Tree (PLMD); trx_hdr (PLMD::molfile); twoGlobs (PLMD); TypesafePtr (PLMD)

V: Value (PLMD); Operation::Variable (PLMD::lepton); Vector (PLMD::metatomic::vesin); VectorBessel (PLMD::function); VectorBetween (PLMD::function); VectorCombine (PLMD::function); VectorCustom (PLMD::function); VectorDifference (PLMD::refdist); VectorEvalGrid (PLMD::gridtools); VectorHighest (PLMD::function); VectorLessThan (PLMD::function); VectorMoments (PLMD::function); VectorMoreThan (PLMD::function); VectorSort (PLMD::function); VectorTyped (PLMD); VesBias (PLMD::ves); VesDeltaF (PLMD::ves); VesinNeighborList (PLMD::metatomic::vesin); VesinOptions (PLMD::metatomic::vesin); VesLinearExpansion (PLMD::ves); VesTools (PLMD::ves); View (PLMD); View2D (PLMD); ColvarOutput::VirialHelper (PLMD); vmdplugin_t (PLMD::molfile); Vola (PLMD::volumes); Volc (PLMD::volumes); VolCav (PLMD::volumes); volenv (PLMD::volumes); Vols (PLMD::volumes); VolTet (PLMD::volumes); Volume (PLMD::colvar); VolumeAround (PLMD::volumes); VolumeAroundShortcut (PLMD::volumes); VolumeCavity (PLMD::volumes); VolumeCavityShortcut (PLMD::volumes); VolumeData (PLMD::volumes); VolumeInCylinder (PLMD::volumes); VolumeInCylinderShortcut (PLMD::volumes); VolumeInEnvelope (PLMD::volumes); VolumeInEnvelopeShortcut (PLMD::volumes); VolumeInput (PLMD::volumes); VolumeInSphere (PLMD::volumes); VolumeInSphereShortcut (PLMD::volumes); VolumeOutput (PLMD::volumes); VolumeShortcut (PLMD::volumes); VolumeTetrapore (PLMD::volumes); VolumeTetraporeShortcut (PLMD::volumes); VonMissesKernelParams (PLMD::gridtools); Voronoi (PLMD::matrixtools); VStack (PLMD::valtools)

X: XAngle (PLMD::multicolvar); XDR (PLMD::xdrfile); XDR::xdr_ops (PLMD::xdrfile); XDRFILE (PLMD::xdrfile); XYTorsions (PLMD::multicolvar)