PLUMED: Class Index

Loading...

Searching...

No Matches

A: ABMD (PLMD::bias); Operation::Abs (PLMD::lepton); Operation::Acos (PLMD::lepton); Action (PLMD); ActionAnyorder (PLMD); ActionAtomistic (PLMD); ActionOptions (PLMD); ActionPilot (PLMD); ActionRegister (PLMD); ActionSet (PLMD); ActionSetup (PLMD); ActionShortcut (PLMD); ActionVolume (PLMD::multicolvar); ActionWithArguments (PLMD); ActionWithAveraging (PLMD::vesselbase); ActionWithGrid (PLMD::gridtools); ActionWithInputGrid (PLMD::gridtools); ActionWithInputMatrix (PLMD::adjmat); ActionWithInputVessel (PLMD::vesselbase); ActionWithIntegral (PLMD::gridtools); ActionWithValue (PLMD); ActionWithVessel (PLMD::vesselbase); ActionWithVirtualAtom (PLMD); ActionWithVirtualAtom (PLMD::vatom); AdaptivePath (PLMD::mapping); Operation::Add (PLMD::lepton); Operation::AddConstant (PLMD::lepton); AdjacencyMatrixBase (PLMD::adjmat); AdjacencyMatrixVessel (PLMD::adjmat); AlignedMatrixBase (PLMD::adjmat); AlphaBeta (PLMD::multicolvar); AlphaRMSD (PLMD::secondarystructure); AltMin (PLMD::vesselbase); AnalysisBase (PLMD::analysis); Angle (PLMD); Angle (PLMD::colvar); Angles (PLMD::multicolvar); annfunc::ANN (PLMD); ANN (PLMD::function::annfunc); AntibetaRMSD (PLMD::secondarystructure); ArgumentOnlyDistance (PLMD); Operation::Asin (PLMD::lepton); AsmJitRuntimePtr (PLMD::lepton); Exception::Assertion (PLMD); Operation::Atan (PLMD::lepton); Operation::Atan2 (PLMD::lepton); AtomNumber (PLMD); Atoms (PLMD); AtomValuePack (PLMD::multicolvar); Average (PLMD::analysis); AverageOnGrid (PLMD::gridtools); AverageVessel (PLMD::analysis); AveragingVessel (PLMD::vesselbase)

C: Caliber (PLMD::isdb); CatomPack (PLMD::multicolvar); Operation::Ceil (PLMD::lepton); Cell (PLMD::colvar); Center (PLMD::vatom); CenterOfMultiColvar (PLMD::multicolvar); CS2Backbone::ChemicalShift (PLMD::isdb); Citations (PLMD); ClassicalMultiDimensionalScaling (PLMD::dimred); CLTool (PLMD); CLTool (PLMD::cltools); CLToolMain (PLMD); CLToolOptions (PLMD); CLToolRegister (PLMD); CLToolSumHills (PLMD::cltools); ClusterAnalysisBase (PLMD::adjmat); ClusterDiameter (PLMD::adjmat); ClusterDistribution (PLMD::adjmat); ClusteringBase (PLMD::adjmat); ClusterProperties (PLMD::adjmat); ClusterSize (PLMD::adjmat); ClusterWithSurface (PLMD::adjmat); CoeffsBase (PLMD::ves); CoeffsMatrix (PLMD::ves); CoeffsVector (PLMD::ves); Colvar (PLMD); Colvar (PLMD::colvar); Colvar (PLMD::sasa); ColvarFake (PLMD::colvar); Combine (PLMD::function); Committor (PLMD::analysis); Communicator (PLMD); CompiledExpression (PLMD::lepton); Completion (PLMD::cltools); ConjugateGradient (PLMD); MatrixSquareBracketsAccess::Const_row (PLMD); Constant (PLMD::colvar); Operation::Constant (PLMD::lepton); Communicator::ConstData (PLMD); ContactAlignedMatrix (PLMD::adjmat); ContactMap (PLMD::colvar); ContactMatrix (PLMD::adjmat); ContourFindingBase (PLMD::gridtools); convergence (PLMD::opes); ConvertToFES (PLMD::gridtools); Coordination (PLMD::colvar); CoordinationBase (PLMD::colvar); CoordinationNumbers (PLMD::multicolvar); Operation::Cos (PLMD::lepton); Operation::Cosh (PLMD::lepton); Operation::Cot (PLMD::lepton); CS2Backbone (PLMD::isdb); CS2BackboneDB (PLMD::isdb); Operation::Csc (PLMD::lepton); Operation::Cube (PLMD::lepton); CubicHarmonicBase (PLMD::crystallization); Custom (PLMD::function); Operation::Custom (PLMD::lepton); CustomFunction (PLMD::lepton)

D: Communicator::Data (PLMD); DataCollectionObject (PLMD::analysis); DataFetchingObject (PLMD); DataFetchingObjectTyped (PLMD); Debug (PLMD::generic); tls::delete_ptr (PLMD::maze); Operation::Delta (PLMD::lepton); Density (PLMD::multicolvar); DFSClustering (PLMD::adjmat); DHEnergy (PLMD::colvar); DihedralCorrelation (PLMD::multicolvar); DimensionalityReductionBase (PLMD::dimred); Dimer (PLMD::colvar); Dipole (PLMD::colvar); Direction (PLMD); Tools::DirectoryChanger (PLMD); Distance (PLMD::colvar); DistanceFromContour (PLMD::multicolvar); Distances (PLMD::multicolvar); Operation::Divide (PLMD::lepton); DLLoader (PLMD); Atoms::DomainDecomposition (PLMD); DotProductDistance (PLMD); Driver (PLMD::cltools); DRMSD (PLMD::colvar); DRMSD (PLMD); DumpAtoms (PLMD::generic); DumpCube (PLMD::gridtools); DumpDerivatives (PLMD::generic); DumpForces (PLMD::generic); DumpGraph (PLMD::adjmat); DumpGrid (PLMD::gridtools); DumpMassCharge (PLMD::generic); DumpMultiColvar (PLMD::multicolvar); DumpProjections (PLMD::generic); DynamicList (PLMD); 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); EndPlumed (PLMD::generic); Energy (PLMD::colvar); Ensemble (PLMD::function); EnvironmentSimilarity (PLMD::crystallization); Operation::Erf (PLMD::lepton); Operation::Erfc (PLMD::lepton); ERMSD (PLMD::colvar); ERMSD (PLMD); EuclideanDissimilarityMatrix (PLMD::analysis); EuclideanDistance (PLMD); Exception (PLMD); Exception (PLMD::lepton); ExceptionDebug (PLMD); ExceptionError (PLMD); ExceptionTypeError (PLMD); ExchangePatterns (PLMD); Operation::Exp (PLMD::lepton); ExpansionCVs (PLMD::opes); exploration (PLMD::opes); ExpressionProgram (PLMD::lepton); ExpressionTreeNode (PLMD::lepton); ExtendedLagrangian (PLMD::bias); External (PLMD::bias); ExtraCV (PLMD::colvar)

F: F1dim (PLMD); FakeFrame (PLMD); FarthestPointSampling (PLMD::analysis); Fccubic (PLMD::crystallization); FermiSwitchingFunction (PLMD::ves); FesWeight (PLMD::ves); IFile::Field (PLMD); OFile::Field (PLMD); FileBase::FieldBase (PLMD); FileBase (PLMD); FilesHandler (PLMD::function); FilterBetween (PLMD::multicolvar); FilterLess (PLMD::multicolvar); FilterMore (PLMD::multicolvar); FindContour (PLMD::gridtools); FindContourSurface (PLMD::gridtools); FindSphericalContour (PLMD::gridtools); fio_iovec (PLMD::molfile); FISST (PLMD::fisst); FitToTemplate (PLMD::generic); FixedAtom (PLMD::vatom); FlexibleBin (PLMD); Operation::Floor (PLMD::lepton); Flush (PLMD::generic); ForwardDecl (PLMD); FourierTransform (PLMD::gridtools); FretEfficiency (PLMD::isdb); FuncPathGeneral (PLMD::function); FuncPathMSD (PLMD::function); FuncSumHills (PLMD::function); Function (PLMD::function); FunctionVessel (PLMD::vesselbase); Funnel (PLMD::funnel); FUNNEL_PS (PLMD::funnel); fusionPoreExpansionP (PLMD::membranefusion); fusionPoreNucleationP (PLMD::membranefusion)

J: JCoupling (PLMD::isdb)

K: OPESmetad::kernel (PLMD::opes); KernelFunctions (PLMD); Keywords::KeyType (PLMD); Keywords (PLMD); kt (PLMD::cltools)

M: MahalanobisDistance (PLMD); Manual (PLMD::cltools); ManyRestraintsBase (PLMD::manyrestraints); Mapping (PLMD::mapping); MarginalWeight (PLMD::ves); Matheval (PLMD::function); Matrix (PLMD); MatrixColumnSums (PLMD::adjmat); MatrixRowSums (PLMD::adjmat); MatrixSquareBracketsAccess (PLMD); Operation::Max (PLMD::lepton); Max (PLMD::vesselbase); 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); MDAtomsBase (PLMD); MDAtomsTyped (PLMD); Mean (PLMD::vesselbase); Member (PLMD::maze); Memetic (PLMD::maze); memFusionP (PLMD::membranefusion); MetaD (PLMD::bias); Metainference (PLMD::isdb); MetainferenceBase (PLMD::isdb); MetricRegister (PLMD); Operation::Min (PLMD::lepton); Min (PLMD::vesselbase); Minimise1DBrent (PLMD); MinimiseBase (PLMD); MolDataClass (PLMD); MoleculeOrientation (PLMD::crystallization); MoleculePlane (PLMD::crystallization); 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::vesselbase); MoreThan (PLMD::vesselbase); MovingRestraint (PLMD::bias); MPI_Comm (PLMD); MPI_Datatype (PLMD); MPI_Request (PLMD); MPI_Status (PLMD); MultiColvarBase (PLMD::multicolvar); MultiColvarCombine (PLMD::multicolvar); MultiColvarDensity (PLMD::multicolvar); MultiColvarFilter (PLMD::multicolvar); MultiColvarProduct (PLMD::multicolvar); MultiDomainRMSD (PLMD); Operation::Multiply (PLMD::lepton); Operation::MultiplyConstant (PLMD::lepton); MultiRMSD (PLMD::colvar); MultiValue (PLMD)

N: n_matrix (PLMD::drr::UIestimator); n_vector (PLMD::drr::UIestimator); Operation::Nandelta (PLMD::lepton); Operation::Negate (PLMD::lepton); NeighborList (PLMD); NOE (PLMD::isdb); NormalizedEuclideanDistance (PLMD); NumberOfLinks (PLMD::multicolvar)

P: FuncPathGeneral::pairordering (PLMD::function); FuncPathMSD::pairordering (PLMD::function); PAMM (PLMD::pamm); PammObject (PLMD::pamm); ParabetaRMSD (PLMD::secondarystructure); ParsedExpression (PLMD::lepton); Parser (PLMD::lepton); ParseToken (PLMD::lepton); Path (PLMD::mapping); PathBase (PLMD::mapping); PathMSD (PLMD::colvar); PathMSDBase (PLMD::colvar); PathReparameterization (PLMD::mapping); PathTools (PLMD::mapping); Pbc (PLMD); PBMetaD (PLMD::bias); PCA (PLMD::dimred); PCARMSD (PLMD::colvar); PCAVars (PLMD::mapping); PDB (PLMD); PdbRenumber (PLMD::cltools); PesMD (PLMD::cltools); Piecewise (PLMD::function); PIV (PLMD::piv); PlaceholderFunction (PLMD::lepton); Plumed (PLMD::generic); plumed; plumed_error; 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); PolymerAngles (PLMD::crystallization); Position (PLMD::colvar); Operation::Power (PLMD::lepton); Operation::PowerConstant (PLMD::lepton); PRE (PLMD::isdb); Print (PLMD::generic); PrintDissimilarityMatrix (PLMD::analysis); ProbWeight (PLMD); ProjectionOnAxis (PLMD::colvar); ProjectNonLandmarkPoints (PLMD::dimred); PropertyMap (PLMD::colvar); PropertyMap (PLMD::mapping); Puckering (PLMD::colvar); pytorch::PytorchModel (PLMD)

Q: Q3 (PLMD::crystallization); Q4 (PLMD::crystallization); Q6 (PLMD::crystallization)

R: Random (PLMD); Random_Acceleration_MD (PLMD::maze); Random_Walk (PLMD::maze); RandomExchanges (PLMD::generic); RDC (PLMD::isdb); Read (PLMD::generic); ReadAnalysisFrames (PLMD::analysis); ReadDissimilarityMatrix (PLMD::analysis); Operation::Reciprocal (PLMD::lepton); ReferenceArguments (PLMD); ReferenceAtoms (PLMD); ReferenceConfiguration (PLMD); ReferenceConfigurationOptions (PLMD); ReferenceValuePack (PLMD); Communicator::Request (PLMD); Rescale (PLMD::isdb); ReselectLandmarks (PLMD::analysis); ResetCell (PLMD::generic); Restart (PLMD::setup); Restraint (PLMD::bias); ReweightBase (PLMD::bias); ReweightBias (PLMD::bias); ReweightMetad (PLMD::bias); ReweightTemperaturePressure (PLMD::bias); ReweightWham (PLMD::bias); CS2Backbone::RingInfo (PLMD::isdb); RMSD (PLMD::colvar); RMSD (PLMD); RMSDBase (PLMD); RMSDCoreData (PLMD); rnd (PLMD::maze); RootFindingBase (PLMD); MatrixSquareBracketsAccess::Row (PLMD)

S: S2ContactModel (PLMD::s2cm); SASA_HASEL (PLMD::sasa); SASA_LCPO (PLMD::sasa); SAXS (PLMD::isdb); Operation::Sec (PLMD::lepton); SecondaryStructureRMSD (PLMD::secondarystructure); Select (PLMD::isdb); Operation::Select (PLMD::lepton); Selector (PLMD::isdb); SelectRandomFrames (PLMD::analysis); SelectWithStride (PLMD::analysis); PIV::SharedData (PLMD::piv); ShortcutVessel (PLMD::vesselbase); SimpleCubic (PLMD::crystallization); SimpleMD (PLMD::cltools); SimpleRMSD (PLMD); Simulated_Annealing (PLMD::maze); Operation::Sin (PLMD::lepton); SingleDomainRMSD (PLMD); Operation::Sinh (PLMD::lepton); SketchMap (PLMD::dimred); SketchMapBase (PLMD::dimred); SketchMapConjGrad (PLMD::dimred); SketchMapPointwise (PLMD::dimred); SketchMapRead (PLMD::dimred); SketchMapSmacof (PLMD::dimred); SMAC (PLMD::crystallization); SMACMatrix (PLMD::adjmat); SMACOF (PLMD::dimred); SmacofMDS (PLMD::dimred); Sort (PLMD::function); SparseGrid (PLMD); SpathVessel (PLMD::mapping); Sprint (PLMD::adjmat); Operation::Sqrt (PLMD::lepton); Operation::Square (PLMD::lepton); Stats (PLMD::function); Communicator::Status (PLMD); Steered_MD (PLMD::maze); Steinhardt (PLMD::crystallization); Operation::Step (PLMD::lepton); Stopwatch (PLMD); StoreDataVessel (PLMD::vesselbase); Subprocess (PLMD); SubprocessPid (PLMD); Operation::Subtract (PLMD::lepton); Sum (PLMD::vesselbase); SwitchingFunction (PLMD)

T: t_trnheader (PLMD::xdrfile); Operation::Tan (PLMD::lepton); Operation::Tanh (PLMD::lepton); Target (PLMD::function); 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); TensorGeneric (PLMD); TensorGenericAux (PLMD); Tetrahedral (PLMD::crystallization); Exception::Throw (PLMD); Time (PLMD::generic); tls (PLMD::maze); Tools (PLMD); TopologyMatrix (PLMD::adjmat); Torsion (PLMD::colvar); Torsion (PLMD); Torsions (PLMD::multicolvar); Tree (PLMD); TrigonometricPathVessel (PLMD::mapping); trx_hdr (PLMD::molfile); TypesafePtr (PLMD)

U: UIestimator (PLMD::drr::UIestimator); Units (PLMD::setup); Units (PLMD); UpdateIf (PLMD::generic); UWalls (PLMD::bias); UWalls (PLMD::manyrestraints)

W: Stopwatch::Watch (PLMD); WaveletGrid (PLMD::ves); WeightBase (PLMD); WellTemperedModifer (PLMD::ves); WhamHistogram (PLMD::analysis); WhamWeights (PLMD::analysis); WholeMolecules (PLMD::generic); WithCmd (PLMD); WrapAround (PLMD::generic)

X: XAngles (PLMD::multicolvar); XDistances (PLMD::multicolvar); XDR (PLMD::xdrfile); XDR::xdr_ops (PLMD::xdrfile); XDRFILE (PLMD::xdrfile); XYDistances (PLMD::multicolvar); XYTorsion (PLMD::multicolvar)

Z: ZpathVessel (PLMD::mapping)

_: Tools::_Unique_if (PLMD); Tools::_Unique_if< T[]> (PLMD); Tools::_Unique_if< T[N]> (PLMD)