Class Index
A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z
  A  
Function (PLMD::function)   
  Q  
FunctionVessel (PLMD::vesselbase)   
ABMD (PLMD::bias)   
  G  
Q3 (PLMD::crystallization)   
Action (PLMD)   Q4 (PLMD::crystallization)   
ActionAtomistic (PLMD)   MetaD::Gaussian (PLMD::bias)   Q6 (PLMD::crystallization)   
ActionOptions (PLMD)   PBMetaD::Gaussian (PLMD::bias)   
  R  
ActionPilot (PLMD)   GenTemplate (PLMD::cltools)   
ActionRegister (PLMD)   Ghost (PLMD::vatom)   Random (PLMD)   
ActionSet (PLMD)   Gradient (PLMD::crystallisation)   RandomExchanges (PLMD::generic)   
ActionSetup (PLMD)   GradientVessel (PLMD::crystallisation)   RDC (PLMD)   
ActionVolume (PLMD::multicolvar)   GREX (PLMD)   Read (PLMD::generic)   
ActionWithArguments (PLMD)   Grid (PLMD)   ReferenceArguments (PLMD)   
ActionWithInputVessel (PLMD::vesselbase)   Group (PLMD::generic)   ReferenceAtoms (PLMD)   
ActionWithValue (PLMD)   Gyration (PLMD::colvar)   ReferenceConfiguration (PLMD)   
ActionWithVessel (PLMD::vesselbase)   
  H  
ReferenceConfigurationOptions (PLMD)   
ActionWithVirtualAtom (PLMD)   ReferenceValuePack (PLMD)   
AdjacencyMatrixAction (PLMD::multicolvar)   Highest (PLMD::vesselbase)   Communicator::Request (PLMD)   
AdjacencyMatrixVessel (PLMD::multicolvar)   Histogram (PLMD::analysis)   Restart (PLMD::setup)   
AlphaBeta (PLMD::multicolvar)   Histogram (PLMD::vesselbase)   Restraint (PLMD::bias)   
AlphaRMSD (PLMD::secondarystructure)   HistogramBead (PLMD)   RMSD (PLMD)   
AltMin (PLMD::mapping)   
  I  
RMSD (PLMD::colvar)   
Analysis (PLMD::analysis)   RMSDBase (PLMD)   
AnalysisWithLandmarks (PLMD::analysis)   IFile (PLMD)   RMSDCoreData (PLMD)   
Angle (PLMD::colvar)   PathMSDBase::ImagePath (PLMD::colvar)   MatrixSquareBracketsAccess::Row (PLMD)   
Angle (PLMD)   IMD (PLMD)   
  S  
Angles (PLMD::multicolvar)   Include (PLMD::generic)   
AntibetaRMSD (PLMD::secondarystructure)   Info (PLMD::cltools)   SecondaryStructureRMSD (PLMD::secondarystructure)   
ArgumentOnlyDistance (PLMD)   InPlaneDistances (PLMD::multicolvar)   SetupMolInfo (PLMD)   
AtomNumber (PLMD)   InterpolateBicubic (PLMD)   ShortcutVessel (PLMD::vesselbase)   
Atoms (PLMD)   InterpolateCubic (PLMD)   SimpleCubic (PLMD::crystallization)   
AtomValuePack (PLMD::multicolvar)   
  K  
SimpleMD (PLMD::cltools)   
  B  
SimpleRMSD (PLMD)   
Kearsley (PLMD)   SingleDomainRMSD (PLMD)   
Between (PLMD::vesselbase)   KernelFunctions (PLMD)   SMAC (PLMD::crystallization)   
Bias (PLMD::bias)   Keywords::KeyType (PLMD)   Sort (PLMD::function)   
BiasRepresentation (PLMD)   Keywords (PLMD)   SparseGrid (PLMD)   
BiasValue (PLMD::bias)   
  L  
SpathVessel (PLMD::mapping)   
BiasWeight (PLMD)   Sprint (PLMD::multicolvar)   
Bridge (PLMD::multicolvar)   LandmarkRegister (PLMD::analysis)   Communicator::Status (PLMD)   
BridgedMultiColvarFunction (PLMD::multicolvar)   LandmarkSelectionBase (PLMD::analysis)   Steinhardt (PLMD::crystallization)   
BridgeVessel (PLMD::vesselbase)   LandmarkSelectionOptions (PLMD::analysis)   Stopwatch (PLMD)   
  C  
LatticeReduction (PLMD)   StoreDataVessel (PLMD::vesselbase)   
LessThan (PLMD::vesselbase)   Sum (PLMD::vesselbase)   
CatomPack (PLMD::multicolvar)   LinkCells (PLMD)   SwitchingFunction (PLMD)   
Cell (PLMD::colvar)   Load (PLMD::setup)   
  T  
Center (PLMD::vatom)   LOCAL_Q3 (PLMD::crystallization)   
CH3Shifts (PLMD)   LOCAL_Q4 (PLMD::crystallization)   Target (PLMD::function)   
CInterpolation (PLMD)   LOCAL_Q6 (PLMD::crystallization)   TargetDist (PLMD)   
Citations (PLMD)   LocalAverage (PLMD::multicolvar)   Template (PLMD::colvar)   
ClassicalMultiDimensionalScaling (PLMD::analysis)   LocalSteinhardt (PLMD::crystallization)   TensorChecks (PLMD)   
ClassicalScaling (PLMD::analysis)   Log (PLMD)   TensorGeneric (PLMD)   
CLTool (PLMD)   LoopUnroller (PLMD)   Tetrahedral (PLMD::crystallization)   
CLToolMain (PLMD)   Lowest (PLMD::vesselbase)   Time (PLMD::generic)   
CLToolOptions (PLMD)   LWalls (PLMD::bias)   Stopwatch::Time (PLMD)   
CLToolRegister (PLMD)   
  M  
Tools (PLMD)   
CLToolSumHills (PLMD::cltools)   Torsion (PLMD)   
Colvar (PLMD)   MahalanobisDistance (PLMD)   Torsion (PLMD::colvar)   
ColvarFake (PLMD::colvar)   Manual (PLMD::cltools)   Torsions (PLMD::multicolvar)   
COM (PLMD::vatom)   ManyRestraintsBase (PLMD::manyrestraints)   
  U  
Combine (PLMD::function)   Mapping (PLMD::mapping)   
Committor (PLMD::analysis)   Matheval (PLMD::function)   Units (PLMD::setup)   
Communicator (PLMD)   Matrix (PLMD)   Units (PLMD)   
MatrixSquareBracketsAccess::Const_row (PLMD)   MatrixSquareBracketsAccess (PLMD)   UWalls (PLMD::bias)   
Constant (PLMD::colvar)   Max (PLMD::vesselbase)   UWalls (PLMD::manyrestraints)   
Communicator::ConstData (PLMD)   MDAtomsBase (PLMD)   
  V  
ContactMap (PLMD::colvar)   MDAtomsTyped (PLMD)   
Coordination (PLMD::colvar)   Mean (PLMD::vesselbase)   Value (PLMD)   
CoordinationBase (PLMD::colvar)   MetaD (PLMD::bias)   ValueVessel (PLMD::vesselbase)   
CoordinationNumbers (PLMD::multicolvar)   MetricRegister (PLMD)   VectorChecks (PLMD)   
CopyAllFrames (PLMD::analysis)   Min (PLMD::vesselbase)   VectorGeneric (PLMD)   
CS2Backbone (PLMD)   MolDataClass (PLMD)   VectorMean (PLMD::crystallization)   
  D  
MoleculeOrientation (PLMD::crystallization)   VectorMultiColvar (PLMD::crystallization)   
MoleculePlane (PLMD::crystallization)   VectorSum (PLMD::crystallization)   
Communicator::Data (PLMD)   MolInfo (PLMD::setup)   Vessel (PLMD::vesselbase)   
Debug (PLMD::generic)   Moments (PLMD::vesselbase)   VesselOptions (PLMD::vesselbase)   
Density (PLMD::multicolvar)   MoreThan (PLMD::vesselbase)   VesselRegister (PLMD::vesselbase)   
DFSBasic (PLMD::crystallization)   MovingRestraint (PLMD::bias)   Volume (PLMD::colvar)   
DFSClusterDiameter (PLMD::crystallization)   MPI_Comm (PLMD)   VolumeAround (PLMD::multicolvar)   
DFSClustering (PLMD::crystallization)   MPI_Datatype (PLMD)   VolumeCavity (PLMD::multicolvar)   
DFSMaxCluster (PLMD::crystallization)   MPI_Request (PLMD)   VolumeGradientBase (PLMD::multicolvar)   
DFSNumberOfClusters (PLMD::crystallization)   MPI_Status (PLMD)   VolumeInCylinder (PLMD::multicolvar)   
DHEnergy (PLMD::colvar)   MultiColvar (PLMD::multicolvar)   VolumeTetrapore (PLMD::multicolvar)   
DihedralCorrelation (PLMD::multicolvar)   MultiColvarBase (PLMD::multicolvar)   
  W  
Dipole (PLMD::colvar)   MultiColvarDensity (PLMD::multicolvar)   
Direction (PLMD)   MultiColvarFilter (PLMD::multicolvar)   Stopwatch::Watch (PLMD)   
Distance (PLMD::colvar)   MultiColvarFunction (PLMD::multicolvar)   WeightBase (PLMD)   
Distances (PLMD::multicolvar)   MultiDomainRMSD (PLMD)   WholeMolecules (PLMD::generic)   
DLLoader (PLMD)   MultiReferenceBase (PLMD)   WithCmd (PLMD)   
Atoms::DomainDecomposition (PLMD)   MultiRMSD (PLMD::colvar)   WrapAround (PLMD::generic)   
DotProductDistance (PLMD)   MultiValue (PLMD)   
  X  
Driver (PLMD::cltools)   
  N  
DRMSD (PLMD)   XDistances (PLMD::multicolvar)   
DRMSD (PLMD::colvar)   NeighborList (PLMD)   XYDistances (PLMD::multicolvar)   
DumpAtoms (PLMD::generic)   NOE (PLMD::colvar)   
  Z  
DumpDerivatives (PLMD::generic)   NormalizedEuclideanDistance (PLMD)   
DumpForces (PLMD::generic)   NumberOfLinks (PLMD::multicolvar)   ZpathVessel (PLMD::mapping)   
DumpMassCharge (PLMD::generic)   
  O  
  f  
DumpMultiColvar (PLMD::multicolvar)   
DumpProjections (PLMD::generic)   OFile (PLMD)   fio_iovec (PLMD::molfile)   
DynamicList (PLMD)   OpenMP (PLMD)   
  i  
  E  
OptimalAlignment (PLMD)   
OptimalRMSD (PLMD)   PathMSDBase::imgOrderByDist (PLMD::colvar)   
EffectiveEnergyDrift (PLMD::generic)   OrderingVessel (PLMD::vesselbase)   PathMSDBase::imgOrderBySimilarity (PLMD::colvar)   
Energy (PLMD::colvar)   OrientationSphere (PLMD::crystallization)   
  k  
Ensemble (PLMD::function)   
  P  
EuclideanDistance (PLMD)   kt (PLMD::cltools)   
Exception (PLMD)   ParabetaRMSD (PLMD::secondarystructure)   
  m  
ExchangePatterns (PLMD)   Path (PLMD::mapping)   
ExtendedLagrangian (PLMD::bias)   PathBase (PLMD::mapping)   md_atom (PLMD::molfile)   
External (PLMD::bias)   PathMSD (PLMD::colvar)   md_box (PLMD::molfile)   
  F  
PathMSDBase (PLMD::colvar)   md_file (PLMD::molfile)   
Pbc (PLMD)   md_header (PLMD::molfile)   
FakeFrame (PLMD)   PBMetaD (PLMD::bias)   md_ts (PLMD::molfile)   
Fccubic (PLMD::crystallization)   PCARMSD (PLMD::colvar)   molfile_atom_t (PLMD::molfile)   
IFile::Field (PLMD)   PCAVars (PLMD::mapping)   molfile_graphics_t (PLMD::molfile)   
OFile::Field (PLMD)   PDB (PLMD)   molfile_metadata_t (PLMD::molfile)   
FileBase::FieldBase (PLMD)   Piecewise (PLMD::function)   molfile_plugin_t (PLMD::molfile)   
FileBase (PLMD)   Plumed (PLMD)   molfile_qm_basis_t (PLMD::molfile)   
FilesHandler (PLMD::function)   PlumedMain (PLMD)   molfile_qm_hessian_t (PLMD::molfile)   
FilterBetween (PLMD::multicolvar)   PlumedMainInitializer (PLMD)   molfile_qm_metadata_t (PLMD::molfile)   
FilterLess (PLMD::multicolvar)   PointWiseMapping (PLMD)   molfile_qm_sysinfo_t (PLMD::molfile)   
FilterMore (PLMD::multicolvar)   Position (PLMD::colvar)   molfile_qm_t (PLMD::molfile)   
FitToTemplate (PLMD::generic)   Print (PLMD::generic)   molfile_qm_timestep_metadata (PLMD::molfile)   
FlexibleBin (PLMD)   ProbWeight (PLMD)   molfile_qm_timestep_t (PLMD::molfile)   
Flush (PLMD::generic)   PropertyMap (PLMD::colvar)   molfile_qm_wavefunction_t (PLMD::molfile)   
FuncPathMSD (PLMD::function)   PropertyMap (PLMD::mapping)   molfile_timestep_metadata (PLMD::molfile)   
FuncSumHills (PLMD::function)   Puckering (PLMD::colvar)   molfile_timestep_t (PLMD::molfile)   
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