Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 123456]

►CPLMD::GridBase::AcceleratorBase	Auxiliary class for accelerating grid calculations
CPLMD::Accelerator< dimension_ >
CPLMD::GridBase::AcceleratorHandler	Auxiliary class for managing AcceleratorBase
►CPLMD::Action	Base class for all the input Actions
►CPLMD::ActionAnyorder
CPLMD::generic::Include	Provides the keyword INCLUDE
CPLMD::GenericMolInfo
CPLMD::setup::Load	Provides the keyword LOAD
►CPLMD::ActionAtomistic
►CPLMD::ActionWithVector
►CPLMD::ActionWithMatrix
►CPLMD::adjmat::AdjacencyMatrixBase
CPLMD::adjmat::BridgeMatrix	Provides the keyword BRIDGE_MATRIX
CPLMD::adjmat::ContactMatrix	Provides the keyword CONTACT_MATRIX_PROPER
CPLMD::adjmat::DistanceMatrix	Provides the keyword DISTANCE_MATRIX
CPLMD::adjmat::HbondMatrix	Provides the keyword HBOND_MATRIX
CPLMD::adjmat::TopologyMatrix	Provides the keyword TOPOLOGY_MATRIX
CPLMD::pamm::HBPammMatrix	Provides the keyword HBPAMM_MATRIX
CPLMD::adjmat::Neighbors	Provides the keyword NEIGHBORS
CPLMD::adjmat::TorsionsMatrix	Provides the keyword TORSIONS_MATRIX
CPLMD::crystdistrib::QuaternionBondProductMatrix	Provides the keyword QUATERNION_BOND_PRODUCT_MATRIX
CPLMD::crystdistrib::QuaternionProductMatrix	Provides the keyword QUATERNION_PRODUCT_MATRIX
CPLMD::function::FunctionOfMatrix< T >
CPLMD::matrixtools::MatrixTimesMatrix	Provides the keyword MATRIX_PRODUCT
CPLMD::matrixtools::MatrixTimesVector	Provides the keyword MATRIX_VECTOR_PRODUCT
CPLMD::matrixtools::OuterProduct	Provides the keyword OUTER_PRODUCT
CPLMD::matrixtools::Voronoi	Provides the keyword VORONOI
CPLMD::valtools::VStack	Provides the keyword VSTACK
CPLMD::colvar::MultiColvarTemplate< T >
CPLMD::colvar::RMSDVector	Provides the keyword RMSD_VECTOR
CPLMD::dimred::ProjectPoints	Provides the keyword PROJECT_POINTS
CPLMD::function::FunctionOfVector< T >
►CPLMD::gridtools::ActionWithGrid
►CPLMD::contour::ContourFindingBase
CPLMD::contour::FindContour	Provides the keyword FIND_CONTOUR
CPLMD::contour::FindContourSurface	Provides the keyword FIND_CONTOUR_SURFACE
CPLMD::contour::FindSphericalContour	Provides the keyword FIND_SPHERICAL_CONTOUR
CPLMD::fourier::FourierTransform	Provides the keyword FOURIER_TRANSFORM
CPLMD::gridtools::FindGridOptimum	Provides the keyword FIND_GRID_MAXIMUM
CPLMD::gridtools::FunctionOfGrid< T >
CPLMD::gridtools::InterpolateGrid	Provides the keyword INTERPOLATE_GRID
CPLMD::gridtools::KDE	Provides the keyword KDE
CPLMD::gridtools::ReadGridInSetup	Provides the keyword REFERENCE_GRID
CPLMD::mapping::GeometricPath	Provides the keyword GEOMETRIC_PATH
CPLMD::refdist::MatrixProductDiagonal	Provides the keyword MATRIX_PRODUCT_DIAGONAL
CPLMD::secondarystructure::SecondaryStructureRMSD	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
CPLMD::symfunc::ThreeBodyGFunctions	Provides the keyword GSYMFUNC_THREEBODY
►CPLMD::volumes::ActionVolume
CPLMD::volumes::VolumeAround	Provides the keyword AROUND_CALC
CPLMD::volumes::VolumeCavity	Provides the keyword CAVITY_CALC
CPLMD::volumes::VolumeInCylinder	Provides the keyword INCYLINDER_CALC
CPLMD::volumes::VolumeInEnvelope	Provides the keyword INENVELOPE_CALC
CPLMD::volumes::VolumeInSphere	Provides the keyword INSPHERE_CALC
CPLMD::volumes::VolumeTetrapore	Provides the keyword TETRAHEDRALPORE_CALC
►CPLMD::ActionWithVirtualAtom	Class to add a single virtual atom to the system
CPLMD::vatom::Center	Provides the keyword CENTER_FAST
CPLMD::vatom::FixedAtom	Provides the keyword FIXEDATOM
CPLMD::vatom::Ghost	Provides the keyword GHOST
►CPLMD::Colvar
CPLMD::colvar::Angle	Provides the keyword ANGLE_SCALAR
CPLMD::colvar::Cell	Provides the keyword CELL
CPLMD::colvar::ColvarFake	Provides the keyword FAKE
CPLMD::colvar::ContactMap	Provides the keyword CONTACTMAP
►CPLMD::colvar::CoordinationBase
CPLMD::colvar::Coordination	Provides the keyword COORDINATION
CPLMD::colvar::DHEnergy	Provides the keyword DHENERGY
CPLMD::colvar::GHBFIX	Provides the keyword GHBFIX
CPLMD::colvar::DihedralCorrelation	Provides the keyword DIHEDRAL_CORRELATION_SCALAR
CPLMD::colvar::Dimer	Provides the keyword <a href="../../user-doc/html/_"_d_i_m_e_r.html"> "DIMER
CPLMD::colvar::Dipole	Provides the keyword DIPOLE_SCALAR
CPLMD::colvar::Distance	Provides the keyword DISTANCE_SCALAR
CPLMD::colvar::EEFSolv	Provides the keyword EEFSOLV
CPLMD::colvar::ERMSD	Provides the keyword ERMSD
CPLMD::colvar::Gyration	Provides the keyword GYRATION_FAST
►CPLMD::colvar::PathMSDBase
CPLMD::colvar::PathMSD	Provides the keyword PATHMSD
CPLMD::colvar::PropertyMap	Provides the keyword PROPERTYMAP
CPLMD::colvar::PCARMSD	Provides the keyword PCARMSD
CPLMD::colvar::Plane	Provides the keyword PLANE_SCALAR
CPLMD::colvar::Position	Provides the keyword POSITION_SCALAR
CPLMD::colvar::ProjectionOnAxis	Provides the keyword PROJECTION_ON_AXIS
CPLMD::colvar::Puckering	Provides the keyword PUCKERING
CPLMD::colvar::RMSD	Provides the keyword RMSD_SCALAR
CPLMD::colvar::SelectMassCharge	Provides the keyword MASS_SCALAR
CPLMD::colvar::Template	Provides the keyword TEMPLATE
CPLMD::colvar::Torsion	Provides the keyword TORSION_SCALAR
CPLMD::colvar::Volume	Provides the keyword VOLUME
CPLMD::crystdistrib::Quaternion	Provides the keyword QUATERNION_SCALAR
CPLMD::funnel::FUNNEL_PS	Provides the keyword FUNNEL_PS
CPLMD::isdb::FretEfficiency	Provides the keyword FRET
CPLMD::isdb::Shadow	Provides the keyword SHADOW
CPLMD::maze::Loss	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__l_o_s_s.html"> "MAZE_LOSS
►CPLMD::maze::Optimizer	Base class for implementing optimizers for ligand unbinding
CPLMD::maze::Memetic	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__m_e_m_e_t_i_c__s_a_m_p_l_i_n_g.html"> "MAZE_MEMETIC_SAMPLING
CPLMD::maze::Random_Acceleration_MD	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__r_a_n_d_o_m__a_c_c_e_l_e_r_a_t_i_o_n__m_d.html"> "MAZE_RANDOM_ACCELERATION_MD
CPLMD::maze::Random_Walk	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__r_a_n_d_o_m__w_a_l_k.html"> "MAZE_RANDOM_WALK
CPLMD::maze::Simulated_Annealing	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__s_i_m_u_l_a_t_e_d__a_n_n_e_a_l_i_n_g.html"> "MAZE_SIMULATED_ANNEALING
CPLMD::maze::Steered_MD	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__s_t_e_e_r_e_d__m_d.html"> "MAZE_STEERED_MD
CPLMD::membranefusion::fusionPoreExpansionP	Provides the keyword <a href="../../user-doc/html/_"_f_u_s_i_o_n_p_o_r_e_e_x_p_a_n_s_i_o_n_p.html"> "FUSIONPOREEXPANSIONP
CPLMD::membranefusion::fusionPoreNucleationP	Provides the keyword <a href="../../user-doc/html/_"_f_u_s_i_o_n_p_o_r_e_n_u_c_l_e_a_t_i_o_n_p.html"> "FUSIONPORENUCLEATIONP
CPLMD::membranefusion::memFusionP	Provides the keyword <a href="../../user-doc/html/_"_m_e_m_f_u_s_i_o_n_p.html"> "MEMFUSIONP
CPLMD::piv::PIV	Provides the keyword PIV
CPLMD::s2cm::S2ContactModel	Provides the keyword S2CM
CPLMD::sasa::SASA_HASEL	Provides the keyword SASA_HASEL
CPLMD::sasa::SASA_LCPO	Provides the keyword SASA_LCPO
CPLMD::sizeshape::position_linear_proj	Provides the keyword <a href="../../user-doc/html/_"_s_i_z_e_s_h_a_p_e__p_o_s_i_t_i_o_n__l_i_n_e_a_r__p_r_o_j.html"> "SIZESHAPE_POSITION_LINEAR_PROJ
CPLMD::sizeshape::position_maha_dist	Provides the keyword SIZESHAPE_POSITION_MAHA_DIST
►CPLMD::contour::DistanceFromContourBase
CPLMD::contour::DistanceFromContour	Provides the keyword DISTANCE_FROM_CONTOUR
CPLMD::contour::DistanceFromSphericalContour	Provides the keyword DISTANCE_FROM_SPHERICAL_CONTOUR
CPLMD::generic::DumpAtoms	Provides the keyword DUMPATOMS
CPLMD::generic::DumpMassCharge	Provides the keyword DUMPMASSCHARGE
CPLMD::generic::FitToTemplate	Provides the keyword FIT_TO_TEMPLATE
CPLMD::generic::Plumed	Provides the keyword PLUMED
CPLMD::generic::PrintNDX	Provides the keyword PRINT_NDX
CPLMD::generic::ResetCell	Provides the keyword RESET_CELL
CPLMD::generic::WholeMolecules	Provides the keyword WHOLEMOLECULES
CPLMD::generic::WrapAround	Provides the keyword WRAPAROUND
CPLMD::GenericMolInfo
CPLMD::Group	Provides the keyword GROUP
CPLMD::isdb::EMMI	Provides the keyword EMMI
►CPLMD::isdb::MetainferenceBase
CPLMD::isdb::CS2Backbone	Provides the keyword CS2BACKBONE
CPLMD::isdb::JCoupling	Provides the keyword <a href="../../user-doc/html/_"_j_c_o_u_p_l_i_n_g.html"> "JCOUPLING
CPLMD::isdb::NOE	Provides the keyword NOE
CPLMD::isdb::PRE	Provides the keyword PRE
CPLMD::isdb::RDC	Provides the keyword RDC
CPLMD::isdb::SAXS	Provides the keyword SAXS
CPLMD::metatensor::MetatensorPlumedAction	Provides the keyword <a href="../../user-doc/html/_"_m_e_t_a_t_e_n_s_o_r.html"> "METATENSOR
►CPLMD::ActionPilot
CPLMD::ActionToGetData	Provides the keyword GET
►CPLMD::bias::Bias
CPLMD::bias::ABMD	Provides the keyword ABMD
CPLMD::bias::BiasValue	Provides the keyword BIASVALUE
CPLMD::bias::ExtendedLagrangian	Provides the keyword EXTENDED_LAGRANGIAN
CPLMD::bias::External	Provides the keyword EXTERNAL
CPLMD::bias::LWalls	Provides the keyword LOWER_WALLS_SCALAR
CPLMD::bias::MaxEnt	Provides the keyword MAXENT
CPLMD::bias::MetaD	Provides the keyword METAD
CPLMD::bias::MovingRestraint	Provides the keyword MOVINGRESTRAINT
CPLMD::bias::PBMetaD	Provides the keyword PBMETAD
CPLMD::bias::Restraint	Provides the keyword RESTRAINT_SCALAR
CPLMD::bias::UWalls	Provides the keyword UPPER_WALLS_SCALAR
CPLMD::eds::EDS	Provides the keyword <a href="../../user-doc/html/_"_e_d_s.html"> "EDS
CPLMD::fisst::FISST	Provides the keyword FISST
CPLMD::funnel::Funnel	Provides the keyword FUNNEL
CPLMD::isdb::Caliber	Provides the keyword CALIBER
CPLMD::isdb::Metainference	Provides the keyword METAINFERENCE
CPLMD::isdb::Rescale	Provides the keyword RESCALE
CPLMD::logmfd::LogMFD	Class for LogMFD parameters, variables and subroutines
CPLMD::maze::OptimizerBias	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__o_p_t_i_m_i_z_e_r__b_i_a_s.html"> "MAZE_OPTIMIZER_BIAS
CPLMD::opes::OPESexpanded	Provides the keyword OPES_EXPANDED
CPLMD::opes::OPESmetad< mode >
►CPLMD::ves::VesBias
CPLMD::ves::VesLinearExpansion	Provides the keyword VES_LINEAR_EXPANSION
CPLMD::ves::VesDeltaF	Provides the keyword VES_DELTA_F
CPLMD::contour::DumpContour	Provides the keyword DUMPCONTOUR
CPLMD::generic::Accumulate	Provides the keyword ACCUMULATE
CPLMD::generic::Collect	Provides the keyword COLLECT
CPLMD::generic::Committor	Provides the keyword COMMITTOR
CPLMD::generic::Debug	Provides the keyword DEBUG
CPLMD::generic::DumpAtoms	Provides the keyword DUMPATOMS
CPLMD::generic::DumpDerivatives	Provides the keyword DUMPDERIVATIVES
CPLMD::generic::DumpForces	Provides the keyword DUMPFORCES
CPLMD::generic::DumpMassCharge	Provides the keyword DUMPMASSCHARGE
CPLMD::generic::DumpPDB	Provides the keyword DUMPPDB
CPLMD::generic::DumpProjections	Provides the keyword DUMPPROJECTIONS
CPLMD::generic::DumpVector	Provides the keyword DUMPVECTOR
CPLMD::generic::EffectiveEnergyDrift	Provides the keyword EFFECTIVE_ENERGY_DRIFT
CPLMD::generic::FitToTemplate	Provides the keyword FIT_TO_TEMPLATE
CPLMD::generic::Flush	Provides the keyword FLUSH
CPLMD::generic::Plumed	Provides the keyword PLUMED
CPLMD::generic::Print	Provides the keyword PRINT
CPLMD::generic::PrintNDX	Provides the keyword PRINT_NDX
CPLMD::generic::Read	Provides the keyword READ
CPLMD::generic::ResetCell	Provides the keyword RESET_CELL
CPLMD::generic::UpdateIf	Provides the keyword UPDATE_IF
CPLMD::generic::WholeMolecules	Provides the keyword WHOLEMOLECULES
CPLMD::generic::WrapAround	Provides the keyword WRAPAROUND
CPLMD::GenericMolInfo
CPLMD::gridtools::DumpGrid	Provides the keyword DUMPCUBE
CPLMD::mapping::PathDisplacements	Provides the keyword AVERAGE_PATH_DISPLACEMENT
CPLMD::mapping::PathReparameterization	Provides the keyword REPARAMETERIZE_PATH
►CPLMD::ves::Optimizer
CPLMD::ves::Opt_Adam	Provides the keyword OPT_ADAM
CPLMD::ves::Opt_BachAveragedSGD	Provides the keyword OPT_AVERAGED_SGD
CPLMD::ves::Opt_Dummy	Provides the keyword OPT_DUMMY
CPLMD::ves::Opt_RobbinsMonroSGD	Provides the keyword OPT_ROBBINS_MONRO_SGD
►CPLMD::ActionSetup
CPLMD::setup::Restart	Provides the keyword RESTART
CPLMD::setup::Units	Provides the keyword UNITS
►CPLMD::ActionShortcut
CPLMD::adjmat::Bridge	Provides the keyword BRIDGE
CPLMD::adjmat::ContactMatrixShortcut	Provides the keyword CONTACT_MATRIX
CPLMD::bias::RestraintShortcut	Provides the keyword RESTRAINT
CPLMD::bias::Walls	Provides the keyword UPPER_WALLS
CPLMD::clusters::ClusterDiameter	Provides the keyword CLUSTER_DIAMETER
CPLMD::clusters::ClusterDistributionShortcut	Provides the keyword CLUSTER_DISTRIBUTION
CPLMD::clusters::ClusterNatoms	Provides the keyword CLUSTER_NATOMS
CPLMD::clusters::ClusterProperties	Provides the keyword CLUSTER_PROPERTIES
CPLMD::clusters::ClusterWithSurface	Provides the keyword CLUSTER_WITHSURFACE
CPLMD::clusters::OutputCluster	Provides the keyword OUTPUT_CLUSTER
CPLMD::colvar::ColvarShortcut< T >
CPLMD::colvar::DRMSD	Provides the keyword DRMSD
CPLMD::colvar::ExtraCV	Provides the keyword EXTRACV
CPLMD::colvar::GyrationShortcut	Provides the keyword GYRATION
CPLMD::colvar::MultiRMSD	Provides the keyword MULTI_RMSD
CPLMD::colvar::RMSDShortcut	Provides the keyword RMSD
CPLMD::crystdistrib::BopsShortcut	Provides the keyword BOPS
CPLMD::crystdistrib::DopsShortcut	Provides the keyword DOPS
CPLMD::crystdistrib::RopsShortcut	Provides the keyword ROPS
CPLMD::dimred::ClassicalMultiDimensionalScaling	Provides the keyword CLASSICAL_MDS
CPLMD::dimred::PCA	Provides the keyword PCA
CPLMD::dimred::SketchMap	Provides the keyword SKETCHMAP
CPLMD::dimred::SketchMapProjection	Provides the keyword SKETCHMAP_PROJECTION
CPLMD::envsim::EnvironmentSimilarity	Provides the keyword ENVIRONMENTSIMILARITY
CPLMD::function::FunctionShortcut< T >
CPLMD::function::Product	Provides the keyword PRODUCT
CPLMD::generic::Average	Provides the keyword AVERAGE
CPLMD::generic::MassChargeInput	Provides the keyword READMASSCHARGE
CPLMD::generic::Ones	Provides the keyword ONES
CPLMD::generic::PDB2Constant	Provides the keyword PDB2CONSTANT
CPLMD::gridtools::ConvertToFES	Provides the keyword CONVERT_TO_FES
CPLMD::gridtools::EvaluateFunctionOnGrid	Provides the keyword EVALUATE_FUNCTION_FROM_GRID
CPLMD::gridtools::Gradient	Provides the keyword GRADIENT
CPLMD::gridtools::Histogram	Provides the keyword HISTOGRAM
CPLMD::gridtools::KLEntropy	Provides the keyword KL_ENTROPY
CPLMD::gridtools::MultiColvarDensity	Provides the keyword MULTICOLVARDENS
CPLMD::gridtools::PairEntropies	Provides the keyword PAIRENTROPIES
CPLMD::gridtools::PairEntropy	Provides the keyword PAIRENTROPY
CPLMD::gridtools::RDF	Provides the keyword RDF
CPLMD::landmarks::CollectFrames	Provides the keyword COLLECT_FRAMES
CPLMD::landmarks::LandmarkSelection	Provides the keyword LANDMARK_SELECT_STRIDE
CPLMD::landmarks::LogSumExp	Provides the keyword LOGSUMEXP
CPLMD::mapping::AdaptivePath	Provides the keyword ADAPTIVE_PATH
CPLMD::mapping::GeometricPathShortcut	Provides the keyword GPATH
CPLMD::mapping::Path	Provides the keyword PATH
CPLMD::mapping::PCAVars	Provides the keyword PCAVARS
CPLMD::matrixtools::CovarianceMatrix	Provides the keyword COVARIANCE_MATRIX
CPLMD::matrixtools::Determinant	Provides the keyword DETERMINANT
CPLMD::multicolvar::AlphaBeta	Provides the keyword ALPHABETA
CPLMD::multicolvar::Angles	Provides the keyword ANGLES
CPLMD::multicolvar::CoordAngles	Provides the keyword COORD_ANGLES
CPLMD::multicolvar::Dihcor	Provides the keyword DIHCOR
CPLMD::multicolvar::Distances	Provides the keyword DISTANCES
CPLMD::multicolvar::DumpMultiColvar	Provides the keyword DUMPMULTICOLVAR
CPLMD::multicolvar::InPlaneDistances	Provides the keyword INPLANEDISTANCES
CPLMD::multicolvar::MFilterLess	Provides the keyword MFILTER_LESS
CPLMD::multicolvar::MFilterMore	Provides the keyword MFILTER_MORE
CPLMD::multicolvar::PlaneShortcut	Provides the keyword PLANES
CPLMD::multicolvar::Torsions	Provides the keyword TORSIONS
CPLMD::multicolvar::UWalls	Provides the keyword UWALLS
CPLMD::multicolvar::XAngle	Provides the keyword XANGLES
CPLMD::multicolvar::XYTorsions	Provides the keyword XYTORSIONS
CPLMD::pamm::HBPammShortcut	Provides the keyword HBPAMM_SD
CPLMD::pamm::PAMM	Provides the keyword PAMM
CPLMD::refdist::Displacement	Provides the keyword DISPLACEMENT
CPLMD::refdist::EuclideanDistance	Provides the keyword EUCLIDEAN_DISTANCE
CPLMD::refdist::Kernel	Provides the keyword KERNEL
CPLMD::refdist::MahalanobisDistance	Provides the keyword MAHALANOBIS_DISTANCE
CPLMD::refdist::NormalizedEuclideanDistance	Provides the keyword NORMALIZED_EUCLIDEAN_DISTANCE
CPLMD::secondarystructure::AlphaRMSD	Provides the keyword ALPHARMSD
CPLMD::secondarystructure::AntibetaRMSD	Provides the keyword ANTIBETARMSD
CPLMD::secondarystructure::ParabetaRMSD	Provides the keyword PARABETARMSD
CPLMD::sprint::Sprint	Provides the keyword SPRINT
CPLMD::symfunc::AngularTetra	Provides the keyword TETRA_ANGULAR
CPLMD::symfunc::AtomicSMAC	Provides the keyword ATOMIC_SMAC
CPLMD::symfunc::CoordinationNumbers	Provides the keyword COORDINATIONNUMBER
CPLMD::symfunc::CoordShellVectorFunction	Provides the keyword FCCUBIC
CPLMD::symfunc::HexacticParameter	Provides the keyword HEXACTIC_PARAMETER
CPLMD::symfunc::LocalAverage	Provides the keyword LOCAL_AVERAGE
CPLMD::symfunc::LocalCrystallinity	Provides the keyword LOCAL_CRYSTALINITY
CPLMD::symfunc::LocalSteinhardt	Provides the keyword LOCAL_Q1
CPLMD::symfunc::RadialTetra	Provides the keyword TETRA_RADIAL
CPLMD::symfunc::SMAC	Provides the keyword SMAC
CPLMD::symfunc::Steinhardt	Provides the keyword Q1
CPLMD::valtools::SelectComponents	Provides the keyword SELECT_COMPONENTS
CPLMD::vatom::CenterShortcut	Provides the keyword CENTER
CPLMD::volumes::Density	Provides the keyword DENSITY
CPLMD::volumes::VolumeShortcut< v >
CPLMD::wham::WhamHistogram	Provides the keyword WHAM_HISTOGRAM
CPLMD::wham::WhamWeights	Provides the keyword WHAM_WEIGHTS
►CPLMD::ActionWithArguments
CPLMD::ActionToGetData	Provides the keyword GET
CPLMD::ActionWithVector
CPLMD::bias::Bias
►CPLMD::bias::ReweightBase
CPLMD::bias::ReweightBias	Provides the keyword REWEIGHT_BIAS
CPLMD::bias::ReweightMetad	Provides the keyword REWEIGHT_METAD
CPLMD::bias::ReweightTemperaturePressure	Provides the keyword REWEIGHT_TEMP_PRESS
CPLMD::clusters::ClusterDistribution	Provides the keyword CLUSTER_DISTRIBUTION_CALC
CPLMD::clusters::ClusterWeights	Provides the keyword CLUSTER_WEIGHTS
CPLMD::contour::DistanceFromContourBase
CPLMD::contour::DumpContour	Provides the keyword DUMPCONTOUR
CPLMD::dimred::ArrangePoints	Provides the keyword ARRANGE_POINTS
►CPLMD::function::Function
CPLMD::function::annfunc::ANN
CPLMD::function::Ensemble	Provides the keyword ENSEMBLE
CPLMD::function::FuncPathGeneral	Provides the keyword <a href="../../user-doc/html/_"_f_u_n_c_p_a_t_h_g_e_n_e_r_a_l.html"> "FUNCPATHGENERAL
CPLMD::function::FuncPathMSD	Provides the keyword FUNCPATHMSD
CPLMD::function::FuncSumHills	Provides the keyword FUNCSUMHILLS
CPLMD::function::FunctionOfScalar< T >
CPLMD::function::LocalEnsemble	Provides the keyword LOCALENSEMBLE
CPLMD::function::Stats	Provides the keyword STATS
CPLMD::isdb::Select	Provides the keyword SELECT
CPLMD::generic::Accumulate	Provides the keyword ACCUMULATE
CPLMD::generic::Collect	Provides the keyword COLLECT
CPLMD::generic::Committor	Provides the keyword COMMITTOR
CPLMD::generic::CreateMask	Provides the keyword CREATE_MASK
CPLMD::generic::DumpAtoms	Provides the keyword DUMPATOMS
CPLMD::generic::DumpDerivatives	Provides the keyword DUMPDERIVATIVES
CPLMD::generic::DumpForces	Provides the keyword DUMPFORCES
CPLMD::generic::DumpPDB	Provides the keyword DUMPPDB
CPLMD::generic::DumpProjections	Provides the keyword DUMPPROJECTIONS
CPLMD::generic::DumpVector	Provides the keyword DUMPVECTOR
CPLMD::generic::GatherReplicas	Provides the keyword GATHER_REPLICAS
CPLMD::generic::Print	Provides the keyword PRINT
CPLMD::generic::PrintNDX	Provides the keyword PRINT_NDX
CPLMD::generic::UpdateIf	Provides the keyword UPDATE_IF
CPLMD::gridtools::DumpGrid	Provides the keyword DUMPCUBE
CPLMD::isdb::EMMI	Provides the keyword EMMI
CPLMD::isdb::MetainferenceBase
CPLMD::mapping::PathDisplacements	Provides the keyword AVERAGE_PATH_DISPLACEMENT
►CPLMD::matrixtools::MatrixOperationBase
►CPLMD::clusters::ClusteringBase
CPLMD::clusters::DFSClustering	Provides the keyword DFSCLUSTERING
CPLMD::landmarks::FarthestPointSampling	Provides the keyword FARTHEST_POINT_SAMPLING
CPLMD::matrixtools::DiagonalizeMatrix	Provides the keyword DIAGONALIZE
CPLMD::matrixtools::InvertMatrix	Provides the keyword INVERT_MATRIX
CPLMD::matrixtools::TransposeMatrix	Provides the keyword TRANSPOSE
►CPLMD::opes::ExpansionCVs
CPLMD::opes::ECVcustom	Provides the keyword ECV_CUSTOM
CPLMD::opes::ECVlinear	Provides the keyword ECV_LINEAR
CPLMD::opes::ECVmultiThermal	Provides the keyword ECV_MULTITHERMAL
CPLMD::opes::ECVmultiThermalBaric	Provides the keyword ECV_MULTITHERMAL_MULTIBARIC
CPLMD::opes::ECVumbrellasFile	Provides the keyword ECV_UMBRELLAS_FILE
CPLMD::opes::ECVumbrellasLine	Provides the keyword ECV_UMBRELLAS_LINE
CPLMD::valtools::Concatenate	Provides the keyword CONCATENATE
CPLMD::valtools::Flatten	Provides the keyword FLATTEN
CPLMD::valtools::SelectWithMask	Provides the keyword SELECT_WITH_MASK
CPLMD::vatom::ArgsToVatom	Provides the keyword ARGS2VATOM
CPLMD::wham::Wham	Provides the keyword WHAM
►CPLMD::ActionWithValue
►CPLMD::ActionForInterface
►CPLMD::ActionToPutData	Provides the keyword PUT
CPLMD::colvar::Energy	Provides the keyword ENERGY
CPLMD::PbcAction	Provides the keyword PBC
CPLMD::DomainDecomposition
CPLMD::ActionWithVector
CPLMD::ActionWithVirtualAtom	Class to add a single virtual atom to the system
CPLMD::bias::Bias
CPLMD::bias::ReweightBase
CPLMD::clusters::ClusterDistribution	Provides the keyword CLUSTER_DISTRIBUTION_CALC
CPLMD::clusters::ClusterWeights	Provides the keyword CLUSTER_WEIGHTS
CPLMD::Colvar
CPLMD::contour::DistanceFromContourBase
CPLMD::dimred::ArrangePoints	Provides the keyword ARRANGE_POINTS
CPLMD::function::Function
CPLMD::generic::Accumulate	Provides the keyword ACCUMULATE
CPLMD::generic::Collect	Provides the keyword COLLECT
CPLMD::generic::Constant	Provides the keyword CONSTANT
CPLMD::generic::CreateMask	Provides the keyword CREATE_MASK
CPLMD::generic::FitToTemplate	Provides the keyword FIT_TO_TEMPLATE
CPLMD::generic::GatherReplicas	Provides the keyword GATHER_REPLICAS
CPLMD::generic::Plumed	Provides the keyword PLUMED
CPLMD::generic::Read	Provides the keyword READ
CPLMD::generic::Time	Provides the keyword TIME
CPLMD::isdb::EMMI	Provides the keyword EMMI
CPLMD::isdb::MetainferenceBase
CPLMD::mapping::PathDisplacements	Provides the keyword AVERAGE_PATH_DISPLACEMENT
CPLMD::matrixtools::MatrixOperationBase
CPLMD::metatensor::MetatensorPlumedAction	Provides the keyword <a href="../../user-doc/html/_"_m_e_t_a_t_e_n_s_o_r.html"> "METATENSOR
CPLMD::opes::ExpansionCVs
CPLMD::valtools::Concatenate	Provides the keyword CONCATENATE
CPLMD::valtools::Flatten	Provides the keyword FLATTEN
CPLMD::valtools::SelectWithMask	Provides the keyword SELECT_WITH_MASK
CPLMD::vatom::ArgsToVatom	Provides the keyword ARGS2VATOM
CPLMD::ves::Optimizer
CPLMD::wham::Wham	Provides the keyword WHAM
CPLMD::generic::EndPlumed	Provides the keyword ENDPLUMED
CPLMD::generic::RandomExchanges	Provides the keyword RANDOM_EXCHANGES
CPLMD::isdb::Selector	Provides the keyword SELECTOR
►CPLMD::ves::BasisFunctions
CPLMD::ves::BF_Chebyshev	Provides the keyword BF_CHEBYSHEV
CPLMD::ves::BF_Combined	Provides the keyword BF_COMBINED
CPLMD::ves::BF_Cosine	Provides the keyword BF_COSINE
CPLMD::ves::BF_CubicBsplines	Provides the keyword BF_CUBIC_B_SPLINES
CPLMD::ves::BF_Custom	Provides the keyword BF_CUSTOM
CPLMD::ves::BF_Fourier	Provides the keyword BF_FOURIER
CPLMD::ves::BF_Gaussians	Provides the keyword BF_GAUSSIANS
CPLMD::ves::BF_Legendre	Provides the keyword BF_LEGENDRE
CPLMD::ves::BF_Powers	Provides the keyword BF_POWERS
CPLMD::ves::BF_Sine	Provides the keyword BF_SINE
CPLMD::ves::BF_Wavelets	Provides the keyword BF_WAVELETS
CPLMD::ves::OutputBasisFunctions	Provides the keyword VES_OUTPUT_BASISFUNCTIONS
CPLMD::ves::OutputFesBias	Provides the keyword VES_OUTPUT_FES
CPLMD::ves::OutputTargetDistribution	Provides the keyword VES_OUTPUT_TARGET_DISTRIBUTION
►CPLMD::ves::TargetDistribution
CPLMD::ves::TD_Chi	Provides the keyword TD_CHI
CPLMD::ves::TD_ChiSquared	Provides the keyword TD_CHISQUARED
CPLMD::ves::TD_Custom	Provides the keyword TD_CUSTOM
CPLMD::ves::TD_Exponential	Provides the keyword TD_EXPONENTIAL
CPLMD::ves::TD_ExponentiallyModifiedGaussian	Provides the keyword TD_EXPONENTIALLY_MODIFIED_GAUSSIAN
CPLMD::ves::TD_Gaussian	Provides the keyword TD_GAUSSIAN
CPLMD::ves::TD_GeneralizedExtremeValue	Provides the keyword TD_GENERALIZED_EXTREME_VALUE
CPLMD::ves::TD_GeneralizedNormal	Provides the keyword TD_GENERALIZED_NORMAL
CPLMD::ves::TD_Grid	Provides the keyword TD_GRID
CPLMD::ves::TD_LinearCombination	Provides the keyword TD_LINEAR_COMBINATION
CPLMD::ves::TD_Multicanonical	Provides the keyword TD_MULTICANONICAL
CPLMD::ves::TD_MultithermalMultibaric	Provides the keyword TD_MULTITHERMAL_MULTIBARIC
CPLMD::ves::TD_ProductCombination	Provides the keyword TD_PRODUCT_COMBINATION
CPLMD::ves::TD_ProductDistribution	Provides the keyword TD_PRODUCT_DISTRIBUTION
CPLMD::ves::TD_Uniform	Provides the keyword TD_UNIFORM
CPLMD::ves::TD_VonMises	Provides the keyword TD_VONMISES
CPLMD::ves::TD_WellTempered	Provides the keyword TD_WELLTEMPERED
CPLMD::ActionOptions	This class is used to bring the relevant information to the Action constructor
CPLMD::ActionRegisterPointers
CPLMD::ActionRegistration< ActionClass >	Each instance of this specialized class represents an action that can be called with the specified directive
►CAllocator
CPLMD::gch::detail::allocator_inliner< Allocator, true >
CPLMD::gch::detail::allocator_inliner< Allocator, AvailableForEBO >
►CPLMD::gch::detail::allocator_inliner< Allocator >
►CPLMD::gch::detail::allocator_interface< Allocator >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >
CPLMD::gch::detail::allocator_inliner< Allocator, false >
CPLMD::Angle
CAngleMulti	Provides the keyword ANGLE_VECTOR
CAngleShortcut	Provides the keyword ANGLE
CANN	Provides the keyword ANN
►Cstd::array< T >	STL class
CPLMD::metatensor::vesin::CellShift	A cell shift represents the displacement along cell axis between the actual position of an atom and a periodic image of this atom
CPLMD::metatensor::vesin::Matrix
CPLMD::metatensor::vesin::Vector
CPLMD::lepton::AsmJitRuntimePtr
CPLMD::Exception::Assertion	Auxiliary containing the failed assertion
CPLMD::AtomNumber
►CPLMD::switchContainers::baseSwitch	Container for the actual switching function used by PLMD::SwitchingFunction
CPLMD::switchContainers::cosinusSwitch
CPLMD::switchContainers::cubicSwitch
CPLMD::switchContainers::exponentialSwitch
CPLMD::switchContainers::fastGaussianSwitch
CPLMD::switchContainers::fixedRational< N,, >
CPLMD::switchContainers::gaussianSwitch
CPLMD::switchContainers::leptonSwitch
CPLMD::switchContainers::nativeqSwitch
CPLMD::switchContainers::rational< isFast, nis2m >
CPLMD::switchContainers::smapSwitch
CPLMD::switchContainers::tanhSwitch
CBesselShortcut	Provides the keyword BESSEL
CBetweenShortcut	Provides the keyword BETWEEN
CPLMD::BiasRepresentation	This class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias
►Cbool_constant
►CPLMD::gch::detail::allocator_interface< Allocator >::is_uninitialized_memcpyable_iterator< U, V >
CPLMD::gch::detail::allocator_interface< Allocator >::is_uninitialized_memcpyable_iterator< std::move_iterator< U >, V >
CPLMD::gch::detail::allocator_interface< Allocator >::is_contiguous_iterator< InputIt >
CPLMD::gch::detail::allocator_interface< Allocator >::is_convertible_pointer< From, To >
►CPLMD::gch::detail::allocator_interface< Allocator >::is_memcpyable_iterator< InputIt >
CPLMD::gch::detail::allocator_interface< Allocator >::is_memcpyable_iterator< std::move_iterator< InputIt > >
CPLMD::gch::detail::allocator_interface< Allocator >::is_uninitialized_memcpyable_iterator< InputIt, V >
CPLMD::gch::detail::allocator_interface< Allocator >::must_use_alloc_construct< A, V, Args >
CPLMD::gch::detail::allocator_interface< Allocator >::must_use_alloc_destroy< A, V >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::allocations_are_movable< A >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::allocations_are_swappable< A >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::relocate_with_move< V >
CPLMD::metatensor::vesin::BoundingBox
CPLMD::Brent1DRootSearch< FCLASS >	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::bypass_tag
CPLMD::metatensor::vesin::cpu::CellList	The cell list is used to sort atoms inside bins/cells
CPLMD::CheckInRange
CPLMD::isdb::CS2Backbone::ChemicalShift
CPLMD::Citations
►CPLMD::CLTool
CPLMD::cltools::CLToolSumHills
CPLMD::cltools::Completion
CPLMD::cltools::Driver< real >
CPLMD::cltools::GenExample
CPLMD::cltools::GenJson
CPLMD::cltools::GenTemplate
CPLMD::cltools::Info
CPLMD::cltools::kt
CPLMD::cltools::Manual
CPLMD::cltools::PdbRenumber
CPLMD::cltools::PesMD
CPLMD::cltools::ShowGraph
CPLMD::cltools::SimpleMD
CPLMD::cltools::SwitchingPlotter
CPLMD::mapping::PathTools
CPLMD::ves::MD_LinearExpansionPES
CPLMD::CLToolOptions
CPLMD::CLToolRegisterPointers
►CPLMD::ves::CoeffsBase
CPLMD::ves::CoeffsMatrix
CPLMD::ves::CoeffsVector
CCombineShortcut	Provides the keyword COMBINE
►CPLMD::Communicator
CPLMD::DomainDecomposition::DomainComms
CPLMD::lepton::CompiledExpression	A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate it many times as quickly as possible
CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Const_row	Small utility class which just contains a pointer to the T and the row number
CPLMD::Communicator::ConstData	Const version of Communicator::Data See Communicator::Data documentation
CPLMD::RegisterBase< Content >::ContentAndFullPath	Auxiliary class
CPLMD::opes::convergence
CPLMD::Tools::CriticalSectionWithKey< Key >	Utility to create named critical sections Key should be usable in a std::map
CPLMD::isdb::CS2BackboneDB
CPLMD::Plumed::CString
►CPLMD::lepton::CustomFunction	This class is the interface for defining your own function that may be included in expressions
CPLMD::lepton::PlaceholderFunction	This class is an implementation of CustomFunction that does no computation
CCustomShortcut	Provides the keyword CUSTOM
CCyHarmShortcut	Provides the keyword CYLINDRICAL_HARMONIC
CPLMD::Communicator::Data	Structure defining a buffer for MPI
►CPLMD::DataPassingObject
CPLMD::DataPassingObjectTyped< T >
►CPLMD::DataPassingTools
CPLMD::DataPassingToolsTyped< T >
CPLMD::gch::default_buffer_size< Allocator >
CPLMD::maze::tls::delete_ptr
CPLMD::PlumedMain::DeprecatedAtoms
CDifferenceShortcut	Provides the keyword DIFFERENCE
CDihedralCorrelationMulti	Provides the keyword DIHEDRAL_CORRELATION_VECTOR
CDihedralCorrelationShortcut	Provides the keyword DIHEDRAL_CORRELATION
CDipoleMulti	Provides the keyword DIPOLE_VECTOR
CDipoleShortcut	Provides the keyword DIPOLE
CPLMD::Tools::DirectoryChanger	Tiny class that changes directory and comes back when going out of scope
CDistanceMulti	Provides the keyword DISTANCE_VECTOR
CDistanceShortcut	Provides the keyword DISTANCE
CPLMD::DLLoader
CDomainDecomposition	Provides the keyword DOMAIN_DECOMPOSITION
CDynamicReferenceRestraining	Provides the keyword <a href="../../user-doc/html/_"_d_r_r.html"> "DRR
CEMMIVOX	Provides the keyword EMMIVOX
CPLMD::DLLoader::EnsureGlobalDLOpen	RAII helper for promoting RTLD_LOCAL loaded objects to RTLD_GLOBAL
CPLMD::ERMSD	A class that implements ERMSD calculations
►Cstd::exception	STL class
CPLMD::Exception
►CPLMD::lepton::Exception	This class is used for all exceptions thrown by lepton
CPLMD::ExceptionDebug	Class representing a debug error (can only be thrown when using debug options)
CPLMD::ExceptionError	Class representing a generic error
CPLMD::ExceptionRegisterError	Class representing an error in a register
CPLMD::ExceptionTypeError	Class representing a type error in the PLMD::Plumed interface
►CPLMD::Plumed::Exception	Base class used to rethrow PLUMED exceptions
CPLMD::Plumed::ExceptionDebug	Used to rethrow a PLMD::ExceptionDebug
CPLMD::Plumed::ExceptionError	Used to rethrow a PLMD::ExceptionError
CPLMD::Plumed::ExceptionTypeError	Thrown when a wrong pointer is passed to the PLUMED interface
CPLMD::Plumed::Invalid	Thrown when trying to access an invalid plumed object
CPLMD::Plumed::LeptonException	Class used to rethrow Lepton exceptions
CPLMD::ExchangePatterns
CPLMD::opes::exploration
CPLMD::lepton::ExpressionProgram	An ExpressionProgram is a linear sequence of Operations for evaluating an expression
CPLMD::lepton::ExpressionTreeNode	This class represents a node in the abstract syntax tree representation of an expression
CPLMD::F1dim< FCLASS >
►Cfalse_type
►CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_construct_check< void, A, V, Args... >
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_construct_impl< typename std::enable_if< is_complete< V >::value >::type, A, V, Args... >
►CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_construct_impl< void, A, V, Args... >
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_construct< A, V, Args >
►CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_destroy_impl< void, A, V >
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_destroy< A, V, typename std::enable_if< is_complete< V >::value >::type >
►CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_emplace_constructible_impl< void, alloc_interface, value_ty, Args... >
►CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_emplace_constructible< value_ty && >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_explicitly_move_insertable< V >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_emplace_constructible< Args >
►CPLMD::gch::detail::allocator_interface< Allocator >::is_trivially_constructible_impl< void, V, Args... >
CPLMD::gch::detail::allocator_interface< Allocator >::is_trivially_constructible< V, Args >
CPLMD::gch::default_buffer_size< Allocator >::is_complete< typename, Enable >
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_construct_check< Void, A, V, Args >
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_construct_impl< Void, A, V, Args >
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_destroy< A, V, Enable >
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_destroy_impl< Void, A, V >
CPLMD::gch::detail::allocator_interface< Allocator >::has_ptr_traits_to_address< typename, typename >
CPLMD::gch::detail::allocator_interface< Allocator >::is_complete< typename, typename >
CPLMD::gch::detail::allocator_interface< Allocator >::is_memcpyable< QualifiedFrom, QualifiedTo, Enable >
CPLMD::gch::detail::allocator_interface< Allocator >::is_memcpyable_integral< typename, typename, typename >
CPLMD::gch::detail::allocator_interface< Allocator >::is_small_vector_iterator< Iterator >
CPLMD::gch::detail::allocator_interface< Allocator >::is_trivially_constructible_impl< Void, T, Args >
CPLMD::gch::detail::allocator_interface< Allocator >::is_trivially_destructible< V, Enable >
CPLMD::gch::detail::allocator_interface< Allocator >::is_uninitialized_memcpyable< To, Args >
CPLMD::gch::detail::small_vector_adl::is_nothrow_swappable< T, Enable >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_emplace_constructible_impl< Void, AI, V, Args >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_eraseable< AI, Enable >
CPLMD::mergeVectorTools::has_size_and_data< T, typename >
CPLMD::wrapper::has_size_and_data< T, typename >	Primary template, assumes T does not have both size() and data() methods
CPLMD::wrapper::is_custom_array< T >	Primary template, assumes T is not a custom structure
CPLMD::Tools::FastStringUnorderedMap< T >	Tiny class implementing faster std::string_view access to an unordered_map It exposes a limited number of methods of std::unordered_map
CPLMD::Tools::FastStringUnorderedMap< PLMD::Stopwatch::Watch >
CFccubicShortcut	Provides the keyword FCCUBIC_FUNC
CPLMD::ves::FermiSwitchingFunction
►CFieldBase
CPLMD::OFile::Field	Class identifying a single field for fielded output
►CPLMD::FileBase::FieldBase	Internal tool
CPLMD::IFile::Field
►CPLMD::FileBase	Base class for dealing with files
CPLMD::IFile
►CPLMD::OFile
CPLMD::Log	Class containing the log stream
CPLMD::function::FilesHandler
CPLMD::Plumed::finalize_plumed_error	Internal class to simplify plumed_error finalization
CPLMD::molfile::fio_iovec
CPLMD::FlexibleBin
CPLMD::switchContainers::leptonSwitch::funcAndDeriv	Lepton expression
►CPLMD::function::FunctionTemplateBase
CPLMD::function::Bessel
CPLMD::function::Between
CPLMD::function::Combine
CPLMD::function::Custom
CPLMD::function::Highest
CPLMD::function::LessThan
CPLMD::function::Moments
CPLMD::function::MoreThan
CPLMD::function::Piecewise
CPLMD::function::Sort
CPLMD::function::Sum
CPLMD::gridtools::EvaluateGridFunction
CPLMD::refdist::Difference
CPLMD::symfunc::CylindricalHarmonic
CPLMD::symfunc::Fccubic
CPLMD::symfunc::SphericalHarmonic
CPLMD::bias::MetaD::Gaussian
CPLMD::bias::PBMetaD::Gaussian
►CPLMD::GridBase
CPLMD::Grid
CPLMD::SparseGrid
CPLMD::gridtools::GridCoordinatesObject
CGridCustom	Provides the keyword CUSTOM_GRID
CPLMD::ves::GridIntegrationWeights
CPLMD::ves::GridLinearInterpolation
CPLMD::gridtools::GridSearch< FCLASS >
CGridSum	Provides the keyword SUM_GRID
CPLMD::metatensor::vesin::cpu::GrowableNeighborList	Wrapper around VesinNeighborList that behaves like a std::vector, automatically growing memory allocations
CPLMD::Stopwatch::Handler	Auxiliary class for handling exception-safe start/pause and start/stop
CPLMD::Subprocess::Handler	Class used to cont/stop a Subprocess in an exception safe manner
CPLMD::Tools::CriticalSectionWithKey< Key >::Handler
CHighestShortcut	Provides the keyword HIGHEST
CPLMD::HistogramBead
CPLMD::RegisterBase< Content >::ID
CPLMD::colvar::PathMSDBase::ImagePath	This class is a general container for path stuff
CPLMD::colvar::PathMSDBase::imgOrderByDist
CPLMD::colvar::PathMSDBase::imgOrderBySimilarity
CPLMD::gch::detail::inline_storage< T, InlineCapacity >
►CPLMD::gch::detail::inline_storage< T, 0 >
CPLMD::gch::detail::small_vector_data< Pointer, SizeT, T, 0 >
CPLMD::gch::detail::inline_storage< value_ty, InlineCapacity >
►Cintegral_constant
CPLMD::gch::detail::small_vector_adl::is_nothrow_swappable< T, decltype(swap(std::declval< T & >(), std::declval< T & >()))>
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_explicitly_copy_insertable< V >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_explicitly_nothrow_copy_insertable< V >
CPLMD::gridtools::Interpolator
CPLMD::gch::detail::allocator_interface< Allocator >::is_memcpyable< QualifiedFrom, QualifiedTo, typename std::enable_if< is_complete< QualifiedFrom >::value >::type >
CPLMD::gch::detail::allocator_interface< Allocator >::is_memcpyable_integral< From, To, typename std::enable_if< is_complete< From >::value >::type >
►Cis_trivially_constructible
CPLMD::gch::detail::allocator_interface< Allocator >::is_trivially_constructible_impl< typename std::enable_if< is_complete< V >::value >::type, V, Args... >
►Cis_trivially_destructible
CPLMD::gch::detail::allocator_interface< Allocator >::is_trivially_destructible< V, typename std::enable_if< is_complete< V >::value >::type >
CPLMD::gch::detail::allocator_interface< Allocator >::is_uninitialized_memcpyable_impl< QualifiedFrom, QualifiedTo >
►CPLMD::gch::detail::allocator_interface< Allocator >::is_uninitialized_memcpyable_impl< From, To >
CPLMD::gch::detail::allocator_interface< Allocator >::is_uninitialized_memcpyable< To, From >
CPLMD::opes::OPESmetad< mode >::kernel
CPLMD::KernelFunctions
CPLMD::Keywords::KeyType	This class lets me pass keyword types easily
CPLMD::Keywords	This class holds the keywords and their documentation
CPLMD::LatticeReduction	Class implementing algorithms for lattice reduction
CPLMD::LeptonCall
CLessThanShortcut	Provides the keyword LESS_THAN
CPLMD::ves::LinearBasisSetExpansion
CPLMD::LinkCells
CPLMD::Exception::Location	Auxiliary containing the location of the exception in the file
CPLMD::LoopUnroller< n >
CPLMD::wrapper::make_void< Ts >	This is to replace c++17 std::void_t
CMatrixBetween	Provides the keyword BETWEEN_MATRIX
CMatrixCombine	Provides the keyword COMBINE_MATRIX
CMatrixCustom	Provides the keyword CUSTOM_MATRIX
CMatrixCyHarm	Provides the keyword CYLINDRICAL_HARMONIC_MATRIX
CMatrixFccubic	Provides the keyword FCCUBIC_FUNC_MATRIX
CMatrixLessThan	Provides the keyword LESS_THAN_MATRIX
CMatrixMoreThan	Provides the keyword MORE_THAN_MATRIX
CMatrixSpHarm	Provides the keyword SPHERICAL_HARMONIC_MATRIX
CPLMD::MatrixSquareBracketsAccess< T, C, I, J >	Utility class to add [][] access
►CPLMD::MatrixSquareBracketsAccess< Matrix< double >, double >
CPLMD::Matrix< double >
►CPLMD::MatrixSquareBracketsAccess< Matrix< std::vector< PLMD::VectorGeneric > >, std::vector< PLMD::VectorGeneric > >
CPLMD::Matrix< std::vector< PLMD::VectorGeneric > >
►CPLMD::MatrixSquareBracketsAccess< Matrix< T >, T >
CPLMD::Matrix< T >	This class stores a full matrix and allows one to do some simple matrix operations
►CPLMD::MatrixSquareBracketsAccess< Matrix< unsigned >, unsigned >
CPLMD::Matrix< unsigned >
►CPLMD::MatrixSquareBracketsAccess< TensorGeneric< n, m >, double >
CPLMD::TensorGeneric< n, m >
CPLMD::TensorGeneric< 4, 4 >
CMatrixSum	Provides the keyword SUM_MATRIX
CPLMD::molfile::md_atom
CPLMD::molfile::md_box
CPLMD::molfile::md_file
CPLMD::molfile::md_header
CPLMD::molfile::md_ts
CPLMD::mdMemoryView< N, STRIDE >
CPLMD::maze::Member	Defines the encoding for a ligand conformation
CPLMD::MemoryView< N >
CPLMD::Minimise1DBrent< FCLASS >	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method
►CPLMD::MinimiseBase< FCLASS >
CPLMD::ConjugateGradient< FCLASS >
►CPLMD::MinimiseBase< PLMD::dimred::ProjectPoints >
CPLMD::ConjugateGradient< PLMD::dimred::ProjectPoints >
CPLMD::MolDataClass	This class provides information on various kinds of molecules for instance the kinds of residues that are in a protein the atoms involved in the backbone of a particular residue etc
CPLMD::molfile::molfile_atom_t	Per-atom attributes and information
CPLMD::molfile::molfile_graphics_t	Individual graphics object/element data
CPLMD::molfile::molfile_metadata_t	File level comments, origin information, and annotations
CPLMD::molfile::molfile_plugin_t	Main file reader API
CPLMD::molfile::molfile_qm_basis_t	Data for QM basis set
CPLMD::molfile::molfile_qm_hessian_t	Data from QM Hessian/normal mode runs
CPLMD::molfile::molfile_qm_metadata_t	Sizes of various QM-related, timestep independent data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data
CPLMD::molfile::molfile_qm_sysinfo_t	QM run info
CPLMD::molfile::molfile_qm_t	QM related information that is timestep independent
CPLMD::molfile::molfile_qm_timestep_metadata	Sizes of various QM-related, per-timestep data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data
CPLMD::molfile::molfile_qm_timestep_t	QM per trajectory timestep info Note that each timestep can contain multiple wavefunctions
CPLMD::molfile::molfile_qm_wavefunction_t	QM wavefunction
CPLMD::molfile::molfile_timestep_metadata
CPLMD::molfile::molfile_timestep_t	Per-timestep atom coordinates, velocities, time, energies and periodic cell info
CPLMD::molfile::molfile_volumetric_readwrite_t	Volumetric dataset read/write structure with both flag/parameter sets and VMD-allocated pointers for fields to be used by the plugin
CPLMD::molfile::molfile_volumetric_t	Metadata for volumetric datasets, read initially and used for subsequent memory allocations and file loading
CMolInfo	Provides the keyword MOLINFO
CMomentsShortcut	Provides the keyword MOMENTS
CMoreThanShortcut	Provides the keyword MORE_THAN
CPLMD::MPI_Comm	Surrogate of MPI_Comm when MPI library is not available
CPLMD::MPI_Datatype	Surrogate of MPI_Datatype when MPI library is not available
CPLMD::MPI_Request	Surrogate of MPI_Request when MPI library is not available
CPLMD::MPI_Status	Surrogate of MPI_Status when MPI library is not available
CMQMulti	Provides the keyword MASS_VECTOR
CMQShortcut	Provides the keyword MASS
CPLMD::multicolvar::MultiColvarShortcuts
CPLMD::MultiValue
CPLMD::drr::UIestimator::n_matrix
CPLMD::drr::UIestimator::n_vector< T >
CPLMD::drr::UIestimator::n_vector< double >
CPLMD::drr::UIestimator::n_vector< int >
CPLMD::drr::UIestimator::n_vector< std::vector< double > >
CPLMD::NeighborList
►Cnothrow
►CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_nothrow_emplace_constructible< value_ty && >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_explicitly_nothrow_move_insertable< V >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_nothrow_emplace_constructible< Args >
CPLMD::OpenMP::OpenMPVars	Singleton struct to treat the openMP setting as a global variables, but with a layer of encapsulation
CPLMD::lepton::Operation	An Operation represents a single step in the evaluation of an expression, such as a function, an operator, or a constant value
COPESmetad_c	Provides the keyword OPES_METAD
COPESmetad_e	Provides the keyword OPES_METAD_EXPLORE
CPLMD::function::FuncPathMSD::ordering
CPLMD::function::FuncPathGeneral::pairordering
CPLMD::function::FuncPathMSD::pairordering
CPLMD::lepton::ParsedExpression	This class represents the result of parsing an expression
CPLMD::lepton::Parser	This class provides the main interface for parsing expressions
CPLMD::lepton::ParseToken
CPLMD::mapping::PathProjectionCalculator
CPLMD::Pbc
CPLMD::PDB	Minimalistic pdb parser
CPiecewiseShortcut	Provides the keyword PIECEWISE
CPlaneMulti	Provides the keyword PLANE_VECTOR
CPlaneShortcut	Provides the keyword PLANE
Cplumed	Main plumed object
CPLMD::Plumed	C++ wrapper for plumed
Cplumed_error	Small structure that is only defined locally to retrieve errors
Cplumed_error_filesystem_path
CPLMD::PlumedMain::plumed_error_handler	Error handler
Cplumed_function_holder
Cplumed_nothrow_handler
Cplumed_nothrow_handler_x
Cplumed_plumedmain_function_holder_x	Container for plumedmain function pointers (create, cmd and finalize)
Cplumed_safeptr	Structure holding a typesafe pointer
Cplumed_safeptr_x
Cplumed_symbol_table_type_x	Container for symbol table
CPLMD::metatensor::vesin::cpu::CellList::Point	Cells themselves are a list of points & corresponding shift to place the point inside the cell
CPositionMulti	Provides the keyword POSITION_VECTOR
CPositionShortcut	Provides the keyword POSITION
CPytorchModel	Provides the keyword PYTORCH_MODEL
CQuaternionMulti	Provides the keyword QUATERNION_VECTOR
CQuaternionShortcut	Provides the keyword QUATERNION
CPLMD::Random
►CPLMD::Register	Base class, with type independent information
CPLMD::RegisterBase< Content >	General register
►CPLMD::RegisterBase< ActionRegisterPointers >
CPLMD::ActionRegister	Register holding all the allowed keywords
►CPLMD::RegisterBase< CLToolRegisterPointers >
CPLMD::CLToolRegister	Same as ActionRegister, but for CLTools
CPLMD::Register::RegistrationLock	Small class to manage registration lock This is used during dlopen, to avoid data races in registrations
CPLMD::Communicator::Request	Wrapper class for MPI_Request
CPLMD::Plumed::rethrow_nested	Internal class used by exception_dispatch
CPLMD::Plumed::rethrow_not_nested	Internal class used by exception_dispatch
CPLMD::isdb::CS2Backbone::RingInfo
CPLMD::RMSD
CPLMD::RMSDCoreData	This is a class which is needed to share information across the various non-threadsafe routines so that the public function of rmsd are threadsafe while the inner core can safely share information
CPLMD::maze::rnd	Mersenne Twister sampler for random variables
CPLMD::RootFindingBase< FCLASS >
CPLMD::RootFindingBase< PLMD::contour::ContourFindingBase >
CPLMD::RootFindingBase< PLMD::contour::DistanceFromContourBase >
CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row	Small utility class which just contains a pointer to the T and the row number
CPLMD::Plumed::SafePtr	Small class that wraps plumed_safeptr in order to make its initialization easier
CScalarBessel	Provides the keyword BESSEL_SCALAR
CScalarCombine	Provides the keyword COMBINE_SCALAR
CScalarCustom	Provides the keyword CUSTOM_SCALAR
CScalarDifference	Provides the keyword DIFFERENCE_SCALAR
CScalarEvalGrid	Provides the keyword EVALUATE_FUNCTION_FROM_GRID_SCALAR
CScalarHighest	Provides the keyword HIGHEST_SCALAR
CScalarMoments	Provides the keyword MOMENTS_SCALAR
CScalarPiecewise	Provides the keyword PIECEWISE_SCALAR
CScalarSort	Provides the keyword SORT_SCALAR
CScalarSum	Provides the keyword SUM_SCALAR
CPLMD::piv::PIV::SharedData	Local structure, used to store data that should be shared across multiple PIV instances
CPLMD::Plumed::SizeLike	Small structure used to pass elements of a shape initializer_list
CPLMD::WithCmd::SizeLike	Small structure used to pass elements of a shape initializer_list
CPLMD::TypesafePtr::SizeLike	Small structure used to pass elements of a shape initializer_list
CPLMD::dimred::SMACOF
CPLMD::gch::small_vector< T, InlineCapacity, Allocator >
CPLMD::gch::small_vector< PLMD::VectorGeneric, maxshiftsize >
►CPLMD::gch::detail::small_vector_data_base< Pointer, SizeT >
CPLMD::gch::detail::small_vector_data< Pointer, SizeT, T, InlineCapacity >
CPLMD::gch::detail::small_vector_data< Pointer, SizeT, T, 0 >
►CPLMD::gch::detail::small_vector_data_base< ptr, size_type >
CPLMD::gch::detail::small_vector_data< ptr, size_type, value_ty, InlineCapacity >
CPLMD::gch::small_vector_iterator< Pointer, DifferenceType >
CSortShortcut	Provides the keyword SORT
CSpHarmShortcut	Provides the keyword SPHERICAL_HARMONIC
CPLMD::isdb::SAXS::SplineCoeffs
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::stack_temporary
CPLMD::Communicator::Status	Wrapper class for MPI_Status
CPLMD::Stopwatch
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::strong_exception_policy
CPLMD::Subprocess	Class managing a subprocess
CPLMD::SubprocessPid	Small utility class, used to avoid inclusion of unistd.h> in a header file
CSumShortcut	Provides the keyword SUM
CPLMD::SwitchingFunction
►CT
CPLMD::Plumed::add_buffer_to< T >
CPLMD::xdrfile::t_trnheader
CPLMD::TargetDist
►CPLMD::ves::TargetDistModifer
CPLMD::ves::WellTemperedModifer
CPLMD::bias::MetaD::TemperingSpecs
CPLMD::TensorGenericAux	Small class to contain local utilities
CPLMD::Exception::Throw	Auxiliary class used to throw exceptions
CPLMD::maze::tls	Helper functions
CPLMD::Tools
CPLMD::Torsion
CTorsionMulti	Provides the keyword TORSION_VECTOR
CTorsionShortcut	Provides the keyword TORSION
CPLMD::Tree
►Ctrue_type
CPLMD::gch::default_buffer_size< Allocator >::is_complete< U, decltype(static_cast< void >(sizeof(U)))>
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_construct_check< void_t< decltype(std::declval< A & >().construct(std::declval< V * >(), std::declval< Args >()...))>, A, V, Args... >
CPLMD::gch::detail::allocator_interface< Allocator >::has_alloc_destroy_impl< void_t< decltype(std::declval< A & >().destroy(std::declval< V * >()))>, A, V >
CPLMD::gch::detail::allocator_interface< Allocator >::has_ptr_traits_to_address< P, void_t< decltype(std::pointer_traits< P >::to_address(std::declval< P >()))> >
CPLMD::gch::detail::allocator_interface< Allocator >::is_complete< U, decltype(static_cast< void >(sizeof(U)))>
CPLMD::gch::detail::allocator_interface< Allocator >::is_small_vector_iterator< small_vector_iterator< Ts... > >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::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... >
CPLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::is_eraseable< AI, void_t< decltype(std::declval< AI & >().destroy(std::declval< value_ty * >()))> >
CPLMD::mergeVectorTools::has_size_and_data< T, std::void_t< decltype(std::declval< T >().size()), decltype(std::declval< T >().data())> >
CPLMD::wrapper::has_size_and_data< T, void_t< decltype(std::declval< T >().size()), decltype(std::declval< T >().data())> >	Specialization for types T that do have both size() and data() methods
CPLMD::wrapper::is_custom_array< std::array< T, N > >	Template specialization for std::array
CPLMD::wrapper::is_custom_array< T[N]>	Template specialization for C arrays
CPLMD::molfile::trx_hdr
CPLMD::TypesafePtr
CPLMD::drr::UIestimator::UIestimator
CPLMD::gch::detail::allocator_interface< Allocator >::underlying_if_enum< T, Enable >
►Cunderlying_type
CPLMD::gch::detail::allocator_interface< Allocator >::underlying_if_enum< T, typename std::enable_if< std::is_enum< T >::value >::type >
►Cstd::unique_ptr< T >	STL class
CPLMD::ForwardDecl< PLMD::ActionSet >
CPLMD::ForwardDecl< PLMD::Citations >
CPLMD::ForwardDecl< PLMD::Communicator >
CPLMD::ForwardDecl< PLMD::DLLoader >
CPLMD::ForwardDecl< PLMD::ExchangePatterns >
CPLMD::ForwardDecl< PLMD::Log >
CPLMD::ForwardDecl< PLMD::Pbc >
CPLMD::ForwardDecl< PLMD::PDB >
CPLMD::ForwardDecl< PLMD::PlumedMain::DeprecatedAtoms >
CPLMD::ForwardDecl< PLMD::Random >
CPLMD::ForwardDecl< PLMD::Stopwatch >
CPLMD::ForwardDecl< PLMD::TypesafePtr >
CPLMD::ForwardDecl< T >	Utility class for forward declaration of references
CPLMD::Units
CPLMD::Value
►Cstd::vector< T >	STL class
CPLMD::ActionSet	Std::vector containing the sequence of Action to be done
CPLMD::metatensor::vesin::cpu::CellList::Cell
CVectorBessel	Provides the keyword BESSEL_VECTOR
CVectorBetween	Provides the keyword BETWEEN_VECTOR
CVectorCombine	Provides the keyword COMBINE_VECTOR
CVectorCustom	Provides the keyword CUSTOM_VECTOR
CVectorDifference	Provides the keyword DIFFERENCE_VECTOR
CVectorEvalGrid	Provides the keyword EVALUATE_FUNCTION_FROM_GRID_VECTOR
CPLMD::VectorGeneric< n >
CPLMD::VectorGeneric< 4 >
CPLMD::VectorGeneric< 6 >
CVectorHighest	Provides the keyword HIGHEST_VECTOR
CVectorLessThan	Provides the keyword LESS_THAN_VECTOR
CVectorMoments	Provides the keyword MOMENTS_VECTOR
CVectorMoreThan	Provides the keyword MORE_THAN_VECTOR
CVectorSort	Provides the keyword SORT_VECTOR
CVectorSum	Provides the keyword SUM_VECTOR
CPLMD::metatensor::vesin::VesinNeighborList	The actual neighbor list
CPLMD::metatensor::vesin::VesinOptions	Options for a neighbor list calculation
CPLMD::ves::VesTools
CPLMD::molfile::vmdplugin_t	Typedef for generic plugin header, individual plugins can make their own structures as long as the header info remains the same as the generic plugin header, most easily done by using the vmdplugin_HEAD macro
CVolumeAroundShortcut	Provides the keyword AROUND
CVolumeCavityShortcut	Provides the keyword CAVITY
CVolumeInCylinderShortcut	Provides the keyword INCYLINDER
CVolumeInEnvelopeShortcut	Provides the keyword INENVELOPE
CVolumeInSphereShortcut	Provides the keyword INSPHERE
CVolumeTetraporeShortcut	Provides the keyword TETRAHEDRALPORE
CPLMD::Stopwatch::Watch	Class to store a single stopwatch
CPLMD::ves::WaveletGrid
►CPLMD::WeightBase
CPLMD::BiasWeight
CPLMD::ProbWeight
CPLMD::ves::FesWeight
CPLMD::ves::MarginalWeight
►CPLMD::WithCmd	Base for classes with cmd() method
CPLMD::CLToolMain	Class providing cmd() access to command line tools
CPLMD::GREX
CPLMD::PlumedHandle	Tiny local class to load a PLUMED kernel
CPLMD::PlumedMain	Main plumed object
CPLMD::xdrfile::XDR
CPLMD::xdrfile::XDR::xdr_ops
CPLMD::xdrfile::XDRFILE	Contents of the abstract XDRFILE data structure