Class Hierarchy

Go to the graphical class hierarchy

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

[detail level 1234567]

▶CAbs public Operation
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
▶CAcos public Operation
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
▶CPLMD::Action	Base class for all the input Actions
▶CPLMD::ActionAtomistic	Action used to create objects that access the positions of the atoms from the MD code
▶CPLMD::ActionWithVirtualAtom	Inherit from here if you are calculating the position of a virtual atom (eg a center of mass)
CPLMD::multicolvar::CenterOfMultiColvar	Provides the keyword CENTER_OF_MULTICOLVAR
CPLMD::vatom::Center	Provides the keyword CENTER
CPLMD::vatom::COM	Provides the keyword COM
CPLMD::vatom::FixedAtom	Provides the keyword FIXEDATOM
CPLMD::vatom::Ghost	Provides the keyword GHOST
▶CPLMD::Colvar	This is the abstract base class to use for implementing new collective variables, within it there is information as to how to go about implementing a new CV
CPLMD::colvar::Angle	Provides the keyword ANGLE
CPLMD::colvar::Cell	Provides the keyword CELL
CPLMD::colvar::ColvarFake	Provides the keyword FAKE
CPLMD::colvar::Constant	Provides the keyword CONSTANT
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::Dimer	Provides the keyword <a href="../../user-doc/html/_"_d_i_m_e_r.html"> "DIMER
CPLMD::colvar::Dipole	Provides the keyword DIPOLE
CPLMD::colvar::Distance	Provides the keyword DISTANCE
CPLMD::colvar::DRMSD	Provides the keyword DRMSD
CPLMD::colvar::EEFSolv	Provides the keyword EEFSOLV
CPLMD::colvar::Energy	Provides the keyword ENERGY
CPLMD::colvar::ERMSD	Provides the keyword ERMSD
CPLMD::colvar::Gyration	Provides the keyword GYRATION
▶CPLMD::colvar::MultiRMSD	Provides the keyword MULTI-RMSD
CPLMD::colvar::Multi_RMSD
▶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::Position	Provides the keyword POSITION
CPLMD::colvar::Puckering	Provides the keyword PUCKERING
CPLMD::colvar::RMSD	Provides the keyword RMSD
CPLMD::colvar::Template	Provides the keyword TEMPLATE
CPLMD::colvar::Torsion	Provides the keyword TORSION
CPLMD::colvar::Volume	Provides the keyword VOLUME
CPLMD::isdb::EMMI	Provides the keyword EMMI
CPLMD::isdb::FretEfficiency	Provides the keyword FRET
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::Group	Provides the keyword GROUP
CPLMD::generic::ResetCell	Provides the keyword RESET_CELL
CPLMD::generic::WholeMolecules	Provides the keyword WHOLEMOLECULES
CPLMD::generic::WrapAround	Provides the keyword WRAPAROUND
▶CPLMD::isdb::MetainferenceBase	This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action
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::mapping::Mapping
CPLMD::mapping::AdaptivePath	Provides the keyword ADAPTIVE_PATH
▶CPLMD::mapping::PathBase
CPLMD::mapping::Path	Provides the keyword PATH
CPLMD::mapping::PropertyMap	Provides the keyword GPROPERTYMAP
CPLMD::mapping::PCAVars	Provides the keyword PCAVARS
CPLMD::multicolvar::DumpMultiColvar	Provides the keyword DUMPMULTICOLVAR
▶CPLMD::multicolvar::MultiColvarBase
▶CPLMD::adjmat::ActionWithInputMatrix
▶CPLMD::adjmat::ClusteringBase
CPLMD::adjmat::ClusterWithSurface	Provides the keyword CLUSTER_WITHSURFACE
CPLMD::adjmat::DFSClustering	Provides the keyword DFSCLUSTERING
CPLMD::adjmat::MatrixColumnSums	Provides the keyword COLUMNSUMS
CPLMD::adjmat::MatrixRowSums	Provides the keyword ROWSUMS
CPLMD::adjmat::Sprint	Provides the keyword SPRINT
▶CPLMD::adjmat::AdjacencyMatrixBase
▶CPLMD::adjmat::AlignedMatrixBase
CPLMD::adjmat::ContactAlignedMatrix	Provides the keyword ALIGNED_MATRIX
CPLMD::adjmat::SMACMatrix	Provides the keyword SMAC_MATRIX
CPLMD::adjmat::ContactMatrix	Provides the keyword CONTACT_MATRIX
CPLMD::adjmat::HBondMatrix	Provides the keyword HBOND_MATRIX
CPLMD::adjmat::TopologyMatrix	Provides the keyword TOPOLOGY_MATRIX
▶CPLMD::adjmat::ClusterAnalysisBase
CPLMD::adjmat::ClusterDiameter	Provides the keyword CLUSTER_DIAMETER
CPLMD::adjmat::ClusterDistribution	Provides the keyword CLUSTER_DISTRIBUTION
CPLMD::adjmat::ClusterProperties	Provides the keyword CLUSTER_PROPERTIES
CPLMD::adjmat::ClusterSize	Provides the keyword CLUSTER_NATOMS
▶CPLMD::crystallization::CubicHarmonicBase
CPLMD::crystallization::Fccubic	Provides the keyword FCCUBIC
CPLMD::crystallization::SimpleCubic	Provides the keyword SIMPLECUBIC
CPLMD::crystallization::Tetrahedral	Provides the keyword TETRAHEDRAL
CPLMD::crystallization::InterMolecularTorsions	Provides the keyword INTERMOLECULARTORSIONS
▶CPLMD::crystallization::OrientationSphere
CPLMD::crystallization::LocalSteinhardt< T >
CPLMD::crystallization::PolymerAngles	Provides the keyword POLYMER_ANGLES
CPLMD::crystallization::SMAC	Provides the keyword SMAC
▶CPLMD::crystallization::VectorMultiColvar
CPLMD::crystallization::BondOrientation	Provides the keyword BOND_DIRECTIONS
CPLMD::crystallization::MoleculeOrientation	Provides the keyword MOLECULES
CPLMD::crystallization::MoleculePlane	Provides the keyword PLANES
▶CPLMD::crystallization::Steinhardt
CPLMD::crystallization::Q3	Provides the keyword Q3
CPLMD::crystallization::Q4	Provides the keyword Q4
CPLMD::crystallization::Q6	Provides the keyword Q6
CPLMD::multicolvar::AlphaBeta	Provides the keyword ALPHABETA
CPLMD::multicolvar::Angles	Provides the keyword ANGLES
CPLMD::multicolvar::Bridge	Provides the keyword BRIDGE
▶CPLMD::multicolvar::BridgedMultiColvarFunction
▶CPLMD::multicolvar::MultiColvarFilter	This is the abstract base class to use for implementing a new way of filtering collective variable values to see whether or not they are within a certain range
CPLMD::multicolvar::FilterBetween	Provides the keyword MFILTER_BETWEEN
CPLMD::multicolvar::FilterLess	Provides the keyword MFILTER_LESS
CPLMD::multicolvar::FilterMore	Provides the keyword MFILTER_MORE
▶CPLMD::multicolvar::VolumeGradientBase
CPLMD::crystallization::Gradient	Provides the keyword GRADIENT
▶CPLMD::multicolvar::ActionVolume	This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box
CPLMD::multicolvar::VolumeAround	Provides the keyword AROUND
CPLMD::multicolvar::VolumeCavity	Provides the keyword CAVITY
CPLMD::multicolvar::VolumeInCylinder	Provides the keyword INCYLINDER
CPLMD::multicolvar::VolumeInEnvelope	Provides the keyword INENVELOPE
CPLMD::multicolvar::VolumeInSphere	Provides the keyword INSPHERE
CPLMD::multicolvar::VolumeTetrapore	Provides the keyword TETRAHEDRALPORE
CPLMD::multicolvar::CoordinationNumbers	Provides the keyword COORDINATIONNUMBER
CPLMD::multicolvar::Density	Provides the keyword DENSITY
CPLMD::multicolvar::DihedralCorrelation	Provides the keyword DIHCOR
CPLMD::multicolvar::DistanceFromContour	Provides the keyword DISTANCE_FROM_CONTOUR
CPLMD::multicolvar::Distances	Provides the keyword DISTANCES
CPLMD::multicolvar::InPlaneDistances	Provides the keyword INPLANEDISTANCES
CPLMD::multicolvar::LocalAverage	Provides the keyword LOCAL_AVERAGE
CPLMD::multicolvar::MultiColvarCombine	Provides the keyword MCOLV_COMBINE
CPLMD::multicolvar::MultiColvarProduct	Provides the keyword MCOLV_PRODUCT
CPLMD::multicolvar::NumberOfLinks	Provides the keyword NLINKS
CPLMD::multicolvar::Torsions	Provides the keyword TORSIONS
CPLMD::multicolvar::XAngles	Provides the keyword XANGLES
CPLMD::multicolvar::XDistances	Provides the keyword XDISTANCES
CPLMD::multicolvar::XYDistances	Provides the keyword XYDISTANCES
CPLMD::multicolvar::XYTorsion	Provides the keyword XYTORSIONS
▶CPLMD::secondarystructure::SecondaryStructureRMSD	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
CPLMD::secondarystructure::AlphaRMSD	Provides the keyword ALPHARMSD
CPLMD::secondarystructure::AntibetaRMSD	Provides the keyword ANTIBETARMSD
CPLMD::secondarystructure::ParabetaRMSD	Provides the keyword PARABETARMSD
CPLMD::SetupMolInfo
▶CPLMD::vesselbase::ActionWithAveraging	This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames
▶CPLMD::analysis::Analysis	This is the abstract base class to use for implementing new methods for analyzing the trajectory, within it there is information as to how to go about implementing a new analysis method
▶CPLMD::analysis::AnalysisWithLandmarks
CPLMD::analysis::ClassicalMultiDimensionalScaling	Provides the keyword CLASSICAL_MDS
CPLMD::analysis::PCA	Provides the keyword PCA
CPLMD::analysis::Average	Provides the keyword AVERAGE
▶CPLMD::gridtools::ActionWithGrid
CPLMD::analysis::Histogram	Provides the keyword HISTOGRAM
▶CPLMD::gridtools::ActionWithInputGrid
▶CPLMD::gridtools::ActionWithIntegral
CPLMD::gridtools::IntegrateGrid	Provides the keyword INTEGRATE_GRID
▶CPLMD::gridtools::ContourFindingBase
CPLMD::gridtools::FindContour	Provides the keyword FIND_CONTOUR
CPLMD::gridtools::FindContourSurface	Provides the keyword FIND_CONTOUR_SURFACE
CPLMD::gridtools::FindSphericalContour	Provides the keyword FIND_SPHERICAL_CONTOUR
CPLMD::gridtools::ConvertToFES	Provides the keyword CONVERT_TO_FES
CPLMD::gridtools::FourierTransform	Provides the keyword FOURIER_TRANSFORM
CPLMD::gridtools::InterpolateGrid	Provides the keyword INTERPOLATE_GRID
CPLMD::multicolvar::MultiColvarDensity	Provides the keyword MULTICOLVARDENS
▶CPLMD::ActionPilot	This is used to create PLMD::Action objects that are run with some set frequency
CPLMD::adjmat::DumpGraph	Provides the keyword DUMPGRAPH
CPLMD::adjmat::OutputCluster	Provides the keyword OUTPUT_CLUSTER
CPLMD::analysis::Committor	Provides the keyword COMMITTOR
▶CPLMD::bias::Bias	This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new 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
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
CPLMD::bias::UWalls	Provides the keyword UPPER_WALLS
CPLMD::eds::EDS	Provides the keyword EDS
CPLMD::isdb::Metainference	Provides the keyword METAINFERENCE
CPLMD::isdb::Rescale	Provides the keyword RESCALE
▶CPLMD::ves::VesBias	Abstract base class for implementing biases the extents the normal Bias.h class to include functions related to the variational approach
CPLMD::ves::VesLinearExpansion	Provides the keyword VES_LINEAR_EXPANSION
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::DumpProjections	Provides the keyword DUMPPROJECTIONS
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::Print	Provides the keyword PRINT
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::gridtools::GridPrintingBase
CPLMD::gridtools::DumpCube	Provides the keyword DUMPCUBE
CPLMD::gridtools::DumpGrid	Provides the keyword DUMPGRID
CPLMD::gridtools::GridToXYZ	Provides the keyword GRID_TO_XYZ
▶CPLMD::manyrestraints::ManyRestraintsBase
CPLMD::manyrestraints::LWalls	Provides the keyword LWALLS
CPLMD::manyrestraints::UWalls	Provides the keyword UWALLS
CPLMD::multicolvar::DumpMultiColvar	Provides the keyword DUMPMULTICOLVAR
▶CPLMD::ves::Optimizer
CPLMD::ves::Opt_BachAveragedSGD	Provides the keyword OPT_AVERAGED_SGD
CPLMD::ves::Opt_Dummy	Provides the keyword OPT_DUMMY
CPLMD::vesselbase::ActionWithAveraging	This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames
▶CPLMD::ActionSetup	Action used to create a PLMD::Action that do something during setup only e.g
CPLMD::setup::Load	Provides the keyword LOAD
CPLMD::setup::Restart	Provides the keyword RESTART
CPLMD::setup::Units	Provides the keyword UNITS
CPLMD::SetupMolInfo
▶CPLMD::ActionWithArguments	This is used to create PLMD::Action objects that take the output from some other Action as input
CPLMD::analysis::Committor	Provides the keyword COMMITTOR
CPLMD::bias::Bias	This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias
▶CPLMD::bias::ReweightBase
CPLMD::bias::ReweightBias	Provides the keyword REWEIGHT_BIAS
CPLMD::bias::ReweightMetad	Provides the keyword REWEIGHT_METAD
CPLMD::bias::ReweightTemperature	Provides the keyword REWEIGHT_TEMP
▶CPLMD::function::Function	This is the abstract base class to use for implementing new CV function, within it there is information as to how to go about implementing a new function
CPLMD::function::Combine	Provides the keyword COMBINE
CPLMD::function::Ensemble	Provides the keyword ENSEMBLE
CPLMD::function::FuncPathMSD	Provides the keyword FUNCPATHMSD
CPLMD::function::FuncSumHills	Provides the keyword FUNCSUMHILLS
CPLMD::function::LocalEnsemble	Provides the keyword LOCALENSEMBLE
▶CPLMD::function::Matheval	Provides the keyword MATHEVAL
CPLMD::function::Custom
CPLMD::function::Piecewise	Provides the keyword PIECEWISE
CPLMD::function::Sort	Provides the keyword SORT
CPLMD::function::Stats	Provides the keyword STATS
CPLMD::function::Target	Provides the keyword TARGET
CPLMD::isdb::Select	Provides the keyword SELECT
CPLMD::generic::DumpDerivatives	Provides the keyword DUMPDERIVATIVES
CPLMD::generic::DumpForces	Provides the keyword DUMPFORCES
CPLMD::generic::DumpProjections	Provides the keyword DUMPPROJECTIONS
CPLMD::generic::Print	Provides the keyword PRINT
CPLMD::generic::UpdateIf	Provides the keyword UPDATE_IF
CPLMD::isdb::MetainferenceBase	This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action
CPLMD::mapping::Mapping
CPLMD::mapping::PCAVars	Provides the keyword PCAVARS
CPLMD::vesselbase::ActionWithAveraging	This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames
▶CPLMD::ActionWithValue	Used to create a PLMD::Action that has some scalar or vectorial output that may or may not have some derivatives
CPLMD::bias::Bias	This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias
CPLMD::bias::ReweightBase
CPLMD::Colvar	This is the abstract base class to use for implementing new collective variables, within it there is information as to how to go about implementing a new CV
CPLMD::function::Function	This is the abstract base class to use for implementing new CV function, within it there is information as to how to go about implementing a new function
CPLMD::generic::FitToTemplate	Provides the keyword FIT_TO_TEMPLATE
CPLMD::generic::Read	Provides the keyword READ
CPLMD::generic::Time	Provides the keyword TIME
CPLMD::isdb::MetainferenceBase	This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action
CPLMD::manyrestraints::ManyRestraintsBase
CPLMD::mapping::Mapping
CPLMD::mapping::PCAVars	Provides the keyword PCAVARS
CPLMD::multicolvar::MultiColvarBase
CPLMD::secondarystructure::SecondaryStructureRMSD	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
CPLMD::ves::Optimizer
CPLMD::vesselbase::ActionWithAveraging	This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames
CPLMD::generic::EndPlumed	Provides the keyword ENDPLUMED
CPLMD::generic::Include	Provides the keyword INCLUDE
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_Custom	Provides the keyword BF_CUSTOM
CPLMD::ves::BF_Fourier	Provides the keyword BF_FOURIER
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::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_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::vesselbase::ActionWithInputVessel
CPLMD::manyrestraints::ManyRestraintsBase
CPLMD::multicolvar::DumpMultiColvar	Provides the keyword DUMPMULTICOLVAR
▶CPLMD::vesselbase::ActionWithVessel	This is used to create PLMD::Action objects that are computed by calculating the same function multiple times
CPLMD::manyrestraints::ManyRestraintsBase
CPLMD::mapping::Mapping
CPLMD::multicolvar::MultiColvarBase
CPLMD::secondarystructure::SecondaryStructureRMSD	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
CPLMD::vesselbase::ActionWithAveraging	This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames
CPLMD::ActionOptions	This class is used to bring the relevant information to the Action constructor
CPLMD::ActionRegister	Register holding all the allowed keywords
▶CAdd public Operation
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
▶CAddConstant public Operation
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
CPLMD::Angle	Class to compute angles
▶CAsin public Operation
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
▶CAtan public Operation
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
CPLMD::AtomNumber	Simple class to store the index of an atom
CPLMD::Atoms	Class containing atom related quantities from the MD code
CPLMD::multicolvar::AtomValuePack
CPLMD::BiasRepresentation	This class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias
CPLMD::Brent1DRootSearch< FCLASS >	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method
CPLMD::multicolvar::CatomPack
▶CCeil public Operation
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
CPLMD::Citations	Class taking care of bibliography
CPLMD::analysis::ClassicalScaling
▶CPLMD::CLTool	This is the abstract base class to use for implementing new command line tool, within it there is information as to how to go about implemneting a new tool
CPLMD::cltools::CLToolSumHills
CPLMD::cltools::Driver< real >
CPLMD::cltools::GenTemplate
CPLMD::cltools::Info
CPLMD::cltools::kt
CPLMD::cltools::Manual
CPLMD::cltools::PesMD
CPLMD::cltools::SimpleMD
CPLMD::mapping::PathTools
CPLMD::ves::MD_LinearExpansionPES
CPLMD::CLToolOptions
CPLMD::CLToolRegister	Same as ActionRegister, but for CLTools
▶CPLMD::ves::CoeffsBase
CPLMD::ves::CoeffsMatrix
CPLMD::ves::CoeffsVector
▶CPLMD::Communicator	Class containing wrappers to MPI
CPLMD::Atoms::DomainDecomposition
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
▶CConstant public Operation
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
CPLMD::Communicator::ConstData	Const version of Communicator::Data See Communicator::Data documentation
▶CCos public Operation
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
▶CCosh public Operation
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
▶CCot public Operation
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
CPLMD::isdb::CS2BackboneDB
▶CCsc public Operation
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
▶CCube public Operation
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
▶CCustom public Operation
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
CPLMD::lepton::CustomFunction	This class is the interface for defining your own function that may be included in expressions
CPLMD::Communicator::Data	Structure defining a buffer for MPI
▶CDelta public Operation
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
▶CDivide public Operation
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
CPLMD::DLLoader	Class taking care of dynamic loading
CPLMD::DynamicList< T >	A class for storing a list that changes which members are active as a function of time
CPLMD::DynamicList< unsigned >
CPLMD::drr::DynamicReferenceRestraining	Provides the keyword <a href="../../user-doc/html/_"_d_r_r.html"> "DRR
▶CErf public Operation
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
▶CErfc public Operation
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
CPLMD::ERMSD	A class that implements ERMSD calculations
▶Cstd::exception	STL class
CPLMD::Exception	Class to deal with Plumed runtime errors
CPLMD::lepton::Exception	This class is used for all exceptions thrown by lepton
CPLMD::ExchangePatterns
▶CExp public Operation
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
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 >
CPLMD::ves::FermiSwitchingFunction	Small class to compute fermi switching function
▶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	Class for input files
▶CPLMD::OFile	Class for output files
CPLMD::Log	Class containing the log stream
CPLMD::function::FilesHandler
CPLMD::molfile::fio_iovec
CPLMD::FlexibleBin
▶CFloor public Operation
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
CPLMD::isdb::CS2Backbone::Fragment
CPLMD::bias::MetaD::Gaussian
CPLMD::bias::PBMetaD::Gaussian
▶CPLMD::Grid
CPLMD::SparseGrid
CPLMD::ves::GridIntegrationWeights
CPLMD::ves::GridLinearInterpolation
CPLMD::HistogramBead	A class for calculating whether or not values are within a given range using : \( \sum_i \int_a^b G( s_i, \sigma*(b-a) ) \)
CPLMD::colvar::PathMSDBase::ImagePath	This class is a general container for path stuff
CPLMD::colvar::PathMSDBase::imgOrderByDist
CPLMD::colvar::PathMSDBase::imgOrderBySimilarity
CPLMD::KernelFunctions
CPLMD::Keywords::KeyType	This class lets me pass keyword types easily
CPLMD::Keywords	This class holds the keywords and their documentation
CPLMD::analysis::LandmarkRegister
▶CPLMD::analysis::LandmarkSelectionBase
CPLMD::analysis::CopyAllFrames
CPLMD::analysis::LandmarkSelectionOptions
CPLMD::LatticeReduction	Class implementing algorithms for lattice reduction
CPLMD::ves::LinearBasisSetExpansion
CPLMD::LinkCells	A class for doing link cells
CPLMD::crystallization::LOCAL_Q3	Provides the keyword LOCAL_Q3
CPLMD::crystallization::LOCAL_Q4	Provides the keyword LOCAL_Q4
CPLMD::crystallization::LOCAL_Q6	Provides the keyword LOCAL_Q6
▶CLog public Operation
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
CPLMD::LoopUnroller< n >	Utiliy class for loop unrolling
CPLMD::MatrixSquareBracketsAccess< T, C, I, J >	Utility class to add [][] access
▶CPLMD::MatrixSquareBracketsAccess< Matrix< double >, double >
CPLMD::Matrix< double >
▶CPLMD::MatrixSquareBracketsAccess< Matrix< PLMD::SwitchingFunction >, PLMD::SwitchingFunction >
CPLMD::Matrix< PLMD::SwitchingFunction >
▶CPLMD::MatrixSquareBracketsAccess< Matrix< PLMD::VectorGeneric >, PLMD::VectorGeneric >
CPLMD::Matrix< PLMD::VectorGeneric >
▶CPLMD::MatrixSquareBracketsAccess< Matrix< std::pair< unsigned, unsigned > >, std::pair< unsigned, unsigned > >
CPLMD::Matrix< std::pair< unsigned, unsigned > >
▶CPLMD::MatrixSquareBracketsAccess< Matrix< std::vector< PLMD::KernelFunctions > >, std::vector< PLMD::KernelFunctions > >
CPLMD::Matrix< std::vector< PLMD::KernelFunctions > >
▶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 >	Class implementing fixed size matrices of doubles
▶CMax public Operation
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
CPLMD::molfile::md_atom
CPLMD::molfile::md_box
CPLMD::molfile::md_file
CPLMD::molfile::md_header
CPLMD::molfile::md_ts
▶CPLMD::MDAtomsBase	Class containing interface to MDAtomsTyped
CPLMD::MDAtomsTyped< T >	Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED
CPLMD::MetricRegister
▶CMin public Operation
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
CPLMD::Minimise1DBrent< FCLASS >	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method
CPLMD::MinimiseBase< FCLASS >
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
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
CPLMD::setup::MolInfo	Provides the keyword MOLINFO
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
▶CMultiply public Operation
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
▶CMultiplyConstant public Operation
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
▶CPLMD::MultiReferenceBase
CPLMD::PointWiseMapping
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 > >
▶CNegate public Operation
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
CPLMD::NeighborList	A class that implements neighbor lists from two lists or a single list of atoms
CPLMD::OpenMP
CPLMD::OpenMPVars
CPLMD::function::FuncPathMSD::ordering
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::PathReparameterization	This class can be used to make a set of reference configurations equidistant
CPLMD::Pbc
CPLMD::PDB	Minimalistic pdb parser
CPLMD::Plumed	C++ wrapper for plumed
Cplumed	Main plumed object
Cplumed_function_holder	Holder for function pointer
Cplumed_plumedmain_function_holder	Container for plumedmain function pointers (create, cmd and finalize)
CPLMD::PlumedMainInitializer	Static object which registers Plumed
▶CPower public Operation
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
▶CPowerConstant public Operation
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
CPLMD::Random
▶CReciprocal public Operation
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
▶CPLMD::ReferenceConfiguration	Abstract base class for calculating the distance from a reference configuration
CPLMD::FakeFrame
▶CPLMD::ReferenceArguments	In many applications (e.g
▶CPLMD::ArgumentOnlyDistance
CPLMD::DotProductDistance
CPLMD::EuclideanDistance
CPLMD::MahalanobisDistance
CPLMD::NormalizedEuclideanDistance
CPLMD::Direction
▶CPLMD::ReferenceAtoms	In many applications (e.g
CPLMD::Direction
CPLMD::MultiDomainRMSD
▶CPLMD::SingleDomainRMSD
▶CPLMD::DRMSD
CPLMD::IntermolecularDRMSD
CPLMD::IntramolecularDRMSD
▶CPLMD::RMSDBase
CPLMD::OptimalRMSD
CPLMD::SimpleRMSD
CPLMD::ReferenceConfigurationOptions
CPLMD::ReferenceValuePack
CPLMD::Communicator::Request	Wrapper class for MPI_Request
CPLMD::isdb::CS2Backbone::RingInfo
CPLMD::RMSD	A class that implements RMSD calculations This is a class that implements the various infrastructure to calculate the RMSD or MSD respect a given frame
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::RootFindingBase< FCLASS >
CPLMD::RootFindingBase< PLMD::gridtools::ContourFindingBase >
CPLMD::RootFindingBase< PLMD::multicolvar::DistanceFromContour >
CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row	Small utility class which just contains a pointer to the T and the row number
▶CSec public Operation
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
▶CSelect public Operation
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
▶CSin public Operation
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
▶CSinh public Operation
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
▶CSqrt public Operation
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
▶CSquare public Operation
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
CPLMD::Communicator::Status	Wrapper class for MPI_Status
▶CStep public Operation
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
CPLMD::Stopwatch	Class implementing stopwatch to time execution
▶CSubtract public Operation
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
CPLMD::SwitchingFunction	Small class to compure switching functions
▶CTan public Operation
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
▶CTanh public Operation
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
CPLMD::TargetDist
▶CPLMD::ves::TargetDistModifer
CPLMD::ves::WellTemperedModifer
CPLMD::bias::MetaD::TemperingSpecs
CPLMD::TensorChecks	Small auxiliary class
CPLMD::Tools	Empty class which just contains several (static) tools
CPLMD::Torsion	Class to compute torsional angles
CPLMD::molfile::trx_hdr
CPLMD::drr::UIestimator::UIestimator
CPLMD::Units	Small utility class that contains information about units
CPLMD::Value	A class for holding the value of a function together with its derivatives
▶CVariable public Operation
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
▶Cstd::vector< T >	STL class
CPLMD::ActionSet	Std::vector containing the sequence of Action to be done
CPLMD::VectorChecks	Small auxiliary class
CPLMD::VectorGeneric< n >	Class implementing fixed size vectors of doubles
CPLMD::VectorGeneric< 6 >
▶CPLMD::vesselbase::Vessel
▶CPLMD::vesselbase::AveragingVessel
CPLMD::analysis::AverageVessel
▶CPLMD::gridtools::GridVessel
▶CPLMD::gridtools::HistogramOnGrid
CPLMD::gridtools::AverageOnGrid
CPLMD::vesselbase::BridgeVessel	This class allows you to calculate the vessel in one ActionWithVessel
▶CPLMD::vesselbase::ShortcutVessel
CPLMD::vesselbase::Histogram
▶CPLMD::vesselbase::StoreDataVessel	Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to store values and derivatives for a set of scalars or vectors that are calculated by a PLMD::vesselbase::ActionWithVessel
CPLMD::adjmat::AdjacencyMatrixVessel
CPLMD::mapping::TrigonometricPathVessel
CPLMD::vesselbase::Moments
▶CPLMD::vesselbase::ValueVessel
▶CPLMD::vesselbase::FunctionVessel	Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\)
CPLMD::crystallization::GradientVessel
CPLMD::crystallization::VectorMean
CPLMD::crystallization::VectorSum
CPLMD::mapping::SpathVessel
CPLMD::mapping::ZpathVessel
CPLMD::vesselbase::AltMin
CPLMD::vesselbase::Between
CPLMD::vesselbase::LessThan
CPLMD::vesselbase::Max
CPLMD::vesselbase::Mean
CPLMD::vesselbase::Min
CPLMD::vesselbase::MoreThan
CPLMD::vesselbase::Sum
▶CPLMD::vesselbase::OrderingVessel
CPLMD::vesselbase::Highest
CPLMD::vesselbase::Lowest
CPLMD::vesselbase::VesselOptions	This class is used to pass the input to Vessels
CPLMD::vesselbase::VesselRegister
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
CPLMD::Stopwatch::Watch	Class to store a single stopwatch
▶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::PlumedMain	Main plumed object