Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 123456]

►NPLMD
►Nadjmat
CAdjacencyMatrixBase
CBridge	Provides the keyword BRIDGE
CBridgeMatrix	Provides the keyword BRIDGE_MATRIX
CContactMatrix	Provides the keyword CONTACT_MATRIX_PROPER
CContactMatrixShortcut	Provides the keyword CONTACT_MATRIX
CDistanceMatrix	Provides the keyword DISTANCE_MATRIX
CHbondMatrix	Provides the keyword HBOND_MATRIX
CNeighbors	Provides the keyword NEIGHBORS
CTopologyMatrix	Provides the keyword TOPOLOGY_MATRIX
CTorsionsMatrix	Provides the keyword TORSIONS_MATRIX
►Nbias
CABMD	Provides the keyword ABMD
CBias
CBiasValue	Provides the keyword BIASVALUE
CExtendedLagrangian	Provides the keyword EXTENDED_LAGRANGIAN
CExternal	Provides the keyword EXTERNAL
CLWalls	Provides the keyword LOWER_WALLS_SCALAR
CMaxEnt	Provides the keyword MAXENT
►CMetaD	Provides the keyword METAD
CGaussian
CTemperingSpecs
CMovingRestraint	Provides the keyword MOVINGRESTRAINT
►CPBMetaD	Provides the keyword PBMETAD
CGaussian
CRestraint	Provides the keyword RESTRAINT_SCALAR
CRestraintShortcut	Provides the keyword RESTRAINT
CReweightBase
CReweightBias	Provides the keyword REWEIGHT_BIAS
CReweightMetad	Provides the keyword REWEIGHT_METAD
CReweightTemperaturePressure	Provides the keyword REWEIGHT_TEMP_PRESS
CUWalls	Provides the keyword UPPER_WALLS_SCALAR
CWalls	Provides the keyword UPPER_WALLS
►Ncltools
CCLToolSumHills
CCompletion
CDriver
CGenExample
CGenJson
CGenTemplate
CInfo
Ckt
CManual
CPdbRenumber
CPesMD
CShowGraph
CSimpleMD
CSwitchingPlotter
►Nclusters
CClusterDiameter	Provides the keyword CLUSTER_DIAMETER
CClusterDistribution	Provides the keyword CLUSTER_DISTRIBUTION_CALC
CClusterDistributionShortcut	Provides the keyword CLUSTER_DISTRIBUTION
CClusteringBase
CClusterNatoms	Provides the keyword CLUSTER_NATOMS
CClusterProperties	Provides the keyword CLUSTER_PROPERTIES
CClusterWeights	Provides the keyword CLUSTER_WEIGHTS
CClusterWithSurface	Provides the keyword CLUSTER_WITHSURFACE
CDFSClustering	Provides the keyword DFSCLUSTERING
COutputCluster	Provides the keyword OUTPUT_CLUSTER
►Ncolvar
CAngle	Provides the keyword ANGLE_SCALAR
CCell	Provides the keyword CELL
CColvarFake	Provides the keyword FAKE
CColvarShortcut
CContactMap	Provides the keyword CONTACTMAP
CCoordination	Provides the keyword COORDINATION
CCoordinationBase
CDHEnergy	Provides the keyword DHENERGY
CDihedralCorrelation	Provides the keyword DIHEDRAL_CORRELATION_SCALAR
CDimer	Provides the keyword <a href="../../user-doc/html/_"_d_i_m_e_r.html"> "DIMER
CDipole	Provides the keyword DIPOLE_SCALAR
CDistance	Provides the keyword DISTANCE_SCALAR
CDRMSD	Provides the keyword DRMSD
CEEFSolv	Provides the keyword EEFSOLV
CEnergy	Provides the keyword ENERGY
CERMSD	Provides the keyword ERMSD
CExtraCV	Provides the keyword EXTRACV
CGHBFIX	Provides the keyword GHBFIX
CGyration	Provides the keyword GYRATION_FAST
CGyrationShortcut	Provides the keyword GYRATION
CMultiColvarTemplate
CMultiRMSD	Provides the keyword MULTI_RMSD
CPathMSD	Provides the keyword PATHMSD
►CPathMSDBase
CImagePath	This class is a general container for path stuff
CimgOrderByDist
CimgOrderBySimilarity
CPCARMSD	Provides the keyword PCARMSD
CPlane	Provides the keyword PLANE_SCALAR
CPosition	Provides the keyword POSITION_SCALAR
CProjectionOnAxis	Provides the keyword PROJECTION_ON_AXIS
CPropertyMap	Provides the keyword PROPERTYMAP
CPuckering	Provides the keyword PUCKERING
CRMSD	Provides the keyword RMSD_SCALAR
CRMSDShortcut	Provides the keyword RMSD
CRMSDVector	Provides the keyword RMSD_VECTOR
CSelectMassCharge	Provides the keyword MASS_SCALAR
CTemplate	Provides the keyword TEMPLATE
CTorsion	Provides the keyword TORSION_SCALAR
CVolume	Provides the keyword VOLUME
►Ncontour
CContourFindingBase
CDistanceFromContour	Provides the keyword DISTANCE_FROM_CONTOUR
CDistanceFromContourBase
CDistanceFromSphericalContour	Provides the keyword DISTANCE_FROM_SPHERICAL_CONTOUR
CDumpContour	Provides the keyword DUMPCONTOUR
CFindContour	Provides the keyword FIND_CONTOUR
CFindContourSurface	Provides the keyword FIND_CONTOUR_SURFACE
CFindSphericalContour	Provides the keyword FIND_SPHERICAL_CONTOUR
►Ncrystdistrib
CBopsShortcut	Provides the keyword BOPS
CDopsShortcut	Provides the keyword DOPS
CQuaternion	Provides the keyword QUATERNION_SCALAR
CQuaternionBondProductMatrix	Provides the keyword QUATERNION_BOND_PRODUCT_MATRIX
CQuaternionProductMatrix	Provides the keyword QUATERNION_PRODUCT_MATRIX
CRopsShortcut	Provides the keyword ROPS
►Ndimred
CArrangePoints	Provides the keyword ARRANGE_POINTS
CClassicalMultiDimensionalScaling	Provides the keyword CLASSICAL_MDS
CPCA	Provides the keyword PCA
CProjectPoints	Provides the keyword PROJECT_POINTS
CSketchMap	Provides the keyword SKETCHMAP
CSketchMapProjection	Provides the keyword SKETCHMAP_PROJECTION
CSMACOF
►Ndrr
►NUIestimator
Cn_matrix
Cn_vector
CUIestimator
►Neds
CEDS	Provides the keyword <a href="../../user-doc/html/_"_e_d_s.html"> "EDS
►Nenvsim
CEnvironmentSimilarity	Provides the keyword ENVIRONMENTSIMILARITY
►Nfisst
CFISST	Provides the keyword FISST
►Nfourier
CFourierTransform	Provides the keyword FOURIER_TRANSFORM
►Nfunction
►Nannfunc
CANN
CBessel
CBetween
CCombine
CCustom
CEnsemble	Provides the keyword ENSEMBLE
CFilesHandler
►CFuncPathGeneral	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
Cpairordering
►CFuncPathMSD	Provides the keyword FUNCPATHMSD
Cordering
Cpairordering
CFuncSumHills	Provides the keyword FUNCSUMHILLS
CFunction
CFunctionOfMatrix
CFunctionOfScalar
CFunctionOfVector
CFunctionShortcut
CFunctionTemplateBase
CHighest
CLessThan
CLocalEnsemble	Provides the keyword LOCALENSEMBLE
CMoments
CMoreThan
CPiecewise
CProduct	Provides the keyword PRODUCT
CSort
CStats	Provides the keyword STATS
CSum
►Nfunnel
CFunnel	Provides the keyword FUNNEL
CFUNNEL_PS	Provides the keyword FUNNEL_PS
►Ngch
►Ndetail
►Nsmall_vector_adl
Cis_nothrow_swappable
Cis_nothrow_swappable< T, decltype(swap(std::declval< T & >(), std::declval< T & >()))>
Callocator_inliner
Callocator_inliner< Allocator, false >
Callocator_inliner< Allocator, true >
►Callocator_interface
Chas_alloc_construct
Chas_alloc_construct_check
Chas_alloc_construct_check< void_t< decltype(std::declval< A & >().construct(std::declval< V * >(), std::declval< Args >()...))>, A, V, Args... >
Chas_alloc_construct_impl
Chas_alloc_construct_impl< typename std::enable_if< is_complete< V >::value >::type, A, V, Args... >
Chas_alloc_destroy
Chas_alloc_destroy< A, V, typename std::enable_if< is_complete< V >::value >::type >
Chas_alloc_destroy_impl
Chas_alloc_destroy_impl< void_t< decltype(std::declval< A & >().destroy(std::declval< V * >()))>, A, V >
Chas_ptr_traits_to_address
Chas_ptr_traits_to_address< P, void_t< decltype(std::pointer_traits< P >::to_address(std::declval< P >()))> >
Cis_complete
Cis_complete< U, decltype(static_cast< void >(sizeof(U)))>
Cis_contiguous_iterator
Cis_convertible_pointer
Cis_memcpyable
Cis_memcpyable< QualifiedFrom, QualifiedTo, typename std::enable_if< is_complete< QualifiedFrom >::value >::type >
Cis_memcpyable_integral
Cis_memcpyable_integral< From, To, typename std::enable_if< is_complete< From >::value >::type >
Cis_memcpyable_iterator
Cis_memcpyable_iterator< std::move_iterator< InputIt > >
Cis_small_vector_iterator
Cis_small_vector_iterator< small_vector_iterator< Ts... > >
Cis_trivially_constructible
Cis_trivially_constructible_impl
Cis_trivially_constructible_impl< typename std::enable_if< is_complete< V >::value >::type, V, Args... >
Cis_trivially_destructible
Cis_trivially_destructible< V, typename std::enable_if< is_complete< V >::value >::type >
Cis_uninitialized_memcpyable
Cis_uninitialized_memcpyable< To, From >
Cis_uninitialized_memcpyable_impl
Cis_uninitialized_memcpyable_iterator
Cis_uninitialized_memcpyable_iterator< std::move_iterator< U >, V >
Cmust_use_alloc_construct
Cmust_use_alloc_destroy
Cunderlying_if_enum
Cunderlying_if_enum< T, typename std::enable_if< std::is_enum< T >::value >::type >
Cinline_storage
Cinline_storage< T, 0 >
►Csmall_vector_base
Callocations_are_movable
Callocations_are_swappable
Cbypass_tag
Cis_emplace_constructible
Cis_emplace_constructible_impl
Cis_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... >
Cis_eraseable
Cis_eraseable< AI, void_t< decltype(std::declval< AI & >().destroy(std::declval< value_ty * >()))> >
Cis_explicitly_copy_insertable
Cis_explicitly_move_insertable
Cis_explicitly_nothrow_copy_insertable
Cis_explicitly_nothrow_move_insertable
Cis_nothrow_emplace_constructible
Crelocate_with_move
Cstack_temporary
Cstrong_exception_policy
Csmall_vector_data
Csmall_vector_data< Pointer, SizeT, T, 0 >
Csmall_vector_data_base
►Cdefault_buffer_size
Cis_complete
Cis_complete< U, decltype(static_cast< void >(sizeof(U)))>
Csmall_vector
Csmall_vector_iterator
►Ngeneric
CAccumulate	Provides the keyword ACCUMULATE
CAverage	Provides the keyword AVERAGE
CCollect	Provides the keyword COLLECT
CCommittor	Provides the keyword COMMITTOR
CConstant	Provides the keyword CONSTANT
CCreateMask	Provides the keyword CREATE_MASK
CDebug	Provides the keyword DEBUG
CDumpAtoms	Provides the keyword DUMPATOMS
CDumpDerivatives	Provides the keyword DUMPDERIVATIVES
CDumpForces	Provides the keyword DUMPFORCES
CDumpMassCharge	Provides the keyword DUMPMASSCHARGE
CDumpPDB	Provides the keyword DUMPPDB
CDumpProjections	Provides the keyword DUMPPROJECTIONS
CDumpVector	Provides the keyword DUMPVECTOR
CEffectiveEnergyDrift	Provides the keyword EFFECTIVE_ENERGY_DRIFT
CEndPlumed	Provides the keyword ENDPLUMED
CFitToTemplate	Provides the keyword FIT_TO_TEMPLATE
CFlush	Provides the keyword FLUSH
CGatherReplicas	Provides the keyword GATHER_REPLICAS
CInclude	Provides the keyword INCLUDE
CMassChargeInput	Provides the keyword READMASSCHARGE
COnes	Provides the keyword ONES
CPDB2Constant	Provides the keyword PDB2CONSTANT
CPlumed	Provides the keyword PLUMED
CPrint	Provides the keyword PRINT
CPrintNDX	Provides the keyword PRINT_NDX
CRandomExchanges	Provides the keyword RANDOM_EXCHANGES
CRead	Provides the keyword READ
CResetCell	Provides the keyword RESET_CELL
CTime	Provides the keyword TIME
CUpdateIf	Provides the keyword UPDATE_IF
CWholeMolecules	Provides the keyword WHOLEMOLECULES
CWrapAround	Provides the keyword WRAPAROUND
►Ngridtools
CActionWithGrid
CConvertToFES	Provides the keyword CONVERT_TO_FES
CDumpGrid	Provides the keyword DUMPCUBE
CEvaluateFunctionOnGrid	Provides the keyword EVALUATE_FUNCTION_FROM_GRID
CEvaluateGridFunction
CFindGridOptimum	Provides the keyword FIND_GRID_MAXIMUM
CFunctionOfGrid
CGradient	Provides the keyword GRADIENT
CGridCoordinatesObject
CGridSearch
CHistogram	Provides the keyword HISTOGRAM
CInterpolateGrid	Provides the keyword INTERPOLATE_GRID
CInterpolator
CKDE	Provides the keyword KDE
CKLEntropy	Provides the keyword KL_ENTROPY
CMultiColvarDensity	Provides the keyword MULTICOLVARDENS
CPairEntropies	Provides the keyword PAIRENTROPIES
CPairEntropy	Provides the keyword PAIRENTROPY
CRDF	Provides the keyword RDF
CReadGridInSetup	Provides the keyword REFERENCE_GRID
►Nisdb
CCaliber	Provides the keyword CALIBER
►CCS2Backbone	Provides the keyword CS2BACKBONE
CChemicalShift
CRingInfo
CCS2BackboneDB
CEMMI	Provides the keyword EMMI
CFretEfficiency	Provides the keyword FRET
CJCoupling	Provides the keyword <a href="../../user-doc/html/_"_j_c_o_u_p_l_i_n_g.html"> "JCOUPLING
CMetainference	Provides the keyword METAINFERENCE
CMetainferenceBase
CNOE	Provides the keyword NOE
CPRE	Provides the keyword PRE
CRDC	Provides the keyword RDC
CRescale	Provides the keyword RESCALE
►CSAXS	Provides the keyword SAXS
CSplineCoeffs
CSelect	Provides the keyword SELECT
CSelector	Provides the keyword SELECTOR
CShadow	Provides the keyword SHADOW
►Nlandmarks
CCollectFrames	Provides the keyword COLLECT_FRAMES
CFarthestPointSampling	Provides the keyword FARTHEST_POINT_SAMPLING
CLandmarkSelection	Provides the keyword LANDMARK_SELECT_STRIDE
CLogSumExp	Provides the keyword LOGSUMEXP
►Nlepton
CAsmJitRuntimePtr
CCompiledExpression	A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate it many times as quickly as possible
CCustomFunction	This class is the interface for defining your own function that may be included in expressions
CException	This class is used for all exceptions thrown by lepton
CExpressionProgram	An ExpressionProgram is a linear sequence of Operations for evaluating an expression
CExpressionTreeNode	This class represents a node in the abstract syntax tree representation of an expression
COperation	An Operation represents a single step in the evaluation of an expression, such as a function, an operator, or a constant value
CParsedExpression	This class represents the result of parsing an expression
CParser	This class provides the main interface for parsing expressions
CParseToken
CPlaceholderFunction	This class is an implementation of CustomFunction that does no computation
►Nlogmfd
CLogMFD	Class for LogMFD parameters, variables and subroutines
►Nmapping
CAdaptivePath	Provides the keyword ADAPTIVE_PATH
CGeometricPath	Provides the keyword GEOMETRIC_PATH
CGeometricPathShortcut	Provides the keyword GPATH
CPath	Provides the keyword PATH
CPathDisplacements	Provides the keyword AVERAGE_PATH_DISPLACEMENT
CPathProjectionCalculator
CPathReparameterization	Provides the keyword REPARAMETERIZE_PATH
CPathTools
CPCAVars	Provides the keyword PCAVARS
►Nmatrixtools
CCovarianceMatrix	Provides the keyword COVARIANCE_MATRIX
CDeterminant	Provides the keyword DETERMINANT
CDiagonalizeMatrix	Provides the keyword DIAGONALIZE
CInvertMatrix	Provides the keyword INVERT_MATRIX
CMatrixOperationBase
CMatrixTimesMatrix	Provides the keyword MATRIX_PRODUCT
CMatrixTimesVector	Provides the keyword MATRIX_VECTOR_PRODUCT
COuterProduct	Provides the keyword OUTER_PRODUCT
CTransposeMatrix	Provides the keyword TRANSPOSE
CVoronoi	Provides the keyword VORONOI
►Nmaze
CLoss	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__l_o_s_s.html"> "MAZE_LOSS
CMember	Defines the encoding for a ligand conformation
CMemetic	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
COptimizer	Base class for implementing optimizers for ligand unbinding
COptimizerBias	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
CRandom_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
CRandom_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
Crnd	Mersenne Twister sampler for random variables
CSimulated_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
CSteered_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
►Ctls	Helper functions
Cdelete_ptr
►Nmembranefusion
CfusionPoreExpansionP	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
CfusionPoreNucleationP	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
CmemFusionP	Provides the keyword <a href="../../user-doc/html/_"_m_e_m_f_u_s_i_o_n_p.html"> "MEMFUSIONP
►NmergeVectorTools
Chas_size_and_data
Chas_size_and_data< T, std::void_t< decltype(std::declval< T >().size()), decltype(std::declval< T >().data())> >
►Nmetatensor
►Nvesin
►Ncpu
►CCellList	The cell list is used to sort atoms inside bins/cells
CCell
CPoint	Cells themselves are a list of points & corresponding shift to place the point inside the cell
CGrowableNeighborList	Wrapper around VesinNeighborList that behaves like a std::vector, automatically growing memory allocations
CBoundingBox
CCellShift	A cell shift represents the displacement along cell axis between the actual position of an atom and a periodic image of this atom
CMatrix
CVector
CVesinNeighborList	The actual neighbor list
CVesinOptions	Options for a neighbor list calculation
CMetatensorPlumedAction	Provides the keyword <a href="../../user-doc/html/_"_m_e_t_a_t_e_n_s_o_r.html"> "METATENSOR
►Nmolfile
Cfio_iovec
Cmd_atom
Cmd_box
Cmd_file
Cmd_header
Cmd_ts
Cmolfile_atom_t	Per-atom attributes and information
Cmolfile_graphics_t	Individual graphics object/element data
Cmolfile_metadata_t	File level comments, origin information, and annotations
Cmolfile_plugin_t	Main file reader API
Cmolfile_qm_basis_t	Data for QM basis set
Cmolfile_qm_hessian_t	Data from QM Hessian/normal mode runs
Cmolfile_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
Cmolfile_qm_sysinfo_t	QM run info
Cmolfile_qm_t	QM related information that is timestep independent
Cmolfile_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
Cmolfile_qm_timestep_t	QM per trajectory timestep info Note that each timestep can contain multiple wavefunctions
Cmolfile_qm_wavefunction_t	QM wavefunction
Cmolfile_timestep_metadata
Cmolfile_timestep_t	Per-timestep atom coordinates, velocities, time, energies and periodic cell info
Cmolfile_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
Cmolfile_volumetric_t	Metadata for volumetric datasets, read initially and used for subsequent memory allocations and file loading
Ctrx_hdr
Cvmdplugin_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
►Nmulticolvar
CAlphaBeta	Provides the keyword ALPHABETA
CAngles	Provides the keyword ANGLES
CCoordAngles	Provides the keyword COORD_ANGLES
CDihcor	Provides the keyword DIHCOR
CDistances	Provides the keyword DISTANCES
CDumpMultiColvar	Provides the keyword DUMPMULTICOLVAR
CInPlaneDistances	Provides the keyword INPLANEDISTANCES
CMFilterLess	Provides the keyword MFILTER_LESS
CMFilterMore	Provides the keyword MFILTER_MORE
CMultiColvarShortcuts
CPlaneShortcut	Provides the keyword PLANES
CTorsions	Provides the keyword TORSIONS
CUWalls	Provides the keyword UWALLS
CXAngle	Provides the keyword XANGLES
CXYTorsions	Provides the keyword XYTORSIONS
►NOpenMP
COpenMPVars	Singleton struct to treat the openMP setting as a global variables, but with a layer of encapsulation
►Nopes
Cconvergence
CECVcustom	Provides the keyword ECV_CUSTOM
CECVlinear	Provides the keyword ECV_LINEAR
CECVmultiThermal	Provides the keyword ECV_MULTITHERMAL
CECVmultiThermalBaric	Provides the keyword ECV_MULTITHERMAL_MULTIBARIC
CECVumbrellasFile	Provides the keyword ECV_UMBRELLAS_FILE
CECVumbrellasLine	Provides the keyword ECV_UMBRELLAS_LINE
CExpansionCVs
Cexploration
COPESexpanded	Provides the keyword OPES_EXPANDED
►COPESmetad
Ckernel
►Npamm
CHBPammMatrix	Provides the keyword HBPAMM_MATRIX
CHBPammShortcut	Provides the keyword HBPAMM_SD
CPAMM	Provides the keyword PAMM
►Npiv
►CPIV	Provides the keyword PIV
CSharedData	Local structure, used to store data that should be shared across multiple PIV instances
►Nrefdist
CDifference
CDisplacement	Provides the keyword DISPLACEMENT
CEuclideanDistance	Provides the keyword EUCLIDEAN_DISTANCE
CKernel	Provides the keyword KERNEL
CMahalanobisDistance	Provides the keyword MAHALANOBIS_DISTANCE
CMatrixProductDiagonal	Provides the keyword MATRIX_PRODUCT_DIAGONAL
CNormalizedEuclideanDistance	Provides the keyword NORMALIZED_EUCLIDEAN_DISTANCE
►Ns2cm
CS2ContactModel	Provides the keyword S2CM
►Nsasa
CSASA_HASEL	Provides the keyword SASA_HASEL
CSASA_LCPO	Provides the keyword SASA_LCPO
►Nsecondarystructure
CAlphaRMSD	Provides the keyword ALPHARMSD
CAntibetaRMSD	Provides the keyword ANTIBETARMSD
CParabetaRMSD	Provides the keyword PARABETARMSD
CSecondaryStructureRMSD	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
►Nsetup
CLoad	Provides the keyword LOAD
CRestart	Provides the keyword RESTART
CUnits	Provides the keyword UNITS
►Nsizeshape
Cposition_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
Cposition_maha_dist	Provides the keyword SIZESHAPE_POSITION_MAHA_DIST
►Nsprint
CSprint	Provides the keyword SPRINT
►NswitchContainers
CbaseSwitch	Container for the actual switching function used by PLMD::SwitchingFunction
CcosinusSwitch
CcubicSwitch
CexponentialSwitch
CfastGaussianSwitch
CfixedRational
CgaussianSwitch
►CleptonSwitch
CfuncAndDeriv	Lepton expression
CnativeqSwitch
Crational
CsmapSwitch
CtanhSwitch
►Nsymfunc
CAngularTetra	Provides the keyword TETRA_ANGULAR
CAtomicSMAC	Provides the keyword ATOMIC_SMAC
CCoordinationNumbers	Provides the keyword COORDINATIONNUMBER
CCoordShellVectorFunction	Provides the keyword FCCUBIC
CCylindricalHarmonic
CFccubic
CHexacticParameter	Provides the keyword HEXACTIC_PARAMETER
CLocalAverage	Provides the keyword LOCAL_AVERAGE
CLocalCrystallinity	Provides the keyword LOCAL_CRYSTALINITY
CLocalSteinhardt	Provides the keyword LOCAL_Q1
CRadialTetra	Provides the keyword TETRA_RADIAL
CSMAC	Provides the keyword SMAC
CSphericalHarmonic
CSteinhardt	Provides the keyword Q1
CThreeBodyGFunctions	Provides the keyword GSYMFUNC_THREEBODY
►Nvaltools
CConcatenate	Provides the keyword CONCATENATE
CFlatten	Provides the keyword FLATTEN
CSelectComponents	Provides the keyword SELECT_COMPONENTS
CSelectWithMask	Provides the keyword SELECT_WITH_MASK
CVStack	Provides the keyword VSTACK
►Nvatom
CArgsToVatom	Provides the keyword ARGS2VATOM
CCenter	Provides the keyword CENTER_FAST
CCenterShortcut	Provides the keyword CENTER
CFixedAtom	Provides the keyword FIXEDATOM
CGhost	Provides the keyword GHOST
►Nves
CBasisFunctions
CBF_Chebyshev	Provides the keyword BF_CHEBYSHEV
CBF_Combined	Provides the keyword BF_COMBINED
CBF_Cosine	Provides the keyword BF_COSINE
CBF_CubicBsplines	Provides the keyword BF_CUBIC_B_SPLINES
CBF_Custom	Provides the keyword BF_CUSTOM
CBF_Fourier	Provides the keyword BF_FOURIER
CBF_Gaussians	Provides the keyword BF_GAUSSIANS
CBF_Legendre	Provides the keyword BF_LEGENDRE
CBF_Powers	Provides the keyword BF_POWERS
CBF_Sine	Provides the keyword BF_SINE
CBF_Wavelets	Provides the keyword BF_WAVELETS
CCoeffsBase
CCoeffsMatrix
CCoeffsVector
CFermiSwitchingFunction
CFesWeight
CGridIntegrationWeights
CGridLinearInterpolation
CLinearBasisSetExpansion
CMarginalWeight
CMD_LinearExpansionPES
COpt_Adam	Provides the keyword OPT_ADAM
COpt_BachAveragedSGD	Provides the keyword OPT_AVERAGED_SGD
COpt_Dummy	Provides the keyword OPT_DUMMY
COpt_RobbinsMonroSGD	Provides the keyword OPT_ROBBINS_MONRO_SGD
COptimizer
COutputBasisFunctions	Provides the keyword VES_OUTPUT_BASISFUNCTIONS
COutputFesBias	Provides the keyword VES_OUTPUT_FES
COutputTargetDistribution	Provides the keyword VES_OUTPUT_TARGET_DISTRIBUTION
CTargetDistModifer
CTargetDistribution
CTD_Chi	Provides the keyword TD_CHI
CTD_ChiSquared	Provides the keyword TD_CHISQUARED
CTD_Custom	Provides the keyword TD_CUSTOM
CTD_Exponential	Provides the keyword TD_EXPONENTIAL
CTD_ExponentiallyModifiedGaussian	Provides the keyword TD_EXPONENTIALLY_MODIFIED_GAUSSIAN
CTD_Gaussian	Provides the keyword TD_GAUSSIAN
CTD_GeneralizedExtremeValue	Provides the keyword TD_GENERALIZED_EXTREME_VALUE
CTD_GeneralizedNormal	Provides the keyword TD_GENERALIZED_NORMAL
CTD_Grid	Provides the keyword TD_GRID
CTD_LinearCombination	Provides the keyword TD_LINEAR_COMBINATION
CTD_Multicanonical	Provides the keyword TD_MULTICANONICAL
CTD_MultithermalMultibaric	Provides the keyword TD_MULTITHERMAL_MULTIBARIC
CTD_ProductCombination	Provides the keyword TD_PRODUCT_COMBINATION
CTD_ProductDistribution	Provides the keyword TD_PRODUCT_DISTRIBUTION
CTD_Uniform	Provides the keyword TD_UNIFORM
CTD_VonMises	Provides the keyword TD_VONMISES
CTD_WellTempered	Provides the keyword TD_WELLTEMPERED
CVesBias
CVesDeltaF	Provides the keyword VES_DELTA_F
CVesLinearExpansion	Provides the keyword VES_LINEAR_EXPANSION
CVesTools
CWaveletGrid
CWellTemperedModifer
►Nvolumes
CActionVolume
CDensity	Provides the keyword DENSITY
CVolumeAround	Provides the keyword AROUND_CALC
CVolumeCavity	Provides the keyword CAVITY_CALC
CVolumeInCylinder	Provides the keyword INCYLINDER_CALC
CVolumeInEnvelope	Provides the keyword INENVELOPE_CALC
CVolumeInSphere	Provides the keyword INSPHERE_CALC
CVolumeShortcut
CVolumeTetrapore	Provides the keyword TETRAHEDRALPORE_CALC
►Nwham
CWham	Provides the keyword WHAM
CWhamHistogram	Provides the keyword WHAM_HISTOGRAM
CWhamWeights	Provides the keyword WHAM_WEIGHTS
►Nwrapper	We use a separate namespace here instead of hiding these classes in the Plumed class, because some of these structs might be specialized by the user
Chas_size_and_data	Primary template, assumes T does not have both size() and data() methods
Chas_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
Cis_custom_array	Primary template, assumes T is not a custom structure
Cis_custom_array< std::array< T, N > >	Template specialization for std::array
Cis_custom_array< T[N]>	Template specialization for C arrays
Cmake_void	This is to replace c++17 std::void_t
►Nxdrfile
Ct_trnheader
►CXDR
Cxdr_ops
CXDRFILE	Contents of the abstract XDRFILE data structure
CAccelerator
CAction	Base class for all the input Actions
CActionAnyorder
CActionAtomistic
CActionForInterface
CActionOptions	This class is used to bring the relevant information to the Action constructor
CActionPilot
CActionRegister	Register holding all the allowed keywords
CActionRegisterPointers
CActionRegistration	Each instance of this specialized class represents an action that can be called with the specified directive
CActionSet	Std::vector containing the sequence of Action to be done
CActionSetup
CActionShortcut
CActionToGetData	Provides the keyword GET
CActionToPutData	Provides the keyword PUT
CActionWithArguments
CActionWithMatrix
CActionWithValue
CActionWithVector
CActionWithVirtualAtom	Class to add a single virtual atom to the system
CAngle
CAtomNumber
CBiasRepresentation	This class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias
CBiasWeight
CBrent1DRootSearch	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method
CCheckInRange
CCitations
CCLTool
CCLToolMain	Class providing cmd() access to command line tools
CCLToolOptions
CCLToolRegister	Same as ActionRegister, but for CLTools
CCLToolRegisterPointers
CColvar
►CCommunicator
CConstData	Const version of Communicator::Data See Communicator::Data documentation
CData	Structure defining a buffer for MPI
CRequest	Wrapper class for MPI_Request
CStatus	Wrapper class for MPI_Status
CConjugateGradient
CDataPassingObject
CDataPassingObjectTyped
CDataPassingTools
CDataPassingToolsTyped
►CDLLoader
CEnsureGlobalDLOpen	RAII helper for promoting RTLD_LOCAL loaded objects to RTLD_GLOBAL
►CDomainDecomposition
CDomainComms
CERMSD	A class that implements ERMSD calculations
►CException
CAssertion	Auxiliary containing the failed assertion
CLocation	Auxiliary containing the location of the exception in the file
CThrow	Auxiliary class used to throw exceptions
CExceptionDebug	Class representing a debug error (can only be thrown when using debug options)
CExceptionError	Class representing a generic error
CExceptionRegisterError	Class representing an error in a register
CExceptionTypeError	Class representing a type error in the PLMD::Plumed interface
CExchangePatterns
CF1dim
►CFileBase	Base class for dealing with files
CFieldBase	Internal tool
CFlexibleBin
CForwardDecl	Utility class for forward declaration of references
CGenericMolInfo
CGREX
CGrid
►CGridBase
CAcceleratorBase	Auxiliary class for accelerating grid calculations
CAcceleratorHandler	Auxiliary class for managing AcceleratorBase
CGroup	Provides the keyword GROUP
CHistogramBead
►CIFile
CField
CKernelFunctions
►CKeywords	This class holds the keywords and their documentation
CKeyType	This class lets me pass keyword types easily
CLatticeReduction	Class implementing algorithms for lattice reduction
CLeptonCall
CLinkCells
CLog	Class containing the log stream
CLoopUnroller
CMatrix	This class stores a full matrix and allows one to do some simple matrix operations
►CMatrixSquareBracketsAccess	Utility class to add [][] access
CConst_row	Small utility class which just contains a pointer to the T and the row number
CRow	Small utility class which just contains a pointer to the T and the row number
CmdMemoryView
CMemoryView
CMinimise1DBrent	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method
CMinimiseBase
CMolDataClass	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
CMPI_Comm	Surrogate of MPI_Comm when MPI library is not available
CMPI_Datatype	Surrogate of MPI_Datatype when MPI library is not available
CMPI_Request	Surrogate of MPI_Request when MPI library is not available
CMPI_Status	Surrogate of MPI_Status when MPI library is not available
CMultiValue
CNeighborList
►COFile
CField	Class identifying a single field for fielded output
CPbc
CPbcAction	Provides the keyword PBC
CPDB	Minimalistic pdb parser
►CPlumed	C++ wrapper for plumed
Cadd_buffer_to
CCString
CException	Base class used to rethrow PLUMED exceptions
CExceptionDebug	Used to rethrow a PLMD::ExceptionDebug
CExceptionError	Used to rethrow a PLMD::ExceptionError
CExceptionTypeError	Thrown when a wrong pointer is passed to the PLUMED interface
Cfinalize_plumed_error	Internal class to simplify plumed_error finalization
CInvalid	Thrown when trying to access an invalid plumed object
CLeptonException	Class used to rethrow Lepton exceptions
Crethrow_nested	Internal class used by exception_dispatch
Crethrow_not_nested	Internal class used by exception_dispatch
CSafePtr	Small class that wraps plumed_safeptr in order to make its initialization easier
CSizeLike	Small structure used to pass elements of a shape initializer_list
CPlumedHandle	Tiny local class to load a PLUMED kernel
►CPlumedMain	Main plumed object
CDeprecatedAtoms
Cplumed_error_handler	Error handler
CProbWeight
CRandom
►CRegister	Base class, with type independent information
CRegistrationLock	Small class to manage registration lock This is used during dlopen, to avoid data races in registrations
►CRegisterBase	General register
CContentAndFullPath	Auxiliary class
CID
CRMSD
CRMSDCoreData	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
CRootFindingBase
CSparseGrid
►CStopwatch
CHandler	Auxiliary class for handling exception-safe start/pause and start/stop
CWatch	Class to store a single stopwatch
►CSubprocess	Class managing a subprocess
CHandler	Class used to cont/stop a Subprocess in an exception safe manner
CSubprocessPid	Small utility class, used to avoid inclusion of unistd.h> in a header file
CSwitchingFunction
CTargetDist
CTensorGeneric
CTensorGenericAux	Small class to contain local utilities
►CTools
►CCriticalSectionWithKey	Utility to create named critical sections Key should be usable in a std::map
CHandler
CDirectoryChanger	Tiny class that changes directory and comes back when going out of scope
CFastStringUnorderedMap	Tiny class implementing faster std::string_view access to an unordered_map It exposes a limited number of methods of std::unordered_map
CTorsion
CTree
►CTypesafePtr
CSizeLike	Small structure used to pass elements of a shape initializer_list
CUnits
CValue
CVectorGeneric
CWeightBase
►CWithCmd	Base for classes with cmd() method
CSizeLike	Small structure used to pass elements of a shape initializer_list
CAngleMulti	Provides the keyword ANGLE_VECTOR
CAngleShortcut	Provides the keyword ANGLE
CANN	Provides the keyword ANN
CBesselShortcut	Provides the keyword BESSEL
CBetweenShortcut	Provides the keyword BETWEEN
CCombineShortcut	Provides the keyword COMBINE
CCustomShortcut	Provides the keyword CUSTOM
CCyHarmShortcut	Provides the keyword CYLINDRICAL_HARMONIC
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
CDistanceMulti	Provides the keyword DISTANCE_VECTOR
CDistanceShortcut	Provides the keyword DISTANCE
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
CFccubicShortcut	Provides the keyword FCCUBIC_FUNC
CGridCustom	Provides the keyword CUSTOM_GRID
CGridSum	Provides the keyword SUM_GRID
CHighestShortcut	Provides the keyword HIGHEST
CLessThanShortcut	Provides the keyword LESS_THAN
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
CMatrixSum	Provides the keyword SUM_MATRIX
CMolInfo	Provides the keyword MOLINFO
CMomentsShortcut	Provides the keyword MOMENTS
CMoreThanShortcut	Provides the keyword MORE_THAN
CMQMulti	Provides the keyword MASS_VECTOR
CMQShortcut	Provides the keyword MASS
COPESmetad_c	Provides the keyword OPES_METAD
COPESmetad_e	Provides the keyword OPES_METAD_EXPLORE
CPiecewiseShortcut	Provides the keyword PIECEWISE
CPlaneMulti	Provides the keyword PLANE_VECTOR
CPlaneShortcut	Provides the keyword PLANE
Cplumed	Main plumed object
Cplumed_error	Small structure that is only defined locally to retrieve errors
Cplumed_error_filesystem_path
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
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
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
CSortShortcut	Provides the keyword SORT
CSpHarmShortcut	Provides the keyword SPHERICAL_HARMONIC
CSumShortcut	Provides the keyword SUM
CTorsionMulti	Provides the keyword TORSION_VECTOR
CTorsionShortcut	Provides the keyword TORSION
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
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
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