| ►NPLMD | |
| ►Nadjmat | |
| CAdjacencyMatrixBase | |
| CAdjacencyMatrixData | |
| CAdjacencyMatrixInput | |
| CBridge | Provides the keyword BRIDGE |
| CBridgeMatrix | |
| CContactMatrix | |
| CContactMatrixShortcut | Provides the keyword CONTACT_MATRIX |
| CDistanceMatrix | |
| CHbondMatrix | |
| CMatrixOutput | |
| CNeighborCalcInput | |
| CNeighbors | |
| CNeighborsShortcut | Provides the keyword NEIGHBORS |
| CNHighInput | |
| CNLowInput | |
| COneHighInput | |
| COneLowInput | |
| CTopologyMatrix | |
| CTorsionsMatrix | Provides the keyword TORSIONS_MATRIX |
| CTorsionsMatrixInput | |
| ►Nbias | |
| CABMD | Provides the keyword ABMD |
| CBias | 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 |
| 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 | |
| CCLTool | 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 |
| 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 |
| CColvar | 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 |
| CColvarFake | Provides the keyword FAKE |
| CColvarInput | |
| 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 |
| CMultiColvarInput | |
| 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 |
| CRMSDVectorData | |
| CSelectMassCharge | Provides the keyword MASS |
| CTemplate | Provides the keyword TEMPLATE |
| CTorsion | Provides the keyword TORSION_SCALAR |
| CVolume | Provides the keyword VOLUME |
| ►Ncontour | |
| CContourFindingObject | |
| 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 |
| CFindContourSurfaceObject | |
| CFindSphericalContour | Provides the keyword FIND_SPHERICAL_CONTOUR |
| CFindSphericalContourObject | |
| ►Ncrystdistrib | |
| CBopsShortcut | Provides the keyword BOPS |
| CDopsShortcut | Provides the keyword DOPS |
| CQuatBondProdMatInput | |
| CQuaternion | Provides the keyword QUATERNION_SCALAR |
| CQuaternionBondProductMatrix | Provides the keyword QUATERNION_BOND_PRODUCT_MATRIX |
| CQuaternionProductMatrix | |
| 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 |
| CProjectPointsInput | |
| 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 |
| ►Nenum_traits | |
| CBitmaskEnum | Struct for setting up bitmask operations on enum types |
| CBitmaskEnum< Keywords::argType > | |
| CBitmaskEnum< Keywords::componentType > | |
| ►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 | |
| Ccomponent | |
| 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 | 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 |
| CFunctionData | |
| CFunctionOfMatrix | |
| CFunctionOfScalar | 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 |
| CFunctionOfVector | |
| CFunctionOptions | |
| CFunctionOutput | |
| CFunctionShortcut | |
| CFunctionWithSingleArgument | |
| CHighest | |
| CLessThan | |
| CLocalEnsemble | Provides the keyword LOCALENSEMBLE |
| CMoments | |
| CMoreThan | |
| CPiecewise | |
| CProduct | Provides the keyword PRODUCT |
| CSort | |
| CSortWithSingleArgument | Provides the keyword SORT_ONEARG |
| CStats | Provides the keyword STATS |
| CSum | Provides the keyword SUM |
| ►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 | |
| ►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 |
| CDiagonalKernelParams | |
| CDiscreteKernel | |
| CDumpGrid | Provides the keyword DUMPCUBE |
| CEvaluateFunctionOnGrid | Provides the keyword EVALUATE_FUNCTION_FROM_GRID |
| CEvaluateGridFunction | |
| CFindGridOptimum | Provides the keyword FIND_GRID_MAXIMUM |
| CFunctionOfGrid | |
| CGetGridVolumeElement | Provides the keyword GET_VOLUME_ELEMENT |
| CGradient | Provides the keyword GRADIENT |
| CGridCoordinatesObject | |
| CGridSearch | |
| CHistogram | Provides the keyword HISTOGRAM |
| CHistogramBeadKernel | |
| CIntegrateGrid | Provides the keyword INTEGRATE_GRID |
| CInterpolateGrid | Provides the keyword INTERPOLATE_GRID |
| CInterpolator | |
| CKDE | |
| CKDEGridTools | |
| CKDEHelper | |
| CKDEShortcut | Provides the keyword KDE |
| CKLEntropy | Provides the keyword KL_ENTROPY |
| CMarginal | Provides the keyword MARGINAL |
| CMarginalInput | |
| CMultiColvarDensity | Provides the keyword MULTICOLVARDENS |
| CNonDiagonalKernelParams | |
| CPairEntropy | Provides the keyword PAIRENTROPY |
| CRDF | Provides the keyword RDF |
| CReadGridInSetup | Provides the keyword REFERENCE_GRID |
| CRegularKernel | |
| CSphericalKDEGridTools | |
| CSumOfKernels | |
| CUniversalVonMisses | |
| CVonMissesKernelParams | |
| ►Nisdb | |
| CBAIES | Provides the keyword BAIES |
| 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 | 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 |
| 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 |
| CAbs | |
| CAcos | |
| CAdd | |
| CAddConstant | |
| CAsin | |
| CAtan | |
| CAtan2 | |
| CCeil | |
| CConstant | |
| CCos | |
| CCosh | |
| CCot | |
| CCsc | |
| CCube | |
| CCustom | |
| CDelta | |
| CDivide | |
| CErf | |
| CErfc | |
| CExp | |
| CFloor | |
| CLog | |
| CMax | |
| CMin | |
| CMultiply | |
| CMultiplyConstant | |
| CNandelta | |
| CNegate | |
| CPower | |
| CPowerConstant | |
| CReciprocal | |
| CSec | |
| CSelect | |
| CSin | |
| CSinh | |
| CSqrt | |
| CSquare | |
| CStep | |
| CSubtract | |
| CTan | |
| CTanh | |
| CVariable | |
| 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 |
| ►Nliquid_crystal | |
| CFerroNematicOrder | Provides the keyword FERRONEMATIC_ORDER |
| CNematicOrder | Provides the keyword NEMATIC_ORDER |
| ►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 |
| CDissimilarities | |
| CInputVectors | |
| CInvertMatrix | Provides the keyword INVERT_MATRIX |
| CMatrixForceIndexInput | |
| CMatrixOperationBase | |
| CMatrixProduct | |
| CMatrixTimesMatrix | |
| CMatrixTimesMatrixInput | |
| CMatrixTimesVector | Provides the keyword MATRIX_VECTOR_PRODUCT |
| CMatrixTimesVectorBase | |
| CMatrixTimesVectorData | |
| CMatrixTimesVectorInput | |
| CMatrixTimesVectorOutput | |
| CMatrixTimesVectorProper | |
| CMatrixTimesVectorRowSums | |
| COuterProduct | Provides the keyword OUTER_PRODUCT |
| COuterProductBase | |
| COuterProductInput | |
| COutputProductFunc | |
| COutputProductMax | |
| COutputProductMin | |
| 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())> > | |
| ►Nmetatomic | |
| ►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 |
| CMetatomicPlumedAction | Provides the keyword <a href="../../user-doc/html/_"_m_e_t_a_t_o_m_i_c.html"> "METATOMIC |
| ►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_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 |
| ►NOpenACC | |
| CfromToDataHelper | This little tool is a RAII helper to put and remove data on the device |
| ►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 | |
| 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 |
| CMatrixProductDiagonalInput | |
| CNormalizedEuclideanDistance | Provides the keyword NORMALIZED_EUCLIDEAN_DISTANCE |
| ►Ns2cm | |
| CS2ContactModel | Provides the keyword S2CM |
| ►Nsasa | |
| CColvar | 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 |
| 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 |
| CflexibleMemory | This is a sort of compact std::vector<std::vector<T>> |
| CParabetaRMSD | Provides the keyword PARABETARMSD |
| CSecondaryStructureBase | Base action for calculating things like AlphRMSD, AntibetaRMSD, etc |
| ►CSecondaryStructureDRMSDInput | |
| CpairDistance | |
| CSecondaryStructureRMSDInput | |
| ►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 | |
| CData | |
| CexponentialSwitch | |
| CfastgaussianSwitch | |
| CfixedRational | |
| CgaussianSwitch | |
| ►CleptonSwitch | |
| CfuncAndDeriv | Lepton expression |
| CnativeqSwitch | |
| Crational | |
| CsmapSwitch | |
| CSwitch | |
| CSwitchInterface | |
| CSwitchInterface_lepton | |
| 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 |
| CThreeBodyGFunctionsInput | |
| ►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 | |
| CActionWithVirtualAtom | Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) |
| 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 | Small class to compute fermi switching function |
| 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 | Abstract base class for implementing biases the extents the normal Bias.h class to include functions related to the variational approach |
| CVesDeltaF | Provides the keyword VES_DELTA_F |
| CVesLinearExpansion | Provides the keyword VES_LINEAR_EXPANSION |
| CVesTools | |
| CWaveletGrid | |
| CWellTemperedModifer | |
| ►Nvolumes | |
| CActionVolume | This is the abstract base class to use for implementing a new way of defining a particular region of the simulation box |
| CDensity | Provides the keyword DENSITY |
| CVolumeAround | |
| CVolumeCavity | |
| CVolumeData | |
| CVolumeInCylinder | |
| CVolumeInEnvelope | |
| CVolumeInput | |
| CVolumeInSphere | |
| ►CVolumeOutput | |
| CRefderHelper | |
| CVolumeShortcut | |
| CVolumeTetrapore | |
| ►Nwham | |
| CWham | Provides the keyword WHAM |
| CWhamHistogram | Provides the keyword WHAM_HISTOGRAM |
| CWhamWeights | Provides the keyword WHAM_WEIGHTS |
| ►Nxdrfile | |
| Ct_trnheader | |
| ►CXDR | |
| Cxdr_ops | |
| CXDRFILE | Contents of the abstract XDRFILE data structure |
| CAccelerator | |
| CAction | Base class for all the input Actions |
| CActionAnyorder | Action used to create a PLMD::Action that can go both before and after ActionSetup actions |
| CActionAtomistic | Action used to create objects that access the positions of the atoms from the MD code |
| CActionForInterface | |
| CActionOptions | This class is used to bring the relevant information to the Action constructor |
| CActionPilot | This is used to create PLMD::Action objects that are run with some set frequency |
| 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 | Action used to create a PLMD::Action that do something during setup only e.g |
| CActionShortcut | Action used to create a command that expands to multiple PLMD::Action commands when read in during input |
| CActionToGetData | Provides the keyword GET |
| CActionToPutData | Provides the keyword PUT |
| CActionWithArguments | |
| CActionWithMatrix | |
| CActionWithValue | Used to create a PLMD::Action that has some scalar or vectorial output that may or may not have some derivatives |
| CActionWithVector | |
| CActionWithVirtualAtom | Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) |
| CAngle | Class to compute angles |
| CArgumentBookeepingHolder | |
| CArgumentsBookkeeping | |
| CAtomDistribution | Tested in regtest/tools/rt-make-AtomicDistribution Acts as a template for any distribution |
| CAtomNumber | Simple class to store the index of an atom |
| 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 | Class taking care of bibliography |
| CCLTool | 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 |
| CCLToolMain | Class providing cmd() access to command line tools |
| CCLToolOptions | |
| CCLToolRegister | Same as ActionRegister, but for CLTools |
| CCLToolRegisterPointers | |
| CColvar | 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 |
| ►CColvarOutput | |
| CDerivHelper | |
| CVirialHelper | |
| ►CCommunicator | Class containing wrappers to MPI |
| 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 | Class taking care of dynamic loading |
| CEnsureGlobalDLOpen | RAII helper for promoting RTLD_LOCAL loaded objects to RTLD_GLOBAL |
| ►CDomainDecomposition | |
| CDomainComms | |
| CERMSD | A class that implements ERMSD calculations |
| ►CException | Class to deal with Plumed runtime errors |
| 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 |
| CfileDeleter | |
| CfileParser | |
| CfileTraj | Atomic distribution from a trajectory file |
| CFlexibleBin | |
| CForceIndexHolder | |
| CForceInput | |
| CForceOutput | |
| 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 | A class for calculating whether or not values are within a given range using : \( \sum_i \int_a^b G( s_i, \sigma*(b-a) ) \) |
| ►CIFile | Class for input files |
| CField | |
| CKernelFunctions | |
| ►CKeywords | This class holds the keywords and their documentation |
| Ccomponent | |
| CkeyInfo | |
| CKeyType | This class lets me pass keyword types easily |
| CLatticeReduction | Class implementing algorithms for lattice reduction |
| CLeptonCall | |
| ►CLinkCells | A class for doing link cells |
| CCellCollection | This struct contains the configuration of cells |
| CLog | Class containing the log stream |
| CLoopUnroller | Utiliy class for loop unrolling |
| ►CMatrix | This class stores a full matrix and allows one to do some simple matrix operations |
| CopenAccVectorHelper | |
| CMatrixElementOutput | |
| ►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 |
| 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 |
| CNeighborList | A class that implements neighbor lists from two lists or a single list of atoms |
| ►COFile | Class for output files |
| CField | Class identifying a single field for fielded output |
| CParallelActionsInput | |
| CParallelActionsOutput | |
| CParallelTaskManager | |
| CPbc | |
| CPbcAction | Provides the keyword PBC |
| CPDB | Minimalistic pdb parser |
| 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 | |
| CrepliedTrajectory | Decorator for replicate the atomic distribution |
| CRequiredMatrixElements | |
| CRequiredMatrixElementsUpdater | |
| CRMSD | 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 |
| 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 | Small class to compute switching functions |
| CSwitchingFunctionAccelerable | Small class to compute switching functions |
| CTargetDist | |
| CTensorGenericAux | Small class to contain local utilities |
| CTensorTyped | Class implementing fixed size matrices of doubles |
| CtheLine | A wiggly line of atoms |
| CtiledSimpleCubic | |
| ►CTokenizedLine | This class abstracts the input line in tokens |
| CpresentAndFound | |
| ►CTools | Empty class which just contains several (static) tools |
| ►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 | Class to compute torsional angles |
| CTrajectoryParser | |
| CTree | |
| CtwoGlobs | Atom randomly distribuited between two not overlapping a spheres |
| ►CTypesafePtr | Class to deal with propoagation of typesafe pointers |
| CSizeLike | Small structure used to pass elements of a shape initializer_list |
| CuniformCube | |
| CuniformSphere | Atom randomly distribuited in a sphere |
| CUniformSphericalVector | |
| CUnits | Small utility class that contains information about units |
| CValue | A class for holding the value of a function together with its derivatives |
| CVectorTyped | Class implementing fixed size vectors of doubles |
| CView | A not-owning view for generic data |
| CView2D | A not-owning view for accessing array witha 2D interface |
| 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 |
| Cbeadkde | Provides the keyword KDE_BEADS |
| CBesselShortcut | Provides the keyword BESSEL |
| CBetweenShortcut | Provides the keyword BETWEEN |
| Cbmap | Provides the keyword BRIDGE_MATRIX |
| Ccmap | Provides the keyword CONTACT_MATRIX_PROPER |
| Ccolv | Provides the keyword SECONDARY_STRUCTURE_DRMSD |
| 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 |
| Cdiscretekde | Provides the keyword KDE_DISCRETE |
| Cdissims | Provides the keyword DISSIMILARITIES |
| CDistance | Provides the keyword DISTANCE2 |
| CDistanceMulti | Provides the keyword DISTANCE_VECTOR |
| CDistanceShortcut | Provides the keyword DISTANCE |
| Cdmap | Provides the keyword DISTANCE_MATRIX |
| 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 |
| Cflatfkde | Provides the keyword KDE_FULLCOVAR |
| Cflatkde | Provides the keyword KDE_KERNELS |
| CGridCustom | Provides the keyword CUSTOM_GRID |
| Chbpmap | Provides the keyword HBPAMM_MATRIX |
| CHighestShortcut | Provides the keyword HIGHEST |
| Chmap | Provides the keyword HBOND_MATRIX |
| 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 |
| CMolInfo | Provides the keyword MOLINFO |
| CMomentsShortcut | Provides the keyword MOMENTS |
| CMoreThanShortcut | Provides the keyword MORE_THAN |
| Cmtimes | Provides the keyword MATRIX_PRODUCT |
| Cmycp | Provides the keyword MATRIX_VECTOR_PRODUCT_PROPER |
| Cmycr | Provides the keyword MATRIX_VECTOR_PRODUCT_ROWSUMS |
| Cnhinp | Provides the keyword NEIGHBORS_NHIGH |
| Cnlinp | Provides the keyword NEIGHBORS_NLOW |
| Cohinp | Provides the keyword NEIGHBORS_1HIGH |
| Colinp | Provides the keyword NEIGHBORS_1LOW |
| COneargHighest | Provides the keyword HIGHEST_ONEARG |
| COPESmetad_c | Provides the keyword OPES_METAD |
| COPESmetad_e | Provides the keyword OPES_METAD_EXPLORE |
| Copfunc | Provides the keyword OUTER_PRODUCT_FUNC |
| Copmax | Provides the keyword OUTER_PRODUCT_MAX |
| Copmin | Provides the keyword OUTER_PRODUCT_MIN |
| 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 |
| Cqpop | Provides the keyword QUATERNION_PRODUCT_MATRIX |
| CQuaternionMulti | Provides the keyword QUATERNION_VECTOR |
| CQuaternionShortcut | Provides the keyword QUATERNION |
| CScalarBessel | Provides the keyword BESSEL_SCALAR |
| CScalarBetween | Provides the keyword BETWEEN_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 |
| CScalarLessThan | Provides the keyword LESS_THAN_SCALAR |
| CScalarMoments | Provides the keyword MOMENTS_SCALAR |
| CScalarMoreThan | Provides the keyword MORE_THAN_SCALAR |
| CScalarPiecewise | Provides the keyword PIECEWISE_SCALAR |
| CScalarSort | Provides the keyword SORT_SCALAR |
| CSingleargMoments | Provides the keyword MOMENTS_ONEARG |
| CSortShortcut | Provides the keyword SORT |
| CSpHarmShortcut | Provides the keyword SPHERICAL_HARMONIC |
| Csphericalkde | Provides the keyword SPHERICAL_KDE |
| Ctmap | Provides the keyword TOPOLOGY_MATRIX |
| 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 |
| CVola | Provides the keyword AROUND_CALC |
| CVolc | Provides the keyword INCYLINDER_CALC |
| CVolCav | Provides the keyword CAVITY_CALC |
| Cvolenv | Provides the keyword INENVELOPE_CALC |
| CVols | Provides the keyword INSPHERE_CALC |
| CVolTet | Provides the keyword TETRAHEDRALPORE_CALC |
| 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 |
1.13.2