| ►NPLMD | |
| ►Nanalysis | |
| CAnalysis | 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 |
| CAnalysisWithLandmarks | |
| CClassicalMultiDimensionalScaling | Provides the keyword CLASSICAL_MDS |
| CClassicalScaling | |
| CCommittor | Provides the keyword COMMITTOR |
| CCopyAllFrames | |
| CHistogram | Provides the keyword HISTOGRAM |
| CLandmarkRegister | |
| CLandmarkSelectionBase | |
| CLandmarkSelectionOptions | |
| ►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 |
| ►CMetaD | Provides the keyword METAD |
| CGaussian | |
| CMovingRestraint | Provides the keyword MOVINGRESTRAINT |
| ►CPBMetaD | Provides the keyword PBMETAD |
| CGaussian | |
| CRestraint | Provides the keyword RESTRAINT |
| CUWalls | Provides the keyword UPPER_WALLS |
| ►Ncltools | |
| CCLToolSumHills | |
| CDriver | |
| CGenTemplate | |
| CInfo | |
| Ckt | |
| CManual | |
| CSimpleMD | |
| ►Ncolvar | |
| CAngle | Provides the keyword ANGLE |
| CCell | Provides the keyword CELL |
| CColvarFake | Provides the keyword FAKE |
| CConstant | Provides the keyword CONSTANT |
| CContactMap | Provides the keyword CONTACTMAP |
| CCoordination | Provides the keyword COORDINATION |
| CCoordinationBase | |
| CDHEnergy | Provides the keyword DHENERGY |
| CDipole | Provides the keyword DIPOLE |
| CDistance | Provides the keyword DISTANCE |
| CDRMSD | Provides the keyword DRMSD |
| CEnergy | Provides the keyword ENERGY |
| CGyration | Provides the keyword GYRATION |
| CMultiRMSD | Provides the keyword MULTI-RMSD |
| CNOE | Provides the keyword NOE |
| CPathMSD | Provides the keyword PATHMSD |
| ►CPathMSDBase | |
| CImagePath | This class is a general container for path stuff |
| CimgOrderByDist | |
| CimgOrderBySimilarity | |
| CPCARMSD | Provides the keyword PCARMSD |
| CPosition | Provides the keyword POSITION |
| CPropertyMap | Provides the keyword PROPERTYMAP |
| CPuckering | Provides the keyword PUCKERING |
| CRMSD | Provides the keyword RMSD |
| CTemplate | Provides the keyword TEMPLATE |
| CTorsion | Provides the keyword TORSION |
| CVolume | Provides the keyword VOLUME |
| ►Ncrystallisation | |
| CGradient | Provides the keyword GRADIENT |
| CGradientVessel | |
| ►Ncrystallization | |
| CDFSBasic | Provides the keyword DFSCLUSTERING |
| CDFSClusterDiameter | Provides the keyword DFSCLUSTERDIAMETER |
| CDFSClustering | |
| CDFSMaxCluster | Provides the keyword DFSMAXCLUSTER |
| CDFSNumberOfClusters | Provides the keyword DFSNUMEROFCLUSTERS |
| CFccubic | Provides the keyword FCCUBIC |
| CLOCAL_Q3 | Provides the keyword LOCAL_Q3 |
| CLOCAL_Q4 | Provides the keyword LOCAL_Q4 |
| CLOCAL_Q6 | Provides the keyword LOCAL_Q6 |
| CLocalSteinhardt | |
| CMoleculeOrientation | Provides the keyword MOLECULES |
| CMoleculePlane | Provides the keyword PLANES |
| COrientationSphere | |
| CQ3 | Provides the keyword Q3 |
| CQ4 | Provides the keyword Q4 |
| CQ6 | Provides the keyword Q6 |
| CSimpleCubic | Provides the keyword SIMPLECUBIC |
| CSMAC | Provides the keyword SMAC |
| CSteinhardt | |
| CTetrahedral | Provides the keyword TETRAHEDRAL |
| CVectorMean | |
| CVectorMultiColvar | |
| CVectorSum | |
| ►Nfunction | |
| CCombine | Provides the keyword COMBINE |
| CEnsemble | Provides the keyword ENSEMBLE |
| CFilesHandler | |
| ►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 |
| CMatheval | Provides the keyword MATHEVAL |
| CPiecewise | Provides the keyword PIECEWISE |
| CSort | Provides the keyword SORT |
| CTarget | Provides the keyword TARGET |
| ►Ngeneric | |
| 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 |
| CDumpProjections | Provides the keyword DUMPPROJECTIONS |
| CEffectiveEnergyDrift | Provides the keyword EFFECTIVE_ENERGY_DRIFT |
| CFitToTemplate | Provides the keyword FIT_TO_TEMPLATE |
| CFlush | Provides the keyword FLUSH |
| CGroup | Provides the keyword GROUP |
| CInclude | Provides the keyword INCLUDE |
| CPrint | Provides the keyword PRINT |
| CRandomExchanges | Provides the keyword RANDOM_EXCHANGES |
| CRead | Provides the keyword READ |
| CTime | Provides the keyword TIME |
| CWholeMolecules | Provides the keyword WHOLEMOLECULES |
| CWrapAround | Provides the keyword WRAPAROUND |
| ►Nmanyrestraints | |
| CManyRestraintsBase | |
| CUWalls | Provides the keyword UWALLS |
| ►Nmapping | |
| CAltMin | |
| CMapping | |
| CPath | Provides the keyword PATH |
| CPathBase | |
| CPCAVars | Provides the keyword PCAVARS |
| CPropertyMap | Provides the keyword GPROPERTYMAP |
| CSpathVessel | |
| CZpathVessel | |
| ►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 | |
| 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 | |
| CActionVolume | This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box |
| CAdjacencyMatrixAction | |
| CAdjacencyMatrixVessel | |
| CAlphaBeta | Provides the keyword ALPHABETA |
| CAngles | Provides the keyword ANGLES |
| CAtomValuePack | |
| CBridge | Provides the keyword BRIDGE |
| CBridgedMultiColvarFunction | |
| CCatomPack | |
| CCoordinationNumbers | Provides the keyword COORDINATIONNUMBER |
| CDensity | Provides the keyword DENSITY |
| CDihedralCorrelation | Provides the keyword DIHCOR |
| CDistances | Provides the keyword DISTANCES |
| CDumpMultiColvar | Provides the keyword DUMPMULTICOLVAR |
| CFilterBetween | Provides the keyword MFILTER_BETWEEN |
| CFilterLess | Provides the keyword MFILTER_LESS |
| CFilterMore | Provides the keyword MFILTER_MORE |
| CInPlaneDistances | Provides the keyword INPLANEDISTANCES |
| CLocalAverage | Provides the keyword LOCAL_AVERAGE |
| CMultiColvar | This is the abstract base class to use for creating distributions of colvars and functions thereof, whtin it there is information as to how to go implementing these types of actions |
| CMultiColvarBase | |
| CMultiColvarDensity | Provides the keyword MULTICOLVARDENS |
| CMultiColvarFilter | 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 |
| CMultiColvarFunction | |
| CNumberOfLinks | Provides the keyword NLINKS |
| CSprint | Provides the keyword SPRINT |
| CTorsions | Provides the keyword TORSIONS |
| CVolumeAround | Provides the keyword AROUND |
| CVolumeCavity | Provides the keyword CAVITY |
| CVolumeGradientBase | |
| CVolumeInCylinder | Provides the keyword INCYLINDER |
| CVolumeTetrapore | Provides the keyword TETRAHEDRALPORE |
| CXDistances | Provides the keyword XDISTANCES |
| CXYDistances | Provides the keyword XYDISTANCES |
| ►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 |
| CMolInfo | Provides the keyword MOLINFO |
| CRestart | Provides the keyword RESTART |
| CUnits | Provides the keyword UNITS |
| ►Nvatom | |
| CCenter | Provides the keyword CENTER |
| CCOM | Provides the keyword COM |
| CGhost | Provides the keyword GHOST |
| ►Nvesselbase | |
| CActionWithInputVessel | |
| CActionWithVessel | This is used to create PLMD::Action objects that are computed by calculating the same function multiple times |
| CBetween | |
| CBridgeVessel | This class allows you to calculate the vessel in one ActionWithVessel |
| CFunctionVessel | Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\) |
| CHighest | |
| CHistogram | |
| CLessThan | |
| CLowest | |
| CMax | |
| CMean | |
| CMin | |
| CMoments | |
| CMoreThan | |
| COrderingVessel | |
| CShortcutVessel | |
| CStoreDataVessel | 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 |
| CSum | |
| CValueVessel | |
| CVessel | |
| CVesselOptions | This class is used to pass the input to Vessels |
| CVesselRegister | |
| CAction | Base class for all the input Actions |
| CActionAtomistic | Action used to create objects that access the positions of the atoms from the MD code |
| 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 |
| 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 |
| CActionWithArguments | This is used to create PLMD::Action objects that take the output from some other Action as input |
| CActionWithValue | Used to create a PLMD::Action that has some scalar or vectorial output that may or may not have some derivatives |
| CActionWithVirtualAtom | Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) |
| CAngle | Class to compute angles |
| CArgumentOnlyDistance | |
| CAtomNumber | Simple class to store the index of an atom |
| ►CAtoms | Class containing atom related quantities from the MD code |
| CDomainDecomposition | |
| CBiasRepresentation | This class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias |
| CBiasWeight | |
| CCH3Shifts | Provides the keyword CH3SHIFTS |
| CCInterpolation | |
| 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 |
| 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 |
| ►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 |
| CCS2Backbone | Provides the keyword CS2BACKBONE |
| CDirection | |
| CDLLoader | Class taking care of dynamic loading |
| CDotProductDistance | |
| CDRMSD | |
| CDynamicList | A class for storing a list that changes which members are active as a function of time |
| CEuclideanDistance | |
| CException | Class to deal with Plumed runtime errors |
| CExchangePatterns | |
| CFakeFrame | |
| ►CFileBase | Base class for dealing with files |
| CFieldBase | Internal tool |
| CFlexibleBin | |
| CGREX | |
| CGrid | |
| 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 | |
| CIMD | Provides the keyword IMD |
| CInterpolateBicubic | |
| CInterpolateCubic | |
| CKearsley | |
| 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 |
| CLinkCells | A class for doing link cells |
| CLog | Class containing the log stream |
| CLoopUnroller | Utiliy class for loop unrolling |
| CMahalanobisDistance | |
| 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 |
| CMDAtomsBase | Class containing interface to MDAtomsTyped |
| CMDAtomsTyped | Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED |
| CMetricRegister | |
| 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 |
| CMultiDomainRMSD | |
| CMultiReferenceBase | |
| CMultiValue | |
| CNeighborList | A class that implements neighbor lists from two lists or a single list of atoms |
| CNormalizedEuclideanDistance | |
| ►COFile | Class for output files |
| CField | Class identifying a single field for fielded output |
| COpenMP | |
| COptimalAlignment | A class that is intended to include or combine various optimal alignment algorithms |
| COptimalRMSD | |
| CPbc | |
| CPDB | Minimalistic pdb parser |
| CPlumed | C++ wrapper for plumed |
| CPlumedMain | Main plumed object |
| CPlumedMainInitializer | Static object which registers Plumed |
| CPointWiseMapping | |
| CProbWeight | |
| CRandom | |
| CRDC | Provides the keyword RDC |
| CReferenceArguments | In many applications (e.g |
| CReferenceAtoms | In many applications (e.g |
| CReferenceConfiguration | Abstract base class for calculating the distance from a reference configuration |
| CReferenceConfigurationOptions | |
| CReferenceValuePack | |
| 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 |
| CRMSDBase | |
| 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 |
| CSetupMolInfo | |
| CSimpleRMSD | |
| CSingleDomainRMSD | |
| CSparseGrid | |
| ►CStopwatch | Class implementing stopwatch to time execution |
| CTime | Class to hold the value of absolute time |
| CWatch | Class to store a single stopwatch |
| CSwitchingFunction | Small class to compure switching functions |
| CTargetDist | |
| CTensorChecks | Small auxiliary class |
| CTensorGeneric | Class implementing fixed size matrices of doubles |
| CTools | Empty class which just contains several (static) tools |
| CTorsion | Class to compute torsional angles |
| CUnits | Small utility class that contains information about units |
| CValue | A class for holding the value of a function together with its derivatives |
| CVectorChecks | Small auxiliary class |
| CVectorGeneric | Class implementing fixed size vectors of doubles |
| CWeightBase | |
| CWithCmd | Base for classes with cmd() method |
| Cplumed | Main plumed object |
| Cplumed_function_holder | Holder for function pointer |
| Cplumed_plumedmain_function_holder | Container for plumedmain function pointers (create, cmd and finalize) |
1.8.10
