| ▼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 |
| CHistogram | Provides the keyword HISTOGRAM |
| ►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 |
| CExternal | Provides the keyword EXTERNAL |
| CLWalls | Provides the keyword LOWER_WALLS |
| ►CMetaD | Provides the keyword METAD |
| CGaussian | |
| CMovingRestraint | Provides the keyword MOVINGRESTRAINT |
| CRestraint | Provides the keyword RESTRAINT |
| CUWalls | Provides the keyword UPPER_WALLS |
| ►Ncltools | |
| CCLToolSumHills | |
| CDriver | |
| CGenTemplate | |
| CInfo | |
| 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 |
| CPathMSD | Provides the keyword PATHMSD |
| ►CPathMSDBase | |
| CImagePath | This class is a general container for path stuff |
| CimgOrderByDist | |
| CimgOrderBySimilarity | |
| CPropertyMap | Provides the keyword PROPERTYMAP |
| CRMSD | Provides the keyword RMSD |
| CTemplate | Provides the keyword TEMPLATE |
| CTorsion | Provides the keyword TORSION |
| CVolume | Provides the keyword VOLUME |
| ►Nfunction | |
| CCombine | Provides the keyword COMBINE |
| 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 |
| CDumpProjections | Provides the keyword DUMPPROJECTIONS |
| 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 |
| ►Nmanyrestraints | |
| CManyRestraintsBase | |
| CSphere | Provides the keyword SPHERICAL_RESTRAINT |
| ►Nmulticolvar | |
| CActionVolume | This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box |
| CAlphaBeta | Provides the keyword ALPHABETA |
| CAngles | Provides the keyword ANGLES |
| CBridge | Provides the keyword BRIDGE |
| CCoordinationNumbers | Provides the keyword COORDINATIONNUMBER |
| CDensity | Provides the keyword DENSITY |
| CDHEnergy | |
| CDistances | Provides the keyword DISTANCES |
| CMoments | |
| 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 | |
| CMultiColvarFunction | |
| CStoreCentralAtomsVessel | |
| CStoreColvarVessel | |
| CVolumeAround | Provides the keyword AROUND |
| ►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 | |
| 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::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\) |
| CHistogram | |
| CLessThan | |
| CMean | |
| CMin | |
| CMoreThan | |
| CShortcutVessel | |
| CSum | |
| 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 |
| 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 | |
| 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 |
| CRequest | |
| CStatus | |
| CCS2Backbone | Provides the keyword CS2BACKBONE |
| CDLLoader | Class taking care of dynamic loading |
| CDRMSD | A class that implements DRMSD calculations |
| CDynamicList | A class for storing a list that changes which members are active as a function of time |
| CException | Class to deal with Plumed runtime errors |
| CExchangePatterns | |
| ►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 |
| CLog | Class containing the log stream |
| 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 |
| CMPI_Comm | Surrogate of MPI types 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 |
| COptimalAlignment | A class that is intended to include or combine various optimal alignment algorithms |
| CPbc | |
| CPDB | Minimalistic pdb parser |
| CPlumed | C++ wrapper for plumed |
| CPlumedMain | Main plumed object |
| CPlumedMainInitializer | Static object which registers Plumed |
| CProbWeight | |
| CRandom | |
| 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 |
| CSetupMolInfo | |
| 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 in the form In the future we might extend it so as to be set using a string: void set(std::string); which can then be parsed for more complex stuff, e.g |
| 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) |
1.8.8
