| ►CPLMD::Action | Base class for all the input Actions |
| ►CPLMD::ActionAtomistic | Action used to create objects that access the positions of the atoms from the MD code |
| ►CPLMD::ActionWithVirtualAtom | Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) |
| CPLMD::vatom::Center | Provides the keyword CENTER |
| CPLMD::vatom::COM | Provides the keyword COM |
| CPLMD::vatom::Ghost | Provides the keyword GHOST |
| ►CPLMD::Colvar | This is the abstract base class to use for implementing new collective variables, within it there is information as to how to go about implementing a new CV |
| CPLMD::colvar::Angle | Provides the keyword ANGLE |
| CPLMD::colvar::Cell | Provides the keyword CELL |
| CPLMD::colvar::ColvarFake | Provides the keyword FAKE |
| CPLMD::colvar::Constant | Provides the keyword CONSTANT |
| CPLMD::colvar::ContactMap | Provides the keyword CONTACTMAP |
| ►CPLMD::colvar::CoordinationBase | |
| CPLMD::colvar::Coordination | Provides the keyword COORDINATION |
| CPLMD::colvar::DHEnergy | Provides the keyword DHENERGY |
| CPLMD::colvar::Dipole | Provides the keyword DIPOLE |
| CPLMD::colvar::Distance | Provides the keyword DISTANCE |
| CPLMD::colvar::DRMSD | Provides the keyword DRMSD |
| CPLMD::colvar::Energy | Provides the keyword ENERGY |
| CPLMD::colvar::Gyration | Provides the keyword GYRATION |
| ►CPLMD::colvar::PathMSDBase | |
| CPLMD::colvar::PathMSD | Provides the keyword PATHMSD |
| CPLMD::colvar::PropertyMap | Provides the keyword PROPERTYMAP |
| CPLMD::colvar::RMSD | Provides the keyword RMSD |
| CPLMD::colvar::Template | Provides the keyword TEMPLATE |
| CPLMD::colvar::Torsion | Provides the keyword TORSION |
| CPLMD::colvar::Volume | Provides the keyword VOLUME |
| CPLMD::generic::DumpAtoms | Provides the keyword DUMPATOMS |
| CPLMD::generic::Group | Provides the keyword GROUP |
| CPLMD::generic::WholeMolecules | Provides the keyword WHOLEMOLECULES |
| CPLMD::IMD | Provides the keyword IMD |
| ►CPLMD::manyrestraints::ManyRestraintsBase | |
| CPLMD::manyrestraints::Sphere | Provides the keyword SPHERICAL_RESTRAINT |
| ►CPLMD::multicolvar::ActionVolume | This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box |
| CPLMD::multicolvar::VolumeAround | Provides the keyword AROUND |
| ►CPLMD::multicolvar::MultiColvarBase | |
| ►CPLMD::multicolvar::MultiColvar | 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 |
| CPLMD::multicolvar::AlphaBeta | Provides the keyword ALPHABETA |
| CPLMD::multicolvar::Angles | Provides the keyword ANGLES |
| CPLMD::multicolvar::Bridge | Provides the keyword BRIDGE |
| CPLMD::multicolvar::CoordinationNumbers | Provides the keyword COORDINATIONNUMBER |
| CPLMD::multicolvar::Density | Provides the keyword DENSITY |
| CPLMD::multicolvar::Distances | Provides the keyword DISTANCES |
| CPLMD::multicolvar::MultiColvarFunction | |
| ►CPLMD::secondarystructure::SecondaryStructureRMSD | Base action for calculating things like AlphRMSD, AntibetaRMSD, etc |
| CPLMD::secondarystructure::AlphaRMSD | Provides the keyword ALPHARMSD |
| CPLMD::secondarystructure::AntibetaRMSD | Provides the keyword ANTIBETARMSD |
| CPLMD::secondarystructure::ParabetaRMSD | Provides the keyword PARABETARMSD |
| CPLMD::SetupMolInfo | |
| ►CPLMD::ActionPilot | This is used to create PLMD::Action objects that are run with some set frequency |
| ►CPLMD::analysis::Analysis | This is the abstract base class to use for implementing new methods for analyzing the trajectory, within it there is information as to how to go about implementing a new analysis method |
| CPLMD::analysis::Histogram | Provides the keyword HISTOGRAM |
| ►CPLMD::bias::Bias | This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias |
| CPLMD::bias::ABMD | Provides the keyword ABMD |
| CPLMD::bias::BiasValue | Provides the keyword BIASVALUE |
| CPLMD::bias::External | Provides the keyword EXTERNAL |
| CPLMD::bias::LWalls | Provides the keyword LOWER_WALLS |
| CPLMD::bias::MetaD | Provides the keyword METAD |
| CPLMD::bias::MovingRestraint | Provides the keyword MOVINGRESTRAINT |
| CPLMD::bias::Restraint | Provides the keyword RESTRAINT |
| CPLMD::bias::UWalls | Provides the keyword UPPER_WALLS |
| CPLMD::generic::Debug | Provides the keyword DEBUG |
| CPLMD::generic::DumpAtoms | Provides the keyword DUMPATOMS |
| CPLMD::generic::DumpDerivatives | Provides the keyword DUMPDERIVATIVES |
| CPLMD::generic::DumpForces | Provides the keyword DUMPFORCES |
| CPLMD::generic::DumpProjections | Provides the keyword DUMPPROJECTIONS |
| CPLMD::generic::Flush | Provides the keyword FLUSH |
| CPLMD::generic::Print | Provides the keyword PRINT |
| CPLMD::generic::Read | Provides the keyword READ |
| CPLMD::generic::WholeMolecules | Provides the keyword WHOLEMOLECULES |
| CPLMD::IMD | Provides the keyword IMD |
| CPLMD::manyrestraints::ManyRestraintsBase | |
| ►CPLMD::ActionSetup | Action used to create a PLMD::Action that do something during setup only e.g |
| CPLMD::setup::Load | Provides the keyword LOAD |
| CPLMD::setup::Restart | Provides the keyword RESTART |
| CPLMD::setup::Units | Provides the keyword UNITS |
| CPLMD::SetupMolInfo | |
| ►CPLMD::ActionWithArguments | This is used to create PLMD::Action objects that take the output from some other Action as input |
| CPLMD::analysis::Analysis | This is the abstract base class to use for implementing new methods for analyzing the trajectory, within it there is information as to how to go about implementing a new analysis method |
| CPLMD::bias::Bias | This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias |
| ►CPLMD::function::Function | This is the abstract base class to use for implementing new CV function, within it there is information as to how to go about implementing a new function |
| CPLMD::function::Combine | Provides the keyword COMBINE |
| CPLMD::function::FuncPathMSD | Provides the keyword FUNCPATHMSD |
| CPLMD::function::FuncSumHills | Provides the keyword FUNCSUMHILLS |
| CPLMD::function::Matheval | Provides the keyword MATHEVAL |
| CPLMD::function::Piecewise | Provides the keyword PIECEWISE |
| CPLMD::function::Sort | Provides the keyword SORT |
| CPLMD::function::Target | Provides the keyword TARGET |
| CPLMD::generic::DumpDerivatives | Provides the keyword DUMPDERIVATIVES |
| CPLMD::generic::DumpForces | Provides the keyword DUMPFORCES |
| CPLMD::generic::DumpProjections | Provides the keyword DUMPPROJECTIONS |
| CPLMD::generic::Print | Provides the keyword PRINT |
| ►CPLMD::ActionWithValue | Used to create a PLMD::Action that has some scalar or vectorial output that may or may not have some derivatives |
| CPLMD::bias::Bias | This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias |
| CPLMD::Colvar | This is the abstract base class to use for implementing new collective variables, within it there is information as to how to go about implementing a new CV |
| CPLMD::function::Function | This is the abstract base class to use for implementing new CV function, within it there is information as to how to go about implementing a new function |
| CPLMD::generic::Read | Provides the keyword READ |
| CPLMD::generic::Time | Provides the keyword TIME |
| CPLMD::manyrestraints::ManyRestraintsBase | |
| CPLMD::multicolvar::ActionVolume | This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box |
| CPLMD::multicolvar::MultiColvarBase | |
| CPLMD::secondarystructure::SecondaryStructureRMSD | Base action for calculating things like AlphRMSD, AntibetaRMSD, etc |
| CPLMD::generic::Include | Provides the keyword INCLUDE |
| CPLMD::generic::RandomExchanges | Provides the keyword RANDOM_EXCHANGES |
| ►CPLMD::vesselbase::ActionWithVessel | This is used to create PLMD::Action objects that are computed by calculating the same function multiple times |
| CPLMD::manyrestraints::ManyRestraintsBase | |
| CPLMD::multicolvar::ActionVolume | This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box |
| CPLMD::multicolvar::MultiColvarBase | |
| CPLMD::secondarystructure::SecondaryStructureRMSD | Base action for calculating things like AlphRMSD, AntibetaRMSD, etc |
| CPLMD::ActionOptions | This class is used to bring the relevant information to the Action constructor |
| CPLMD::ActionRegister | Register holding all the allowed keywords |
| CPLMD::Angle | Class to compute angles |
| CPLMD::AtomNumber | Simple class to store the index of an atom |
| CPLMD::Atoms | Class containing atom related quantities from the MD code |
| CPLMD::BiasRepresentation | This class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias |
| ►CPLMD::CInterpolation | |
| CPLMD::InterpolateBicubic | |
| CPLMD::InterpolateCubic | |
| CPLMD::Citations | Class taking care of bibliography |
| ►CPLMD::CLTool | This is the abstract base class to use for implementing new command line tool, within it there is information as to how to go about implemneting a new tool |
| CPLMD::cltools::CLToolSumHills | |
| CPLMD::cltools::Driver< real > | |
| CPLMD::cltools::GenTemplate | |
| CPLMD::cltools::Info | |
| CPLMD::cltools::Manual | |
| CPLMD::cltools::SimpleMD | |
| CPLMD::CLToolOptions | |
| CPLMD::CLToolRegister | Same as ActionRegister, but for CLTools |
| ►CPLMD::Communicator | Class containing wrappers to MPI |
| CPLMD::Atoms::DomainDecomposition | |
| CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Const_row | Small utility class which just contains a pointer to the T and the row number |
| CPLMD::CS2Backbone | Provides the keyword CS2BACKBONE |
| CPLMD::DLLoader | Class taking care of dynamic loading |
| CPLMD::DRMSD | A class that implements DRMSD calculations |
| CPLMD::DynamicList< T > | A class for storing a list that changes which members are active as a function of time |
| CPLMD::DynamicList< PLMD::AtomNumber > | |
| CPLMD::DynamicList< unsigned > | |
| ►Cstd::exception | STL class |
| CPLMD::Exception | Class to deal with Plumed runtime errors |
| CPLMD::ExchangePatterns | |
| CPLMD::FileBase::FieldBase | Internal tool |
| ►CFieldBase | |
| CPLMD::IFile::Field | |
| CPLMD::OFile::Field | Class identifying a single field for fielded output |
| ►CPLMD::FileBase | Base class for dealing with files |
| CPLMD::IFile | Class for input files |
| ►CPLMD::OFile | Class for output files |
| CPLMD::Log | Class containing the log stream |
| CPLMD::function::FilesHandler | |
| CPLMD::FlexibleBin | |
| CPLMD::bias::MetaD::Gaussian | |
| ►CPLMD::Grid | |
| CPLMD::SparseGrid | |
| CPLMD::HistogramBead | A class for calculating whether or not values are within a given range using : \( \sum_i \int_a^b G( s_i, \sigma*(b-a) ) \) |
| CPLMD::colvar::PathMSDBase::ImagePath | This class is a general container for path stuff |
| CPLMD::colvar::PathMSDBase::imgOrderByDist | |
| CPLMD::colvar::PathMSDBase::imgOrderBySimilarity | |
| CPLMD::Kearsley | |
| CPLMD::KernelFunctions | |
| CPLMD::Keywords::KeyType | This class lets me pass keyword types easily |
| CPLMD::Keywords | This class holds the keywords and their documentation |
| CPLMD::LatticeReduction | Class implementing algorithms for lattice reduction |
| CPLMD::MatrixSquareBracketsAccess< T, C, I, J > | Utility class to add [][] access |
| ►CPLMD::MatrixSquareBracketsAccess< Matrix< double >, double > | |
| CPLMD::Matrix< double > | |
| ►CPLMD::MatrixSquareBracketsAccess< Matrix< int >, int > | |
| CPLMD::Matrix< int > | |
| ►CPLMD::MatrixSquareBracketsAccess< Matrix< T >, T > | |
| CPLMD::Matrix< T > | This class stores a full matrix and allows one to do some simple matrix operations |
| ►CPLMD::MatrixSquareBracketsAccess< TensorGeneric< n, m >, double > | |
| CPLMD::TensorGeneric< n, m > | Class implementing fixed size matrices of doubles |
| ►CPLMD::MDAtomsBase | Class containing interface to MDAtomsTyped |
| CPLMD::MDAtomsTyped< T > | Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED |
| CPLMD::setup::MolInfo | Provides the keyword MOLINFO |
| CPLMD::MPI_Comm | Surrogate of MPI types when MPI library is not available |
| CPLMD::NeighborList | A class that implements neighbor lists from two lists or a single list of atoms |
| CPLMD::OptimalAlignment | A class that is intended to include or combine various optimal alignment algorithms |
| CPLMD::function::FuncPathMSD::ordering | |
| CPLMD::function::FuncPathMSD::pairordering | |
| CPLMD::Pbc | |
| CPLMD::PDB | Minimalistic pdb parser |
| CPLMD::Plumed | C++ wrapper for plumed |
| Cplumed | Main plumed object |
| Cplumed_function_holder | Holder for function pointer |
| Cplumed_plumedmain_function_holder | Container for plumedmain function pointers (create, cmd and finalize) |
| CPLMD::PlumedMainInitializer | Static object which registers Plumed |
| CPLMD::Random | |
| CPLMD::Communicator::Request | |
| CPLMD::RMSD | A class that implements RMSD calculations This is a class that implements the various infrastructure to calculate the RMSD or MSD respect a given frame |
| CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row | Small utility class which just contains a pointer to the T and the row number |
| CPLMD::Communicator::Status | |
| CPLMD::Stopwatch | Class implementing stopwatch to time execution |
| CPLMD::SwitchingFunction | 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 |
| CPLMD::TargetDist | |
| CPLMD::TensorChecks | Small auxiliary class |
| CPLMD::Stopwatch::Time | Class to hold the value of absolute time |
| CPLMD::Tools | Empty class which just contains several (static) tools |
| CPLMD::Torsion | Class to compute torsional angles |
| CPLMD::Units | Small utility class that contains information about units |
| CPLMD::Value | A class for holding the value of a function together with its derivatives |
| ►Cstd::vector< T > | STL class |
| CPLMD::ActionSet | Std::vector containing the sequence of Action to be done |
| CPLMD::VectorChecks | Small auxiliary class |
| CPLMD::VectorGeneric< n > | Class implementing fixed size vectors of doubles |
| ►CPLMD::vesselbase::Vessel | |
| CPLMD::multicolvar::StoreCentralAtomsVessel | |
| ►CPLMD::multicolvar::StoreColvarVessel | |
| CPLMD::multicolvar::Moments | |
| CPLMD::vesselbase::BridgeVessel | This class allows you to calculate the vessel in one ActionWithVessel |
| ►CPLMD::vesselbase::FunctionVessel | Objects that inherit from FunctionVessel can be used (in tandem with PLMD::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\) |
| CPLMD::multicolvar::DHEnergy | |
| CPLMD::vesselbase::Between | |
| CPLMD::vesselbase::LessThan | |
| CPLMD::vesselbase::Mean | |
| CPLMD::vesselbase::Min | |
| CPLMD::vesselbase::MoreThan | |
| CPLMD::vesselbase::Sum | |
| ►CPLMD::vesselbase::ShortcutVessel | |
| CPLMD::vesselbase::Histogram | |
| CPLMD::vesselbase::VesselOptions | This class is used to pass the input to Vessels |
| CPLMD::vesselbase::VesselRegister | |
| CPLMD::Stopwatch::Watch | Class to store a single stopwatch |
| ►CPLMD::WeightBase | |
| CPLMD::BiasWeight | |
| CPLMD::ProbWeight | |
| ►CPLMD::WithCmd | Base for classes with cmd() method |
| CPLMD::CLToolMain | Class providing cmd() access to command line tools |
| CPLMD::GREX | |
| CPLMD::PlumedMain | Main plumed object |
1.8.8
