Collective Variables Module - Developer Documentation
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234567]
 CArithmeticPathCV::ArithmeticPathBase< scalar_type >
 CArithmeticPathCV::ArithmeticPathBase< cvm::real >
 CArithmeticPathImpl
 Ccolvarmodule::atomStores numeric id, mass and all mutable data for an atom, mostly used by a colvar::cvc
 CcolvardepsParent class for a member object of a bias, cv or cvc etc. containing features and their dependencies, and handling dependency resolution
 CcolvarA collective variable (main class); to be defined, it needs at least one object of a derived class of colvar::cvc; it calculates and returns a colvarvalue object
 Ccolvar::cvcColvar component (base class for collective variables)
 CcolvarbiasCollective variable bias, base class
 Ccolvarbias_restraint_movingOptions to change the restraint configuration over time (shared between centers and k moving)
 Ccolvarmodule::atom_groupGroup of atom objects, mostly used by a colvar::cvc object to gather all atomic data
 CcolvarmoduleCollective variables module (main class)
 Ccolvarparams
 CcolvarparseBase class containing parsing functions; all objects which need to parse input inherit from this
 Ccolvarproxy_atom_groupsContainer of atom group data (allow collection of aggregated atomic data)
 Ccolvarproxy
 Ccolvarproxy_atomsContainer of atomic data for processing by Colvars
 Ccolvarproxy
 Ccolvarproxy_ioMethods for data input/output
 Ccolvarproxy
 Ccolvarproxy_replicasMethods for multiple-replica communication
 Ccolvarproxy
 Ccolvarproxy_scriptMethods for scripting language interface (Tcl or Python)
 Ccolvarproxy
 Ccolvarproxy_smpMethods for SMP parallelization
 Ccolvarproxy
 Ccolvarproxy_systemMethods for accessing the simulation system (PBCs, integrator, etc)
 Ccolvarproxy
 Ccolvarproxy_tclMethods for using Tcl within Colvars
 Ccolvarproxy
 Ccolvarproxy_volmapsContainer of grid-based objects
 Ccolvarproxy
 Ccolvarscript
 CcolvarvalueValue of a collective variable: this is a metatype which can be set at runtime. By default it is set to be a scalar number, and can be treated as such in all operations (this is done by most colvar::cvc implementations)
 CLAMMPS_NS::commdata
 CneuralnetworkCV::denseLayer
 CGeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::doCompareFrameDistance
 Ccolvardeps::feature
 Ccolvardeps::feature_stateThis contains the current state of each feature for each object
 CFix
 CLAMMPS_NS::FixColvars
 CGeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
 CGeometricPathCV::GeometricPathBase< colvarvalue, cvm::real, GeometricPathCV::path_sz::S >
 Ccolvar::gspathCVColvar component: alternative path collective variable using geometry, variable s Allow any combination of existing (scalar) CVs For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html Diaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601
 CGeometricPathCV::GeometricPathBase< colvarvalue, cvm::real, GeometricPathCV::path_sz::Z >
 Ccolvar::gzpathCV
 CGeometricPathCV::GeometricPathBase< cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S >
 Ccolvar::gspathColvar component: alternative path collective variable using geometry, variable s For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html Diaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601
 CGeometricPathCV::GeometricPathBase< cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::Z >
 Ccolvar::gzpathColvar component: alternative path collective variable using geometry, variable z This should be merged with gspath in the same class by class inheritance or something else
 CGlobalMaster
 Ccolvarproxy_namdCommunication between colvars and NAMD (implementation of colvarproxy)
 Ccolvarbias_meta::hillA hill for the metadynamics bias
 CIntHash_NS::inthash_node_t
 CIntHash_NS::inthash_t
 Ccolvarmodule::matrix2d< T >Arbitrary size array (two dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions)
 Ccvm::memory_stream
 CUIestimator::n_matrix
 CUIestimator::n_vector< T >
 CUIestimator::n_vector< double >
 CUIestimator::n_vector< int >
 CUIestimator::n_vector< std::vector< double > >
 CneuralnetworkCV::neuralNetworkCompute
 Ccolvarmodule::quaternion1-dimensional vector of real numbers with four components and a quaternion algebra
 Ccolvarparse::read_block
 Ccolvarmodule::rmatrix2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector)
 Ccolvarmodule::rotationA rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion)
 Crotation_derivative< T1, T2 >Helper class for calculating the derivative of rotation
 Crotation_derivative< colvarmodule::atom, colvarmodule::rvector >
 Crotation_derivative< cvm::atom_pos, cvm::atom_pos >
 Ccolvar::orientation::rotation_derivative_impl_
 Ccolvarmodule::matrix2d< T >::row
 Ccolvarmodule::rvectorVector of real numbers with three components
 CUIestimator::UIestimator
 Ccolvarmodule::usageTrack usage of Colvars features
 Ccolvarmodule::vector1d< T >Arbitrary size array (one dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions)
 Ccolvarmodule::vector1d< cvm::real >