Collective Variables Module - Developer Documentation
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123]
 NUIestimator
 Cn_matrix
 Cn_vector
 CUIestimator
 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
 Calpha_anglesColvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of phi/psi dihedral angles and hydrogen bonds (colvarvalue::type_scalar type, range [0:1])
 CangleColvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI])
 Ccartesian
 CcoordnumColvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2])
 CcvcColvar component (base class for collective variables)
 CdihedPCColvar component: dihedPC Projection of the config onto a dihedral principal component See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007) Based on a set of 'dihedral' cvcs
 CdihedralColvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI])
 Cdipole_angleColvar component: angle between the dipole of a molecule and an axis formed by two groups of atoms(colvarvalue::type_scalar type, range [0:PI])
 CdistanceColvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*))
 Cdistance_dirColvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unit3vector type, range [-1:1]x[-1:1]x[-1:1])
 Cdistance_invColvar component: average distance between two groups of atoms, weighted as the sixth power, as in NMR refinements(colvarvalue::type_scalar type, range (0:*))
 Cdistance_pairsColvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component)
 Cdistance_vec
 Cdistance_xyColvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*))
 Cdistance_zColvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*))
 CeigenvectorColvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-*:*))
 CgroupcoordnumColvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2])
 CgyrationColvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*))
 Ch_bondColvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1])
 CinertiaColvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*))
 Cinertia_zColvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*))
 CorientationColvar component: orientation in space of an atom group, with respect to a set of reference coordinates (colvarvalue::type_quaternion type, range [-1:1]x[-1:1]x[-1:1]x[-1:1])
 Corientation_angleColvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI))
 Corientation_projColvar component: cosine of the angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [-1:1])
 Cpolar_phiColvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180])
 Cpolar_thetaColvar component: polar coordinate theta of a group (colvarvalue::type_scalar type, range [0:180])
 CrmsdColvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses colvar::orientation to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*))
 CselfcoordnumColvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2])
 Cspin_angleColvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI])
 CtiltColvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1])
 Ccolvar_gridGrid of values of a function of several collective variables
 Ccolvar_grid_countColvar_grid derived class to hold counters in discrete n-dim colvar space
 Ccolvar_grid_gradientClass for accumulating the gradient of a scalar function on a grid
 Ccolvar_grid_scalarClass for accumulating a scalar function on a grid
 CcolvarbiasCollective variable bias, base class
 Ccolvarbias_abfABF bias
 Ccolvarbias_alb
 Ccolvarbias_histogramHistogram "bias" (does as the name says)
 Ccolvarbias_metaMetadynamics bias (implementation of colvarbias)
 ChillA hill for the metadynamics bias
 Ccolvarbias_restraintMost general definition of a colvar restraint: see derived classes for specific types (implementation of colvarbias)
 Ccolvarbias_restraint_centersDefinition and parsing of the restraint centers
 Ccolvarbias_restraint_centers_movingOptions to change the restraint centers over time
 Ccolvarbias_restraint_harmonicHarmonic bias restraint (implementation of colvarbias_restraint)
 Ccolvarbias_restraint_harmonic_wallsWall restraint (implementation of colvarbias_restraint)
 Ccolvarbias_restraint_histogramRestrain the 1D histogram of a set of variables (or of a multidimensional one)
 Ccolvarbias_restraint_kDefinition and parsing of the force constant
 Ccolvarbias_restraint_k_movingOptions to change the restraint force constant over time
 Ccolvarbias_restraint_linearLinear bias restraint (implementation of colvarbias_restraint)
 Ccolvarbias_restraint_movingOptions to change the restraint configuration over time (shared between centers and k moving)
 Ccolvarbias_tiBase class for unconstrained thermodynamic-integration FE estimator
 CcolvardepsParent class for a member object of a bias, cv or cvc etc. containing features and their dependencies, and handling dependency resolution
 Cfeature
 Cfeature_stateThis contains the current state of each feature for each object
 CcolvarmoduleCollective variables module (main class)
 CatomStores numeric id, mass and all mutable data for an atom, mostly used by a cvc
 Catom_groupGroup of atom objects, mostly used by a cvc object to gather all atomic data
 Cmatrix2dArbitrary size array (two dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions)
 Crow
 Cquaternion1-dimensional vector of real numbers with four components and a quaternion algebra
 Crmatrix2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector)
 CrotationA rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion)
 CrvectorVector of real numbers with three components
 Cvector1dArbitrary size array (one dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions)
 CcolvarparseBase class containing parsing functions; all objects which need to parse input inherit from this
 Cread_blockHelper class to read a block of the type "key { ... }" from a stream and store it in a string
 CcolvarproxyInterface between the collective variables module and the simulation or analysis program (NAMD, VMD, LAMMPS...). This is the base class: each interfaced program is supported by a derived class. Only pure virtual functions ("= 0") must be reimplemented to ensure baseline functionality
 Ccolvarproxy_atom_groupsContainer of atom group data (allow collection of aggregated atomic data)
 Ccolvarproxy_atomsContainer of atomic data for processing by Colvars
 Ccolvarproxy_ioMethods for data input/output
 Ccolvarproxy_namdCommunication between colvars and NAMD (implementation of colvarproxy)
 Ccolvarproxy_replicasMethods for multiple-replica communication
 Ccolvarproxy_scriptMethod for scripting language interface (Tcl or Python)
 Ccolvarproxy_smpMethods for SMP parallelization
 Ccolvarproxy_systemMethods for accessing the simulation system (PBCs, integrator, etc)
 Ccolvarproxy_vmdCommunication between colvars and VMD (implementation of colvarproxy)
 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 cvc implementations)
 CScriptTcl
 CSimParameters