▼NUIestimator | |
Cn_matrix | |
Cn_vector | |
CUIestimator | |
▼Ccolvar | A 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_angles | Colvar 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]) |
Cangle | Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]) |
Ccartesian | |
Ccoordnum | Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) |
Ccvc | Colvar component (base class for collective variables) |
CdihedPC | Colvar 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 |
Cdihedral | Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI]) |
Cdipole_angle | Colvar component: angle between the dipole of a molecule and an axis formed by two groups of atoms(colvarvalue::type_scalar type, range [0:PI]) |
Cdistance | Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)) |
Cdistance_dir | Colvar 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_inv | Colvar component: average distance between two groups of atoms, weighted as the sixth power, as in NMR refinements(colvarvalue::type_scalar type, range (0:*)) |
Cdistance_pairs | Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component) |
Cdistance_vec | |
Cdistance_xy | Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*)) |
Cdistance_z | Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*)) |
Ceigenvector | Colvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-*:*)) |
Cgroupcoordnum | Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) |
Cgyration | Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*)) |
Ch_bond | Colvar 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]) |
Cinertia | Colvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*)) |
Cinertia_z | Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*)) |
Corientation | Colvar 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_angle | Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI)) |
Corientation_proj | Colvar component: cosine of the angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [-1:1]) |
Cpolar_phi | Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180]) |
Cpolar_theta | Colvar component: polar coordinate theta of a group (colvarvalue::type_scalar type, range [0:180]) |
Crmsd | Colvar 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:*)) |
Cselfcoordnum | Colvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2]) |
Cspin_angle | Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI]) |
Ctilt | Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1]) |
Ccolvar_grid | Grid of values of a function of several collective variables |
Ccolvar_grid_count | Colvar_grid derived class to hold counters in discrete n-dim colvar space |
Ccolvar_grid_gradient | Class for accumulating the gradient of a scalar function on a grid |
Ccolvar_grid_scalar | Class for accumulating a scalar function on a grid |
Ccolvarbias | Collective variable bias, base class |
Ccolvarbias_abf | ABF bias |
Ccolvarbias_alb | |
Ccolvarbias_histogram | Histogram "bias" (does as the name says) |
▼Ccolvarbias_meta | Metadynamics bias (implementation of colvarbias) |
Chill | A hill for the metadynamics bias |
Ccolvarbias_restraint | Most general definition of a colvar restraint: see derived classes for specific types (implementation of colvarbias) |
Ccolvarbias_restraint_centers | Definition and parsing of the restraint centers |
Ccolvarbias_restraint_centers_moving | Options to change the restraint centers over time |
Ccolvarbias_restraint_harmonic | Harmonic bias restraint (implementation of colvarbias_restraint) |
Ccolvarbias_restraint_harmonic_walls | Wall restraint (implementation of colvarbias_restraint) |
Ccolvarbias_restraint_histogram | Restrain the 1D histogram of a set of variables (or of a multidimensional one) |
Ccolvarbias_restraint_k | Definition and parsing of the force constant |
Ccolvarbias_restraint_k_moving | Options to change the restraint force constant over time |
Ccolvarbias_restraint_linear | Linear bias restraint (implementation of colvarbias_restraint) |
Ccolvarbias_restraint_moving | Options to change the restraint configuration over time (shared between centers and k moving) |
Ccolvarbias_ti | Base class for unconstrained thermodynamic-integration FE estimator |
▼Ccolvardeps | Parent class for a member object of a bias, cv or cvc etc. containing features and their dependencies, and handling dependency resolution |
Cfeature | |
Cfeature_state | This contains the current state of each feature for each object |
▼Ccolvarmodule | Collective variables module (main class) |
Catom | Stores numeric id, mass and all mutable data for an atom, mostly used by a cvc |
Catom_group | Group of atom objects, mostly used by a cvc object to gather all atomic data |
▼Cmatrix2d | Arbitrary size array (two dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions) |
Crow | |
Cquaternion | 1-dimensional vector of real numbers with four components and a quaternion algebra |
Crmatrix | 2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector) |
Crotation | A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion) |
Crvector | Vector of real numbers with three components |
Cvector1d | Arbitrary size array (one dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions) |
▼Ccolvarparse | Base class containing parsing functions; all objects which need to parse input inherit from this |
Cread_block | Helper class to read a block of the type "key { ... }" from a stream and store it in a string |
Ccolvarproxy | Interface 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_groups | Container of atom group data (allow collection of aggregated atomic data) |
Ccolvarproxy_atoms | Container of atomic data for processing by Colvars |
Ccolvarproxy_io | Methods for data input/output |
Ccolvarproxy_namd | Communication between colvars and NAMD (implementation of colvarproxy) |
Ccolvarproxy_replicas | Methods for multiple-replica communication |
Ccolvarproxy_script | Method for scripting language interface (Tcl or Python) |
Ccolvarproxy_smp | Methods for SMP parallelization |
Ccolvarproxy_system | Methods for accessing the simulation system (PBCs, integrator, etc) |
Ccolvarproxy_vmd | Communication between colvars and VMD (implementation of colvarproxy) |
Ccolvarscript | |
Ccolvarvalue | Value 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 | |