| CArithmeticPathCV::ArithmeticPathBase< scalar_type > | |
| ▼CArithmeticPathCV::ArithmeticPathBase< cvm::real > | |
| CArithmeticPathImpl | |
| Ccolvarmodule::atom | Stores numeric id, mass and all mutable data for an atom, mostly used by a colvar::cvc |
| ▼Ccolvardeps | Parent class for a member object of a bias, cv or cvc etc. containing features and their dependencies, and handling dependency resolution |
| 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 |
| ►Ccolvar::cvc | Colvar component (base class for collective variables) |
| ►Ccolvar::CVBasedPath | |
| Ccolvar::aspathCV | |
| Ccolvar::azpathCV | |
| Ccolvar::gspathCV | Colvar 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 |
| Ccolvar::gzpathCV | |
| ►Ccolvar::CartesianBasedPath | |
| Ccolvar::aspath | |
| Ccolvar::azpath | |
| Ccolvar::gspath | Colvar 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 |
| Ccolvar::gzpath | Colvar 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 |
| Ccolvar::alch_Flambda | |
| Ccolvar::alch_lambda | |
| Ccolvar::alpha_angles | Colvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of Ca-Ca-Ca angles and hydrogen bonds (colvarvalue::type_scalar type, range [0:1]) |
| Ccolvar::angle | Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]) |
| Ccolvar::cartesian | |
| Ccolvar::coordnum | Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) |
| Ccolvar::dihedPC | 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 |
| Ccolvar::dihedral | Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI]) |
| Ccolvar::dipole_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]) |
| Ccolvar::dipole_magnitude | Colvar component: dipole magnitude of a molecule |
| ►Ccolvar::distance | Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)) |
| Ccolvar::distance_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]) |
| Ccolvar::distance_vec | |
| Ccolvar::groupcoordnum | Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) |
| Ccolvar::distance_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:*)) |
| Ccolvar::distance_pairs | Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component) |
| ►Ccolvar::distance_z | Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*)) |
| Ccolvar::distance_xy | Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*)) |
| Ccolvar::eigenvector | Colvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-*:*)) |
| ►Ccolvar::gyration | Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*)) |
| ►Ccolvar::inertia | Colvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*)) |
| Ccolvar::inertia_z | Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*)) |
| Ccolvar::h_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]) |
| ►Ccolvar::linearCombination | Current only linear combination of sub-CVCs is available |
| Ccolvar::customColvar | Custom expression of colvars |
| Ccolvar::neuralNetwork | |
| Ccolvar::map_total | |
| ►Ccolvar::orientation | 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]) |
| ►Ccolvar::orientation_angle | |
| Ccolvar::euler_phi | |
| Ccolvar::euler_psi | |
| Ccolvar::euler_theta | |
| ►Ccolvar::orientation_proj | Colvar component: cosine of the angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [-1:1]) |
| ►Ccolvar::tilt | Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1]) |
| Ccolvar::spin_angle | Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI]) |
| Ccolvar::polar_phi | Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180]) |
| Ccolvar::polar_theta | Colvar component: polar coordinate theta of a group (colvarvalue::type_scalar type, range [0:180]) |
| Ccolvar::rmsd | 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:*)) |
| Ccolvar::selfcoordnum | Colvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2]) |
| Ccolvar::torchANN | |
| ►Ccolvarbias | Collective variable bias, base class |
| Ccolvarbias_abf | ABF bias |
| Ccolvarbias_alb | |
| ►Ccolvarbias_histogram | Histogram "bias" (does as the name says) |
| Ccolvarbias_reweightaMD | |
| Ccolvarbias_meta | Metadynamics bias (implementation of colvarbias) |
| Ccolvarbias_opes | |
| ►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_linear | Linear bias restraint (implementation of colvarbias_restraint) |
| ►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_harmonic | Harmonic bias restraint (implementation of colvarbias_restraint) |
| Ccolvarbias_restraint_harmonic_walls | Wall restraint (implementation of colvarbias_restraint) |
| Ccolvarbias_restraint_linear | Linear bias restraint (implementation of colvarbias_restraint) |
| Ccolvarbias_restraint_histogram | Restrain the 1D histogram of a set of variables (or of a multidimensional one) |
| ►Ccolvarbias_ti | Base class for unconstrained thermodynamic-integration FE estimator |
| Ccolvarbias_abmd | Adiabatic Bias MD |
| Ccolvarbias_meta | Metadynamics bias (implementation of colvarbias) |
| Ccolvarbias_restraint | Most general definition of a colvar restraint: see derived classes for specific types (implementation of colvarbias) |
| ►Ccolvarbias_restraint_moving | Options to change the restraint configuration over time (shared between centers and k moving) |
| Ccolvarbias_restraint_centers_moving | Options to change the restraint centers over time |
| Ccolvarbias_restraint_k_moving | Options to change the restraint force constant over time |
| Ccolvarmodule::atom_group | Group of atom objects, mostly used by a colvar::cvc object to gather all atomic data |
| Ccolvarmodule | Collective variables module (main class) |
| ▼Ccolvarparams | |
| ►Ccolvarparse | Base class containing parsing functions; all objects which need to parse input inherit from this |
| ►Ccolvar_grid< size_t > | |
| Ccolvar_grid_count | Colvar_grid derived class to hold counters in discrete n-dim colvar space |
| ►Ccolvar_grid< cvm::real > | |
| 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 |
| Cintegrate_potential | Integrate (1D, 2D or 3D) gradients |
| 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 |
| Ccolvar::cvc | Colvar component (base class for collective variables) |
| Ccolvar_grid< T > | Grid of values of a function of several collective variables |
| Ccolvarbias | Collective variable bias, base class |
| Ccolvarbias_restraint_moving | Options to change the restraint configuration over time (shared between centers and k moving) |
| Ccolvarmodule::atom_group | Group of atom objects, mostly used by a colvar::cvc object to gather all atomic data |
| ▼Ccolvarproxy_atom_groups | Container of atom group data (allow collection of aggregated atomic data) |
| ►Ccolvarproxy | |
| Ccolvarproxy_lammps | Communication between colvars and LAMMPS (implementation of colvarproxy) |
| Ccolvarproxy_namd | Communication between colvars and NAMD (implementation of colvarproxy) |
| Ccolvarproxy_vmd | Communication between colvars and VMD (implementation of colvarproxy) |
| ▼Ccolvarproxy_atoms | Container of atomic data for processing by Colvars |
| Ccolvarproxy | |
| ▼Ccolvarproxy_io | Methods for data input/output |
| Ccolvarproxy | |
| ▼Ccolvarproxy_replicas | Methods for multiple-replica communication |
| Ccolvarproxy | |
| ▼Ccolvarproxy_script | Methods for scripting language interface (Tcl or Python) |
| Ccolvarproxy | |
| ▼Ccolvarproxy_smp | Methods for SMP parallelization |
| Ccolvarproxy | |
| ▼Ccolvarproxy_system | Methods for accessing the simulation system (PBCs, integrator, etc) |
| Ccolvarproxy | |
| ▼Ccolvarproxy_tcl | Methods for using Tcl within Colvars |
| Ccolvarproxy | |
| ▼Ccolvarproxy_volmaps | Container of grid-based objects |
| Ccolvarproxy | |
| 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 colvar::cvc implementations) |
| CLAMMPS_NS::commdata | |
| CneuralnetworkCV::denseLayer | |
| CGeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::doCompareFrameDistance | |
| Ccolvardeps::feature | |
| Ccolvardeps::feature_state | This 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::gspathCV | Colvar 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::gspath | Colvar 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::gzpath | Colvar 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_namd | Communication between colvars and NAMD (implementation of colvarproxy) |
| Ccolvarmodule::atom_group::group_force_object | A helper class for applying forces on an atom group in a way that is aware of the fitting group. NOTE: you are encouraged to use get_group_force_object() to get an instance of group_force_object instead of constructing directly |
| Ccolvarbias_meta::hill | A hill for the metadynamics bias |
| CIntHash_NS::inthash_node_t | |
| CIntHash_NS::inthash_t | |
| Ccolvarbias_opes::kernel | The Gaussian kernel data structure |
| 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::quaternion | 1-dimensional vector of real numbers with four components and a quaternion algebra |
| Ccolvarparse::read_block | |
| Ccolvarmodule::rmatrix | 2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector) |
| Ccolvarmodule::rotation | A 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::rvector | Vector of real numbers with three components |
| Ccolvarbias_opes::traj_line | |
| CUIestimator::UIestimator | |
| Ccolvarmodule::usage | Track 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 > | |
