Collective Variables Module - Developer Documentation
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123]
oCcolvarA 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
|oCalpha_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])
|oCangleColvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI])
|oCcartesian
|oCcoordnumColvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2])
|oCcvcColvar component (base class); most implementations of cvc utilize one or more colvarmodule::atom or colvarmodule::atom_group objects to access atoms
|oCdihedPCColvar 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
|oCdihedralColvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI])
|oCdipole_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])
|oCdistanceColvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*))
|oCdistance_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])
|oCdistance_invColvar component: average distance between two groups of atoms, weighted as the sixth power, as in NMR refinements(colvarvalue::type_scalar type, range (0:*))
|oCdistance_pairsColvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component)
|oCdistance_vec
|oCdistance_xyColvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*))
|oCdistance_zColvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*))
|oCeigenvectorColvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-*:*))
|oCgroupcoordnumColvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2])
|oCgyrationColvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*))
|oCh_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])
|oCinertiaColvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*))
|oCinertia_zColvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*))
|oCorientationColvar 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])
|oCorientation_angleColvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI))
|oCorientation_projColvar component: cosine of the angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [-1:1])
|oCrmsdColvar 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:*))
|oCselfcoordnumColvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2])
|oCspin_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])
oCcolvar_gridGrid of values of a function of several collective variables
oCcolvar_grid_countColvar_grid derived class to hold counters in discrete n-dim colvar space
oCcolvar_grid_gradientClass for accumulating the gradient of a scalar function on a grid
oCcolvar_grid_scalarClass for accumulating a scalar function on a grid
oCcolvarbiasCollective variable bias, base class
oCcolvarbias_abfABF bias
oCcolvarbias_alb
oCcolvarbias_histogramHistogram "bias" (does as the name says)
oCcolvarbias_metaMetadynamics bias (implementation of colvarbias)
|\ChillA hill for the metadynamics bias
oCcolvarbias_restraintMost general definition of a colvar restraint: see derived classes for specific types (implementation of colvarbias)
oCcolvarbias_restraint_centersDefinition and parsing of the restraint centers
oCcolvarbias_restraint_centers_movingOptions to change the restraint centers over time
oCcolvarbias_restraint_harmonicHarmonic bias restraint (implementation of colvarbias_restraint)
oCcolvarbias_restraint_harmonic_wallsWall restraint (implementation of colvarbias_restraint)
oCcolvarbias_restraint_histogramRestrain the 1D histogram of a set of variables (or of a multidimensional one)
oCcolvarbias_restraint_kDefinition and parsing of the force constant
oCcolvarbias_restraint_k_movingOptions to change the restraint force constant over time
oCcolvarbias_restraint_linearLinear bias restraint (implementation of colvarbias_restraint)
oCcolvarbias_restraint_movingOptions to change the restraint configuration over time (shared between centers and k moving)
oCcolvardepsParent class for a member object of a bias, cv or cvc etc. containing features and their dependencies, and handling dependency resolution
|oCfeature
|\Cfeature_stateThis contains the current state of each feature for each object
oCcolvarmoduleCollective variables module (main class)
|oCatomStores numeric id, mass and all mutable data for an atom, mostly used by a cvc
|oCatom_groupGroup of atom objects, mostly used by a cvc object to gather all atomic data
|oCmatrix2dArbitrary size array (two dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions)
||\Crow
|oCquaternion1-dimensional vector of real numbers with four components and a quaternion algebra
|oCrmatrix2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector)
|oCrotationA rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion)
|oCrvectorVector 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)
oCcolvarparseBase 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
oCcolvarproxyInterface 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
oCcolvarproxy_namdCommunication between colvars and NAMD (implementation of colvarproxy)
oCcolvarproxy_vmdCommunication between colvars and VMD (implementation of colvarproxy)
oCcolvarscript
oCcolvarvalueValue 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)
oCScriptTcl
\CSimParameters