#include "colvarmodule.h"
#include "colvar.h"
#include "colvaratoms.h"
#include "colvar_arithmeticpath.h"
#include <map>
Go to the source code of this file.
Compounds | |
class | colvar::azpathCV |
class | colvar::aspathCV |
class | colvar::CartesianBasedPath |
class | colvar::alch_Flambda |
class | colvar::alch_lambda |
class | colvar::cartesian |
class | colvar::alpha_angles |
\brief 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]). More... | |
class | colvar::angle |
\brief Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]). More... | |
class | colvar::cvc |
\brief Colvar component (base class for collective variables) A colvar::cvc object (or an object of a cvc-derived class) implements the calculation of a collective variable, its gradients and any other related physical quantities that depend on microscopic degrees of freedom. No restriction is set to what kind of calculation a colvar::cvc object performs (usually an analytical function of atomic coordinates). The only constraints are that:
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class | colvar::distance |
\brief Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)). More... | |
class | colvar::distance_vec |
class | colvar::distance_dir |
\brief 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]). More... | |
class | colvar::distance_z |
\brief Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*)). More... | |
class | colvar::distance_xy |
\brief Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*)). More... | |
class | colvar::polar_phi |
\brief Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180]). More... | |
class | colvar::polar_theta |
\brief Colvar component: polar coordinate theta of a group (colvarvalue::type_scalar type, range [0:180]). More... | |
class | colvar::distance_inv |
\brief Colvar component: average distance between two groups of atoms, weighted as the sixth power, as in NMR refinements(colvarvalue::type_scalar type, range (0:*)). More... | |
class | colvar::distance_pairs |
\brief Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component). More... | |
class | colvar::dipole_magnitude |
\brief Colvar component: dipole magnitude of a molecule. More... | |
class | colvar::gyration |
\brief Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*)). More... | |
class | colvar::inertia |
\brief Colvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*)). More... | |
class | colvar::inertia_z |
\brief Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*)). More... | |
class | colvar::eigenvector |
\brief Colvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-*:*)). More... | |
class | colvar::dipole_angle |
\brief 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]). More... | |
class | colvar::dihedral |
\brief Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI]). More... | |
class | colvar::coordnum |
\brief Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]). More... | |
class | colvar::selfcoordnum |
\brief Colvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2]). More... | |
class | colvar::groupcoordnum |
\brief Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]). More... | |
class | colvar::h_bond |
\brief 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]). More... | |
class | colvar::dihedPC |
\brief 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. More... | |
class | colvar::orientation |
\brief 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]). More... | |
class | colvar::orientation_angle |
\brief Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI)). More... | |
class | colvar::orientation_proj |
\brief Colvar component: cosine of the angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [-1:1]). More... | |
class | colvar::tilt |
\brief Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1]). More... | |
class | colvar::spin_angle |
\brief Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI]). More... | |
class | colvar::euler_phi |
class | colvar::euler_psi |
class | colvar::euler_theta |
class | colvar::rmsd |
\brief 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:*)). More... | |
class | colvar::componentDisabled |
class | colvar::linearCombination |
class | colvar::CVBasedPath |
class | colvar::gspath |
class | colvar::gzpath |
class | colvar::gspathCV |
class | colvar::gzpathCV |
class | colvar::neuralNetwork |
class | colvar::map_total |
Defines | |
#define | simple_scalar_dist_functions(TYPE) |
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Value: \ \ cvm::real colvar::TYPE::dist2(colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \ } \ \ \ colvarvalue colvar::TYPE::dist2_lgrad(colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return 2.0 * (x1.real_value - x2.real_value); \ } \ \ \ colvarvalue colvar::TYPE::dist2_rgrad(colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return this->dist2_lgrad(x2, x1); \ } \ Definition at line 1882 of file colvarcomp.h. |