colvarcomp.h File Reference

#include <fstream>
#include <cmath>
#include "colvarmodule.h"
#include "colvar.h"
#include "colvaratoms.h"

Go to the source code of this file.

Classes
class	colvar::cvc
	Colvar component (base class); most implementations of utilize one or more or objects to access atoms. More...
class	colvar::distance
	Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)). More...
class	colvar::distance_dir
	Colvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unitvector type, range [-1:1]x[-1:1]x[-1:1]). More...
class	colvar::distance_z
	Colvar component: projection of the distance vector along an axis (colvarvalue::type_scalar type, range (-*:*)). More...
class	colvar::distance_xy
	Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*)). More...
class	colvar::min_distance
	Colvar component: projection of the distance vector along a fixed axis (colvarvalue::type_scalar type, range (-*:*)). More...
class	colvar::gyration
	Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*)). More...
class	colvar::eigenvector
	Colvar component: projection of 3N coordinates onto an eigenvector (colvarvalue::type_scalar type, range (-*:*)). More...
class	colvar::angle
	Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]). More...
class	colvar::dihedral
	Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI]). More...
class	colvar::coordnum
	Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]). More...
class	colvar::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]). More...
class	colvar::alpha_dihedrals
	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]). More...
class	colvar::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]). More...
class	colvar::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]). More...
class	colvar::orientation_angle
	Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI)). More...
class	colvar::rmsd
	Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*)). More...
class	colvar::logmsd
	Colvar component: mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*)). More...
Defines
#define	simple_scalar_dist_functions(TYPE)
Functions
	simple_scalar_dist_functions (distance) simple_scalar_dist_functions(distance_xy) simple_scalar_dist_functions(distance_z) simple_scalar_dist_functions(min_distance) simple_scalar_dist_functions(angle) simple_scalar_dist_functions(coordnum) simple_scalar_dist_functions(h_bond) simple_scalar_dist_functions(gyration) simple_scalar_dist_functions(rmsd) simple_scalar_dist_functions(logmsd) simple_scalar_dist_functions(orientation_angle) simple_scalar_dist_functions(eigenvector) simple_scalar_dist_functions(alpha_dihedrals) simple_scalar_dist_functions(alpha_angles) inline cvm

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Define Documentation

#define simple_scalar_dist_functions (  TYPE   )

Value: \ inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return ::pow (x1.real_value - x2.real_value, int (2)); \ } \ \ inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return 2.0 * (x1.real_value - x2.real_value); \ } \ \ inline colvarvalue colvar::TYPE::dist2_rgrad (colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return this->dist2_lgrad (x2, x1); \ } \ \ inline cvm::real colvar::TYPE::compare (colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return this->dist2_lgrad (x1, x2); \ } \ \ Definition at line 1003 of file colvarcomp.h.

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Function Documentation

simple_scalar_dist_functions (  distance   )

Definition at line 1030 of file colvarcomp.h. References cvm, colvarmodule::quaternion::dist2(), and colvarvalue::quaternion_value. { // return (x1.rvector_value - x2.rvector_value).norm2(); // } // inline colvarvalue colvar::distance_vec::dist2_lgrad (colvarvalue const &x1, // colvarvalue const &x2) const // { // return (x1.rvector_value - x2.rvector_value); // } // inline colvarvalue colvar::distance_vec::dist2_rgrad (colvarvalue const &x1, // colvarvalue const &x2) const // { // return (x2.rvector_value - x1.rvector_value); // } // inline cvm::real colvar::distance_vec::compare (colvarvalue const &x1, // colvarvalue const &x2) const // { // cvm::fatal_error ("Error: cannot compare() two distance vectors.\n"); // return 0.0; // } // distance between quaternions inline cvm::real colvar::orientation::dist2 (colvarvalue const &x1, colvarvalue const &x2) const { return x1.quaternion_value.dist2 (x2); }

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