colvar::angle Class Reference

Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::angle:

List of all members.

Public Member Functions
	angle (std::string const &conf)
	Initialize by parsing the configuration.
	angle (cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3)
	Initialize the three groups after three atoms.
	angle ()
virtual	~angle ()
virtual void	calc_value ()
	Calculate the variable.
virtual void	calc_gradients ()
	Calculate the atomic gradients, to be reused later in order to apply forces.
virtual void	apply_force (colvarvalue const &force)
	Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function).
virtual cvm::real	dist2 (colvarvalue const &x1, colvarvalue const &x2) const
	Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue	dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue	dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual cvm::real	compare (colvarvalue const &x1, colvarvalue const &x2) const
	Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error.
Protected Attributes
cvm::atom_group	group1
	Atom group.
cvm::atom_group	group2
	Atom group.
cvm::atom_group	group3
	Atom group.
cvm::rvector	r21
	Inter site vectors.
cvm::rvector	r23
	Inter site vectors.
cvm::real	r21l
	Inter site vector norms.
cvm::real	r23l
	Inter site vector norms.

---

Detailed Description

Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]).

Definition at line 556 of file colvarcomp.h.

---

Constructor & Destructor Documentation

colvar::angle::angle (  std::string const &  conf  )

Initialize by parsing the configuration. Definition at line 10 of file colvarcomp_angles.C. References group1, group2, group3, colvar::cvc::parse_group(), and colvarvalue::type(). : cvc (conf) { function_type = "angle"; parse_group (conf, "group1", group1); parse_group (conf, "group2", group2); parse_group (conf, "group3", group3); x.type (colvarvalue::type_scalar); }

colvar::angle::angle (  cvm::atom const &  a1, cvm::atom const &  a2, cvm::atom const &  a3 )

Initialize the three groups after three atoms. Definition at line 21 of file colvarcomp_angles.C. References cvm, and colvarvalue::type(). : group1 (std::vector<cvm::atom> (1, a1)), group2 (std::vector<cvm::atom> (1, a2)), group3 (std::vector<cvm::atom> (1, a3)) { function_type = "angle"; x.type (colvarvalue::type_scalar); }

colvar::angle::angle (   )

Definition at line 33 of file colvarcomp_angles.C. References colvarvalue::type(). { function_type = "angle"; x.type (colvarvalue::type_scalar); }

virtual colvar::angle::~angle (   )  [inline, virtual]

Definition at line 580 of file colvarcomp.h. {}

---

Member Function Documentation

void colvar::angle::apply_force (  colvarvalue const &  force  )  [virtual]

Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function). Note: multiple calls to this function within the same simulation step will add the forces altogether Parameters: cvforce  The collective variable force, usually coming from the biases and eventually manipulated by the parent object Implements colvar::cvc. Definition at line 91 of file colvarcomp_angles.C. References colvarmodule::atom_group::apply_colvar_force(), group1, group2, group3, colvarmodule::atom_group::noforce, and colvarvalue::real_value. { if (!group1.noforce) group1.apply_colvar_force (force.real_value); if (!group2.noforce) group2.apply_colvar_force (force.real_value); if (!group3.noforce) group3.apply_colvar_force (force.real_value); }

void colvar::angle::calc_gradients (   )  [virtual]

Calculate the atomic gradients, to be reused later in order to apply forces. Implements colvar::cvc. Definition at line 61 of file colvarcomp_angles.C. References group1, group2, group3, r21, r21l, r23, r23l, and colvarmodule::atom_group::total_mass. { cvm::real const cos_theta = (r21*r23)/(r21l*r23l); cvm::real const dxdcos = -1.0 / ::sqrt (1.0 - cos_theta*cos_theta); cvm::rvector const dthetadr21 = (180.0/PI) * dxdcos * ( (r23)/(r21l*r23l) + (r21l*cos_theta) * (-1.0/(r21l*r21l)) * r21/r21l ); cvm::rvector const dthetadr23 = (180.0/PI) * dxdcos * ( (r21)/(r21l*r23l) + (r23l*cos_theta) * (-1.0/(r23l*r23l)) * r23/r23l ); for (size_t i = 0; i < group1.size(); i++) { group1[i].grad = (group1[i].mass/group1.total_mass) * (dthetadr21); } for (size_t i = 0; i < group2.size(); i++) { group2[i].grad = (group2[i].mass/group2.total_mass) * (dthetadr21 + dthetadr23) * (-1.0); } for (size_t i = 0; i < group3.size(); i++) { group3[i].grad = (group3[i].mass/group3.total_mass) * (dthetadr23); } }

void colvar::angle::calc_value (   )  [virtual]

Calculate the variable. Implements colvar::cvc. Definition at line 40 of file colvarcomp_angles.C. References colvarmodule::atom_pos, colvarmodule::atom_group::center_of_mass(), group1, group2, group3, colvarmodule::rvector::norm(), colvarmodule::position_distance(), r21, r21l, r23, r23l, colvarmodule::atom_group::read_positions(), and colvarvalue::real_value. { group1.read_positions(); group2.read_positions(); group3.read_positions(); cvm::atom_pos const g1_pos = group1.center_of_mass(); cvm::atom_pos const g2_pos = group2.center_of_mass(); cvm::atom_pos const g3_pos = group3.center_of_mass(); r21 = cvm::position_distance (g1_pos, g2_pos); r21l = r21.norm(); r23 = cvm::position_distance (g3_pos, g2_pos); r23l = r23.norm(); cvm::real const cos_theta = (r21*r23)/(r21l*r23l); x.real_value = (180.0/PI) * ::acos (cos_theta); }

virtual cvm::real colvar::angle::compare (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error. Reimplemented from colvar::cvc.

virtual cvm::real colvar::angle::dist2 (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities). colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object. If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients. If constraints are present (and not already implemented by any of the types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface. Finally, another useful application, if you are performing very many operations with these functions, could be to override the member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar type. Reimplemented from colvar::cvc.

virtual colvarvalue colvar::angle::dist2_lgrad (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). Reimplemented from colvar::cvc.

virtual colvarvalue colvar::angle::dist2_rgrad (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). Reimplemented from colvar::cvc.

---

Member Data Documentation

cvm::atom_group colvar::angle::group1 [protected]

Atom group. Definition at line 562 of file colvarcomp.h. Referenced by angle(), apply_force(), calc_gradients(), and calc_value().

cvm::atom_group colvar::angle::group2 [protected]

Atom group. Definition at line 564 of file colvarcomp.h. Referenced by angle(), apply_force(), calc_gradients(), and calc_value().

cvm::atom_group colvar::angle::group3 [protected]

Atom group. Definition at line 566 of file colvarcomp.h. Referenced by angle(), apply_force(), calc_gradients(), and calc_value().

cvm::rvector colvar::angle::r21 [protected]

Inter site vectors. Definition at line 569 of file colvarcomp.h. Referenced by calc_gradients(), and calc_value().

cvm::real colvar::angle::r21l [protected]

Inter site vector norms. Definition at line 571 of file colvarcomp.h. Referenced by calc_gradients(), and calc_value().

cvm::rvector colvar::angle::r23 [protected]

Inter site vectors. Definition at line 569 of file colvarcomp.h. Referenced by calc_gradients(), and calc_value().

cvm::real colvar::angle::r23l [protected]

Inter site vector norms. Definition at line 571 of file colvarcomp.h. Referenced by calc_gradients(), and calc_value().

---

The documentation for this class was generated from the following files:

• colvarcomp.h
• colvarcomp_angles.C

---