colvar::distance_z Class Reference

Colvar component: projection of the distance vector along an axis (colvarvalue::type_scalar type, range (-*:*)). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::distance_z:

List of all members.

Public Member Functions
	distance_z (std::string const &conf)
	distance_z ()
virtual	~distance_z ()
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	calc_force_invgrads ()
	Calculate the total force from the system using the inverse atomic gradients.
virtual void	calc_Jacobian_derivative ()
	Calculate the divergence of the inverse atomic gradients.
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.
virtual void	wrap (colvarvalue &x) const
	Redefined to make use of the user-provided period.
Protected Attributes
cvm::atom_group	main
	Main atom group.
cvm::atom_group	ref1
	Reference atom group.
cvm::atom_group	ref2
	Optional, second ref atom group.
bool	b_no_PBC
	Use absolute positions, ignoring PBCs when present.
bool	b_1site_force
cvm::rvector	axis
	Vector on which the distance vector is projected.
cvm::real	axis_norm
	Norm of the axis.
cvm::rvector	dist_v
	Vector distance, cached to be recycled.
bool	fixed_axis
	Flag: using a fixed axis vector?

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Detailed Description

Colvar component: projection of the distance vector along an axis (colvarvalue::type_scalar type, range (-*:*)).

Definition at line 398 of file colvarcomp.h.

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Constructor & Destructor Documentation

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

Definition at line 132 of file colvarcomp_distances.C. References axis, b_1site_force, b_no_PBC, colvarmodule::fatal_error(), fixed_axis, colvarparse::key_lookup(), colvarmodule::log(), colvarmodule::rvector::norm2(), colvar::cvc::parse_group(), ref1, ref2, colvarvalue::type(), and colvarmodule::rvector::unit(). : cvc (conf) { function_type = "distance_z"; b_inverse_gradients = true; b_Jacobian_derivative = true; x.type (colvarvalue::type_scalar); // TODO detect PBC from MD engine (in simple cases) // and then update period in real time if (period != 0.0) b_periodic = true; if ((wrap_center != 0.0) && (period == 0.0)) { cvm::fatal_error ("Error: wrapAround was defined in a distanceZ component," " but its period has not been set.\n"); } parse_group (conf, "main", main); parse_group (conf, "ref", ref1); atom_groups.push_back (&main); atom_groups.push_back (&ref1); // this group is optional parse_group (conf, "ref2", ref2, true); if (ref2.size()) { atom_groups.push_back (&ref2); cvm::log ("Using axis joining the centers of mass of groups \"ref\" and \"ref2\""); fixed_axis = false; if (key_lookup (conf, "axis")) cvm::log ("Warning: explicit axis definition will be ignored!"); } else { if (get_keyval (conf, "axis", axis, cvm::rvector (0.0, 0.0, 1.0))) { if (axis.norm2() == 0.0) cvm::fatal_error ("Axis vector is zero!"); if (axis.norm2() != 1.0) { axis = axis.unit(); cvm::log ("The normalized axis is: "+cvm::to_str (axis)+".\n"); } } fixed_axis = true; } if (get_keyval (conf, "forceNoPBC", b_no_PBC, false)) { cvm::log ("Computing distance using absolute positions (not minimal-image)"); } if (get_keyval (conf, "oneSiteSystemForce", b_1site_force, false)) { cvm::log ("Computing system force on group \"main\" only"); } }

colvar::distance_z::distance_z (   )

Definition at line 183 of file colvarcomp_distances.C. References colvarvalue::type(). { function_type = "distance_z"; b_inverse_gradients = true; b_Jacobian_derivative = true; x.type (colvarvalue::type_scalar); }

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

Definition at line 424 of file colvarcomp.h. {}

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Member Function Documentation

void colvar::distance_z::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. Reimplemented in colvar::distance_xy. Definition at line 256 of file colvarcomp_distances.C. References colvarmodule::atom_group::apply_colvar_force(), colvarmodule::atom_group::noforce, colvarvalue::real_value, ref1, and ref2. { if (!ref1.noforce) ref1.apply_colvar_force (force.real_value); if (ref2.size() && !ref2.noforce) ref2.apply_colvar_force (force.real_value); if (!main.noforce) main.apply_colvar_force (force.real_value); }

void colvar::distance_z::calc_force_invgrads (   )  [virtual]

Calculate the total force from the system using the inverse atomic gradients. Reimplemented from colvar::cvc. Reimplemented in colvar::distance_xy. Definition at line 239 of file colvarcomp_distances.C. References fixed_axis, colvarmodule::atom_group::read_system_forces(), colvarvalue::real_value, ref1, and colvarmodule::atom_group::system_force(). { main.read_system_forces(); if (fixed_axis && !b_1site_force) { ref1.read_system_forces(); ft.real_value = 0.5 * ((main.system_force() - ref1.system_force()) * axis); } else { ft.real_value = main.system_force() * axis; } }

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

Calculate the atomic gradients, to be reused later in order to apply forces. Implements colvar::cvc. Reimplemented in colvar::distance_xy. Definition at line 218 of file colvarcomp_distances.C. References axis, axis_norm, colvarmodule::atom_group::center_of_mass(), colvarvalue::real_value, ref1, ref2, and colvarmodule::atom_group::set_weighted_gradient(). { main.set_weighted_gradient ( axis ); if (fixed_axis) { ref1.set_weighted_gradient (-1.0 * axis); } else { if (b_no_PBC) { ref1.set_weighted_gradient ( 1.0 / axis_norm * (main.center_of_mass() - ref2.center_of_mass() - x.real_value * axis )); ref2.set_weighted_gradient ( 1.0 / axis_norm * (ref1.center_of_mass() - main.center_of_mass() + x.real_value * axis )); } else { ref1.set_weighted_gradient ( 1.0 / axis_norm * ( cvm::position_distance (ref2.center_of_mass(), main.center_of_mass()) - x.real_value * axis )); ref2.set_weighted_gradient ( 1.0 / axis_norm * ( cvm::position_distance (main.center_of_mass(), ref1.center_of_mass()) + x.real_value * axis )); } } }

void colvar::distance_z::calc_Jacobian_derivative (   )  [virtual]

Calculate the divergence of the inverse atomic gradients. Reimplemented from colvar::cvc. Reimplemented in colvar::distance_xy. Definition at line 251 of file colvarcomp_distances.C. References colvarvalue::real_value. { jd.real_value = 0.0; }

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

Calculate the variable. Implements colvar::cvc. Reimplemented in colvar::distance_xy. Definition at line 191 of file colvarcomp_distances.C. References axis, axis_norm, colvarmodule::atom_group::center_of_mass(), dist_v, colvarmodule::rvector::norm(), colvarmodule::position_distance(), colvarvalue::real_value, ref1, ref2, colvarmodule::rvector::unit(), and wrap(). { if (fixed_axis) { if (b_no_PBC) { dist_v = main.center_of_mass() - ref1.center_of_mass(); } else { dist_v = cvm::position_distance (ref1.center_of_mass(), main.center_of_mass()); } } else { if (b_no_PBC) { dist_v = main.center_of_mass() - (0.5 * (ref1.center_of_mass() + ref2.center_of_mass())); axis = ref2.center_of_mass() - ref1.center_of_mass(); } else { dist_v = cvm::position_distance (0.5 * (ref1.center_of_mass() + ref2.center_of_mass()), main.center_of_mass()); axis = cvm::position_distance (ref1.center_of_mass(), ref2.center_of_mass()); } axis_norm = axis.norm(); axis = axis.unit(); } x.real_value = axis * dist_v; this->wrap (x); }

cvm::real colvar::distance_z::compare (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [inline, 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. Reimplemented in colvar::distance_xy. Definition at line 1323 of file colvarcomp.h. References dist2_lgrad(). { return dist2_lgrad (x1, x2); }

virtual cvm::real colvar::distance_z::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. Reimplemented in colvar::distance_xy.

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

Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). Reimplemented from colvar::cvc. Reimplemented in colvar::distance_xy. Definition at line 1301 of file colvarcomp.h. References colvarvalue::real_value. Referenced by compare(). { cvm::real diff = x1.real_value - x2.real_value; if (period != 0.0) { cvm::real shift = std::floor (diff/period + 0.5); diff -= shift * period; } return 2.0 * diff; }

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

Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). Reimplemented from colvar::cvc. Reimplemented in colvar::distance_xy. Definition at line 1312 of file colvarcomp.h. References colvarvalue::real_value. { cvm::real diff = x1.real_value - x2.real_value; if (period != 0.0) { cvm::real shift = std::floor (diff/period + 0.5); diff -= shift * period; } return (-2.0) * diff; }

void colvar::distance_z::wrap (  colvarvalue &  x  )  const [inline, virtual]

Redefined to make use of the user-provided period. Reimplemented from colvar::cvc. Definition at line 1329 of file colvarcomp.h. References colvarvalue::real_value. Referenced by calc_value(). { if (! this->b_periodic) { // don't wrap if the period has not been set return; } cvm::real shift = std::floor ((x.real_value - wrap_center) / period + 0.5); x.real_value -= shift * period; return; }

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Member Data Documentation

cvm::rvector colvar::distance_z::axis [protected]

Vector on which the distance vector is projected. Definition at line 414 of file colvarcomp.h. Referenced by calc_gradients(), calc_value(), and distance_z().

cvm::real colvar::distance_z::axis_norm [protected]

Norm of the axis. Definition at line 416 of file colvarcomp.h. Referenced by calc_gradients(), and calc_value().

bool colvar::distance_z::b_1site_force [protected]

Compute system force on one site only to avoid unwanted coupling to other colvars (see e.g. Ciccotti et al., 2005) Definition at line 412 of file colvarcomp.h. Referenced by distance_z().

bool colvar::distance_z::b_no_PBC [protected]

Use absolute positions, ignoring PBCs when present. Definition at line 409 of file colvarcomp.h. Referenced by distance_z().

cvm::rvector colvar::distance_z::dist_v [protected]

Vector distance, cached to be recycled. Definition at line 418 of file colvarcomp.h. Referenced by calc_value().

bool colvar::distance_z::fixed_axis [protected]

Flag: using a fixed axis vector? Definition at line 420 of file colvarcomp.h. Referenced by calc_force_invgrads(), and distance_z().

cvm::atom_group colvar::distance_z::main [protected]

Main atom group. Definition at line 403 of file colvarcomp.h.

cvm::atom_group colvar::distance_z::ref1 [protected]

Reference atom group. Definition at line 405 of file colvarcomp.h. Referenced by apply_force(), calc_force_invgrads(), calc_gradients(), calc_value(), and distance_z().

cvm::atom_group colvar::distance_z::ref2 [protected]

Optional, second ref atom group. Definition at line 407 of file colvarcomp.h. Referenced by apply_force(), calc_gradients(), calc_value(), and distance_z().

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

• colvarcomp.h
• colvarcomp_distances.C

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