colvar::orientation Class Reference

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...

#include <colvarcomp.h>

Inheritance diagram for colvar::orientation:

List of all members.

Public Member Functions
	orientation (std::string const &conf)
	orientation ()
virtual	~orientation ()
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	atoms
	Atom group.
cvm::atom_pos	atoms_cog
	Center of geometry of the group.
std::vector< cvm::atom_pos >	ref_pos
	Reference coordinates.
cvm::rotation	rot
	Rotation object.
cvm::quaternion	ref_quat
	This is used to remove jumps in the sign of the quaternion, which may be annoying in the colvars trajectory.

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Detailed Description

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]).

Definition at line 832 of file colvarcomp.h.

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Constructor & Destructor Documentation

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

Definition at line 11 of file colvarcomp_rotations.C. References atoms, colvarmodule::rotation::b_debug_gradients, colvarmodule::fatal_error(), colvarmodule::load_coords(), colvarmodule::log(), colvarmodule::atom_group::noforce, colvar::cvc::parse_group(), colvarmodule::real, ref_pos, ref_quat, colvarmodule::rotation::request_group2_gradients(), rot, and colvarvalue::type(). : cvc (conf) { function_type = "orientation"; parse_group (conf, "atoms", atoms); x.type (colvarvalue::type_quaternion); ref_pos.reserve (atoms.size()); if (get_keyval (conf, "refPositions", ref_pos, ref_pos)) { cvm::log ("Using reference positions from input file.\n"); if (ref_pos.size() != atoms.size()) { cvm::fatal_error ("Error: reference positions do not " "match the number of atom indexes.\n"); } } { std::string file_name; if (get_keyval (conf, "refPositionsFile", file_name)) { std::string file_col; get_keyval (conf, "refPositionsCol", file_col, std::string ("O")); double file_col_value; bool found = get_keyval (conf, "refPositionsColValue", file_col_value, 0.0); if (found && !file_col_value) cvm::fatal_error ("Error: refPositionsColValue, " "if provided, must be non-zero.\n"); ref_pos.resize (atoms.size()); cvm::load_coords (file_name.c_str(), ref_pos, file_col, file_col_value); } } if (!ref_pos.size()) { cvm::fatal_error ("Error: must define a set of " "reference coordinates.\n"); } cvm::log ("Centering the reference coordinates: it is " "assumed that each atom is the closest " "periodic image to the center of geometry.\n"); cvm::rvector cog (0.0, 0.0, 0.0); for (size_t i = 0; i < ref_pos.size(); i++) { cog += ref_pos[i]; } cog /= cvm::real (ref_pos.size()); for (size_t i = 0; i < ref_pos.size(); i++) { ref_pos[i] -= cog; } get_keyval (conf, "closestToQuaternion", ref_quat, cvm::quaternion (1.0, 0.0, 0.0, 0.0)); // initialize rot member data if (!atoms.noforce) { rot.request_group2_gradients (atoms.size()); } rot.b_debug_gradients = this->b_debug_gradients; }

colvar::orientation::orientation (   )

Definition at line 75 of file colvarcomp_rotations.C. References colvarvalue::type(). : cvc () { function_type = "orientation"; x.type (colvarvalue::type_quaternion); }

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

Definition at line 856 of file colvarcomp.h. {}

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Member Function Documentation

void colvar::orientation::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::orientation_angle, colvar::rmsd, and colvar::logmsd. Definition at line 109 of file colvarcomp_rotations.C. References colvarmodule::atom_group::apply_force(), atoms, colvarmodule::rotation::dQ0_2, colvarmodule::atom_group::noforce, colvarvalue::quaternion_value, and rot. { cvm::quaternion const &FQ = force.quaternion_value; if (!atoms.noforce) { for (size_t ia = 0; ia < atoms.size(); ia++) { for (size_t i = 0; i < 4; i++) { atoms[ia].apply_force (FQ[i] * rot.dQ0_2[ia][i]); } } } }

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

Calculate the atomic gradients, to be reused later in order to apply forces. Implements colvar::cvc. Reimplemented in colvar::orientation_angle, colvar::rmsd, and colvar::logmsd. Definition at line 100 of file colvarcomp_rotations.C. { // gradients have already been calculated and stored within the // member object "rot"; we're not using the "grad" member of each // atom object, because it only can represent the gradient of a // scalar colvar }

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

Calculate the variable. Implements colvar::cvc. Reimplemented in colvar::orientation_angle, colvar::rmsd, and colvar::logmsd. Definition at line 83 of file colvarcomp_rotations.C. References atoms, atoms_cog, colvarmodule::rotation::calc_optimal_rotation(), colvarmodule::atom_group::center_of_geometry(), colvarmodule::atom_group::positions_shifted(), colvarmodule::rotation::q, colvarvalue::quaternion_value, colvarmodule::atom_group::read_positions(), ref_pos, ref_quat, colvarmodule::atom_group::reset_atoms_data(), and rot. { atoms.reset_atoms_data(); atoms.read_positions(); atoms_cog = atoms.center_of_geometry(); rot.calc_optimal_rotation (ref_pos, atoms.positions_shifted (-1.0 * atoms_cog)); if ((rot.q).inner (ref_quat) >= 0.0) { x.quaternion_value = rot.q; } else { x.quaternion_value = -1.0 * rot.q; } }

cvm::real colvar::orientation::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::orientation_angle, colvar::rmsd, and colvar::logmsd. Definition at line 1098 of file colvarcomp.h. References colvarmodule::fatal_error(). { cvm::fatal_error ("Error: cannot compare() two quaternions.\n"); return 0.0; }

virtual cvm::real colvar::orientation::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::orientation_angle, colvar::rmsd, and colvar::logmsd.

colvarvalue colvar::orientation::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::orientation_angle, colvar::rmsd, and colvar::logmsd. Definition at line 1086 of file colvarcomp.h. References colvarmodule::quaternion::dist2_grad(), and colvarvalue::quaternion_value. { return x1.quaternion_value.dist2_grad (x2); }

colvarvalue colvar::orientation::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::orientation_angle, colvar::rmsd, and colvar::logmsd. Definition at line 1092 of file colvarcomp.h. References colvarmodule::quaternion::dist2_grad(), and colvarvalue::quaternion_value. { return x2.quaternion_value.dist2_grad (x1); }

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Member Data Documentation

cvm::atom_group colvar::orientation::atoms [protected]

Atom group. Definition at line 838 of file colvarcomp.h. Referenced by apply_force(), calc_value(), and orientation().

cvm::atom_pos colvar::orientation::atoms_cog [protected]

Center of geometry of the group. Definition at line 840 of file colvarcomp.h. Referenced by calc_value().

std::vector<cvm::atom_pos> colvar::orientation::ref_pos [protected]

Reference coordinates. Definition at line 843 of file colvarcomp.h. Referenced by calc_value(), and orientation().

cvm::quaternion colvar::orientation::ref_quat [protected]

This is used to remove jumps in the sign of the quaternion, which may be annoying in the colvars trajectory. Definition at line 850 of file colvarcomp.h. Referenced by calc_value(), and orientation().

cvm::rotation colvar::orientation::rot [protected]

Rotation object. Definition at line 846 of file colvarcomp.h. Referenced by apply_force(), calc_value(), and orientation().

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

• colvarcomp.h
• colvarcomp_rotations.C

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