colvar::eigenvector Class Reference

Colvar component: projection of 3N coordinates onto an eigenvector (colvarvalue::type_scalar type, range (-*:*)). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::eigenvector:

List of all members.

Public Member Functions
	eigenvector (std::string const &conf)
	Constructor.
virtual	~eigenvector ()
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.
Protected Attributes
cvm::atom_group	atoms
	Atom group.
std::vector< cvm::atom_pos >	ref_pos
	Reference coordinates.
std::vector< cvm::rvector >	eigenvec
	Eigenvector (of a normal or essential mode).
cvm::real	eigenvec_invnorm2
	Inverse square norm of the eigenvector.

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Detailed Description

Colvar component: projection of 3N coordinates onto an eigenvector (colvarvalue::type_scalar type, range (-*:*)).

Definition at line 515 of file colvarcomp.h.

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Constructor & Destructor Documentation

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

Constructor. Definition at line 780 of file colvarcomp_distances.C. References atoms, eigenvec, eigenvec_invnorm2, colvarmodule::fatal_error(), colvarmodule::load_coords(), colvarmodule::log(), colvarmodule::rvector::norm2(), colvar::cvc::parse_group(), ref_pos, colvarmodule::rotation::request_group1_gradients(), colvarmodule::rotation::request_group2_gradients(), colvarmodule::atom_group::rot, and colvarvalue::type(). : cvc (conf) { b_inverse_gradients = true; b_Jacobian_derivative = true; function_type = "eigenvector"; x.type (colvarvalue::type_scalar); parse_group (conf, "atoms", atoms); 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); } } // now load the eigenvector if (get_keyval (conf, "vector", eigenvec, eigenvec)) { cvm::log ("Using reference positions from input file.\n"); if (eigenvec.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, "vectorFile", file_name)) { std::string file_col; get_keyval (conf, "vectorCol", file_col, std::string ("O")); double file_col_value; bool found = get_keyval (conf, "vectorColValue", file_col_value, 0.0); if (found && !file_col_value) cvm::fatal_error ("Error: eigenvectorColValue, " "if provided, must be non-zero.\n"); eigenvec.resize (atoms.size()); cvm::load_coords (file_name.c_str(), eigenvec, file_col, file_col_value); } } if (!ref_pos.size() || !eigenvec.size()) { cvm::fatal_error ("Error: must define both reference " "coordinates and eigenvector.\n"); } cvm::rvector center (0.0, 0.0, 0.0); eigenvec_invnorm2 = 0.0; for (size_t i = 0; i < atoms.size(); i++) { center += eigenvec[i]; } cvm::log ("Subtracting sum of eigenvector components: " + cvm::to_str (center) + "\n"); for (size_t i = 0; i < atoms.size(); i++) { eigenvec[i] = eigenvec[i] - center; eigenvec_invnorm2 += eigenvec[i].norm2(); } eigenvec_invnorm2 = 1.0 / eigenvec_invnorm2; // request derivatives of optimal rotation wrt 2nd group // for Jacobian atoms.rot.request_group1_gradients(atoms.size()); atoms.rot.request_group2_gradients(atoms.size()); }

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

Definition at line 536 of file colvarcomp.h. {}

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Member Function Documentation

void colvar::eigenvector::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 893 of file colvarcomp_distances.C. References colvarmodule::atom_group::apply_colvar_force(), atoms, colvarmodule::atom_group::noforce, and colvarvalue::real_value. { if (!atoms.noforce) atoms.apply_colvar_force (force.real_value); }

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

Calculate the total force from the system using the inverse atomic gradients. Reimplemented from colvar::cvc. Definition at line 900 of file colvarcomp_distances.C. References atoms, eigenvec_invnorm2, colvarmodule::atom_group::read_system_forces(), colvarvalue::real_value, and colvarmodule::atom_group::system_force(). { atoms.read_system_forces(); ft.real_value = 0.0; for (size_t ia = 0; ia < atoms.size(); ia++) { ft.real_value += eigenvec_invnorm2 * atoms[ia].grad * atoms[ia].system_force; } }

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

Calculate the atomic gradients, to be reused later in order to apply forces. Implements colvar::cvc. Definition at line 882 of file colvarcomp_distances.C. References atoms, and eigenvec. { for (size_t i = 0; i < atoms.size(); i++) { atoms[i].grad = eigenvec[i]; } // WARNING: either the gradient must be rotated, or the automatic // rotation of forces within the atom group should be disabled. }

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

Calculate the divergence of the inverse atomic gradients. Reimplemented from colvar::cvc. Definition at line 912 of file colvarcomp_distances.C. References colvarmodule::atom_pos, atoms, colvarmodule::rotation::dQ0_1, eigenvec, eigenvec_invnorm2, j, colvarmodule::rotation::q, colvarvalue::real_value, and colvarmodule::atom_group::rot. { // gradient of the rotation matrix cvm::matrix2d <cvm::rvector, 3, 3> grad_rot_mat; cvm::quaternion &quat0 = atoms.rot.q; // gradients of products of 2 quaternion components cvm::rvector g11, g22, g33, g01, g02, g03, g12, g13, g23; cvm::atom_pos x_relative; cvm::real sum = 0.0; for (size_t ia = 0; ia < atoms.size(); ia++) { // Gradient of optimal quaternion wrt current Cartesian position // trick: d(R^-1)/dx = d(R^t)/dx = (dR/dx)^t // we can just transpose the derivatives of the direct matrix cvm::vector1d< cvm::rvector, 4 > &dq_1 = atoms.rot.dQ0_1[ia]; g11 = 2.0 * quat0[1]*dq_1[1]; g22 = 2.0 * quat0[2]*dq_1[2]; g33 = 2.0 * quat0[3]*dq_1[3]; g01 = quat0[0]*dq_1[1] + quat0[1]*dq_1[0]; g02 = quat0[0]*dq_1[2] + quat0[2]*dq_1[0]; g03 = quat0[0]*dq_1[3] + quat0[3]*dq_1[0]; g12 = quat0[1]*dq_1[2] + quat0[2]*dq_1[1]; g13 = quat0[1]*dq_1[3] + quat0[3]*dq_1[1]; g23 = quat0[2]*dq_1[3] + quat0[3]*dq_1[2]; // Gradient of the inverse rotation matrix wrt current Cartesian position // (transpose of the gradient of the direct rotation) grad_rot_mat[0][0] = -2.0 * (g22 + g33); grad_rot_mat[0][1] = 2.0 * (g12 + g03); grad_rot_mat[0][2] = 2.0 * (g13 - g02); grad_rot_mat[1][0] = 2.0 * (g12 - g03); grad_rot_mat[1][1] = -2.0 * (g11 + g33); grad_rot_mat[1][2] = 2.0 * (g01 + g23); grad_rot_mat[2][0] = 2.0 * (g02 + g13); grad_rot_mat[2][1] = 2.0 * (g23 - g01); grad_rot_mat[2][2] = -2.0 * (g11 + g22); for (size_t i = 0; i < 3; i++) { for (size_t j = 0; j < 3; j++) { sum += grad_rot_mat[i][j][i] * eigenvec[ia][j]; } } } jd.real_value = sum * sqrt (eigenvec_invnorm2); }

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

Calculate the variable. Implements colvar::cvc. Definition at line 870 of file colvarcomp_distances.C. References atoms, eigenvec, colvarmodule::atom_group::read_positions(), colvarvalue::real_value, ref_pos, and colvarmodule::atom_group::reset_atoms_data(). { atoms.reset_atoms_data(); atoms.read_positions(); x.real_value = 0.0; for (size_t i = 0; i < atoms.size(); i++) { x.real_value += (atoms[i].pos - ref_pos[i]) * eigenvec[i]; } }

virtual cvm::real colvar::eigenvector::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::eigenvector::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::eigenvector::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::eigenvector::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.

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Member Data Documentation

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

Atom group. Definition at line 521 of file colvarcomp.h. Referenced by apply_force(), calc_force_invgrads(), calc_gradients(), calc_Jacobian_derivative(), calc_value(), and eigenvector().

std::vector<cvm::rvector> colvar::eigenvector::eigenvec [protected]

Eigenvector (of a normal or essential mode). Definition at line 527 of file colvarcomp.h. Referenced by calc_gradients(), calc_Jacobian_derivative(), calc_value(), and eigenvector().

cvm::real colvar::eigenvector::eigenvec_invnorm2 [protected]

Inverse square norm of the eigenvector. Definition at line 530 of file colvarcomp.h. Referenced by calc_force_invgrads(), calc_Jacobian_derivative(), and eigenvector().

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

Reference coordinates. Definition at line 524 of file colvarcomp.h. Referenced by calc_value(), and eigenvector().

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

• colvarcomp.h
• colvarcomp_distances.C

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