#include <colvarcomp.h>
Inheritance diagram for colvar::orientation_angle:
Public Member Functions | |
| orientation_angle (std::string const &conf) | |
| orientation_angle () | |
| virtual | ~orientation_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. | |
Definition at line 874 of file colvarcomp.h.
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Definition at line 124 of file colvarcomp_rotations.C. References colvarvalue::type(). 00125 : orientation (conf) 00126 { 00127 function_type = "orientation_angle"; 00128 x.type (colvarvalue::type_scalar); 00129 }
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Definition at line 132 of file colvarcomp_rotations.C. References colvarvalue::type(). 00133 : orientation() 00134 { 00135 function_type = "orientation_angle"; 00136 x.type (colvarvalue::type_scalar); 00137 }
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Definition at line 881 of file colvarcomp.h. 00881 {}
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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
Reimplemented from colvar::orientation. Definition at line 170 of file colvarcomp_rotations.C. References colvarmodule::atom_group::apply_colvar_force(), colvarmodule::atom_group::noforce, and colvarvalue::real_value. 00171 {
00172 cvm::real const &fw = force.real_value;
00173
00174 if (!atoms.noforce) {
00175 atoms.apply_colvar_force (fw);
00176 }
00177 }
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Calculate the atomic gradients, to be reused later in order to apply forces.
Reimplemented from colvar::orientation. Definition at line 157 of file colvarcomp_rotations.C. References colvarmodule::rotation::dQ0_2, and colvarmodule::rotation::q. 00158 {
00159 cvm::real const dxdq0 =
00160 ( ((rot.q).q0 * (rot.q).q0 < 1.0) ?
00161 ((180.0 / PI) * (-2.0) / ::sqrt (1.0 - ((rot.q).q0 * (rot.q).q0))) :
00162 0.0 );
00163
00164 for (size_t ia = 0; ia < atoms.size(); ia++) {
00165 atoms[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
00166 }
00167 }
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Calculate the variable.
Reimplemented from colvar::orientation. Definition at line 140 of file colvarcomp_rotations.C. References colvarmodule::rotation::calc_optimal_rotation(), colvarmodule::atom_group::center_of_geometry(), colvarmodule::atom_group::positions_shifted(), colvarmodule::rotation::q, colvarmodule::atom_group::read_positions(), colvarvalue::real_value, and colvarmodule::atom_group::reset_atoms_data(). 00141 {
00142 atoms.reset_atoms_data();
00143 atoms.read_positions();
00144
00145 atoms_cog = atoms.center_of_geometry();
00146
00147 rot.calc_optimal_rotation (ref_pos, atoms.positions_shifted (-1.0 * atoms_cog));
00148
00149 if ((rot.q).q0 >= 0.0) {
00150 x.real_value = (180.0/PI) * 2.0 * ::acos ((rot.q).q0);
00151 } else {
00152 x.real_value = (180.0/PI) * 2.0 * ::acos (-1.0 * (rot.q).q0);
00153 }
00154 }
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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::orientation. |
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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::orientation. |
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Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
Reimplemented from colvar::orientation. |
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Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
Reimplemented from colvar::orientation. |
1.3.9.1