#include <colvarcomp.h>
Inheritance diagram for colvar::orientation_angle:
Public Methods | |||
| orientation_angle (std::string const &conf) | |||
| virtual int | init (std::string const &conf) | ||
An init function should be defined for every class inheriting from cvc
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| virtual | ~orientation_angle () | ||
| virtual void | calc_value () | ||
| \brief Calculate the variable. More... | |||
| virtual void | calc_gradients () | ||
| \brief Calculate the atomic gradients, to be reused later in order to apply forces. More... | |||
| virtual void | apply_force (colvarvalue const &force) | ||
\brief Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function) Note: multiple calls to this function within the same simulation step will add the forces altogether
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| virtual cvm::real | dist2 (colvarvalue const &x1, colvarvalue const &x2) const | ||
| \brief 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 colvarvalue 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 colvarvalue 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 colvarvalue type. More... | |||
| virtual colvarvalue | dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const | ||
| \brief Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). More... | |||
| virtual colvarvalue | dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const | ||
| \brief Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). More... | |||
Definition at line 1250 of file colvarcomp.h.
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Definition at line 165 of file colvarcomp_rotations.C. References conf, colvardeps::enable, colvardeps::f_cvc_explicit_gradient, colvar::cvc::init_as_angle, and colvar::cvc::set_function_type. |
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Definition at line 1257 of file colvarcomp.h. |
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\brief Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft 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 208 of file colvarcomp_rotations.C. References colvar::orientation::atoms, force, and colvarvalue::real_value. |
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\brief Calculate the atomic gradients, to be reused later in order to apply forces.
Reimplemented from colvar::orientation. Definition at line 195 of file colvarcomp_rotations.C. References colvar::orientation::atoms, PI, colvar::orientation::rot, and colvarmodule::sqrt. |
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\brief Calculate the variable.
Reimplemented from colvar::orientation. Definition at line 181 of file colvarcomp_rotations.C. References colvarmodule::acos, colvar::orientation::atoms, colvar::orientation::atoms_cog, PI, colvarvalue::real_value, colvar::orientation::ref_pos, colvar::orientation::rot, and colvar::cvc::x. |
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\brief 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 colvarvalue 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 colvarvalue 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 colvarvalue type.
Reimplemented from colvar::orientation. |
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\brief 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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\brief Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
Reimplemented from colvar::orientation. |
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An init function should be defined for every class inheriting from cvc
Reimplemented from colvar::orientation. Definition at line 175 of file colvarcomp_rotations.C. References conf. |
1.2.14 written by Dimitri van Heesch,
© 1997-2002