Main Page Namespace List Class Hierarchy Alphabetical List Compound List File List Namespace Members Compound Members File Members Related Pages

colvar::dihedPC Class Reference

\brief Colvar component: dihedPC Projection of the config onto a dihedral principal component See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007) Based on a set of 'dihedral' cvcs. More...

#include <colvarcomp.h>

Inheritance diagram for colvar::dihedPC:

List of all members.

Public Methods

dihedPC (std::string const &conf)

dihedPC ()

virtual

~dihedPC ()

void

calc_value ()

\brief Calculate the variable. More...

void

calc_gradients ()

\brief Calculate the atomic gradients, to be reused later in order to apply forces. More...

void

collect_gradients (std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients)

Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs. More...

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
Parameters:

cvforce The collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object.

More...

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...

Protected Attributes

std::vector< dihedral * >

theta

std::vector< cvm::real >

coeffs

Detailed Description

\brief Colvar component: dihedPC Projection of the config onto a dihedral principal component See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007) Based on a set of 'dihedral' cvcs.

Definition at line 1176 of file colvarcomp.h.

Constructor & Destructor Documentation

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

colvar::dihedPC::dihedPC ( )

Definition at line 419 of file colvarcomp_protein.C.
References colvardeps::enable, colvardeps::f_cvc_explicit_gradient, colvar::cvc::set_function_type, colvarvalue::type, colvarvalue::type_scalar, and colvar::cvc::x.

colvar::dihedPC::~dihedPC ( ) [virtual]

Definition at line 429 of file colvarcomp_protein.C.
References colvar::cvc::atom_groups, and theta.

Member Function Documentation

void colvar::dihedPC::apply_force ( colvarvalue const & force ) [virtual]

\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
Parameters:

cvforce The collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object.

Implements colvar::cvc.
Definition at line 483 of file colvarcomp_protein.C.
References coeffs, colvarmodule::cos, force, PI, colvarmodule::sin, and theta.

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

\brief Calculate the atomic gradients, to be reused later in order to apply forces.

Reimplemented from colvar::cvc.
Definition at line 452 of file colvarcomp_protein.C.
References theta.

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

\brief Calculate the variable.

Implements colvar::cvc.
Definition at line 440 of file colvarcomp_protein.C.
References coeffs, colvarmodule::cos, PI, colvarvalue::real_value, colvarmodule::sin, theta, and colvar::cvc::x.

void colvar::dihedPC::collect_gradients ( std::vector< int > const & atom_ids,

std::vector< cvm::rvector > & atomic_gradients

) [virtual]

Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs.

Reimplemented from colvar::cvc.
Definition at line 460 of file colvarcomp_protein.C.
References colvar::atom_ids, colvar::atomic_gradients, coeffs, colvarmodule::cos, colvarmodule::integer_power, PI, colvarmodule::real, colvarmodule::sin, colvar::cvc::sup_coeff, colvar::cvc::sup_np, theta, and colvar::cvc::value.

virtual cvm::real colvar::dihedPC::dist2 ( colvarvalue const & x1,

colvarvalue const & x2

) const [virtual]

\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::cvc.

virtual colvarvalue colvar::dihedPC::dist2_lgrad ( colvarvalue const & x1,

colvarvalue const & x2

) const [virtual]

\brief 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::dihedPC::dist2_rgrad ( colvarvalue const & x1,

colvarvalue const & x2

) const [virtual]

\brief Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).

Reimplemented from colvar::cvc.

Member Data Documentation

std::vector<cvm::real> colvar::dihedPC::coeffs [protected]

Definition at line 1182 of file colvarcomp.h.
Referenced by apply_force, calc_value, and collect_gradients.

std::vector<dihedral *> colvar::dihedPC::theta [protected]

Definition at line 1181 of file colvarcomp.h.
Referenced by apply_force, calc_gradients, calc_value, collect_gradients, and ~dihedPC.

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

Generated on Sat Apr 20 02:44:50 2024 for VMD (current) by