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colvar::h_bond Class Reference

\brief Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1]). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::h_bond:

List of all members.

Public Methods

h_bond (std::string const &conf)

h_bond (cvm::atom const &acceptor, cvm::atom const &donor, cvm::real r0, int en, int ed)

Constructor for atoms already allocated. More...

h_bond ()

virtual

~h_bond ()

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
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

cvm::real

\brief "Cutoff" distance between acceptor and donor. More...

int

Integer exponent of the function numerator. More...

int

Integer exponent of the function denominator. More...

Detailed Description

\brief Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1]).

Definition at line 1054 of file colvarcomp.h.

Constructor & Destructor Documentation

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

colvar::h_bond::h_bond ( cvm::atom const & acceptor,

cvm::atom const & donor,

cvm::real r0,

int en,

int ed

)

Constructor for atoms already allocated.

Definition at line 350 of file colvarcomp_coordnums.C.
References colvar::cvc::atom_groups, colvar::cvc::init_scalar_boundaries, colvar::cvc::register_atom_group, colvar::cvc::set_function_type, colvarvalue::type, colvarvalue::type_scalar, and colvar::cvc::x.

colvar::h_bond::h_bond ( )

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

Definition at line 1071 of file colvarcomp.h.

Member Function Documentation

void colvar::h_bond::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 388 of file colvarcomp_coordnums.C.
References colvar::cvc::atom_groups, and force.

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

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

Reimplemented from colvar::cvc.
Definition at line 377 of file colvarcomp_coordnums.C.
References colvar::cvc::atom_groups, ed, en, NULL, and r0.

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

\brief Calculate the variable.

Implements colvar::cvc.
Definition at line 365 of file colvarcomp_coordnums.C.
References colvar::cvc::atom_groups, ed, en, NULL, r0, colvarvalue::real_value, and colvar::cvc::x.

virtual cvm::real colvar::h_bond::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::h_bond::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::h_bond::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

int colvar::h_bond::ed [protected]

Integer exponent of the function denominator.

Definition at line 1063 of file colvarcomp.h.
Referenced by calc_gradients, and calc_value.

int colvar::h_bond::en [protected]

Integer exponent of the function numerator.

Definition at line 1061 of file colvarcomp.h.
Referenced by calc_gradients, and calc_value.

cvm::real colvar::h_bond::r0 [protected]

\brief "Cutoff" distance between acceptor and donor.

Definition at line 1059 of file colvarcomp.h.
Referenced by calc_gradients, and calc_value.

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

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