gmx::Site Class Reference

#include <gromacs/restraint/restraintmdmodule_impl.h>

Description

Abstraction for a restraint interaction site.

A restraint may operate on a single atom or some other entity, such as a selection of atoms. The Restraint implementation is very independent from how coordinates are provided or what they mean.

First implementation can only represent single atoms in a global context.

Ultimately, this should be replaced with a more universal facility for acting on distributed atom data or simple transformations thereof.

Public Member Functions
	Site (int globalIndex)
	Construct from global atom indices. More...
	Site (const Site &site)
	Explicitly define copies. More...
Site &	operator= (const Site &)=delete
	Disallow assignment. More...
int	index () const
	Get the global atom index of an atomic site. More...
RVec	centerOfMass (const t_commrec &cr, size_t nx, ArrayRef< const RVec > x, double gmx_unused t)
	Get the position of this site at time t. More...

Constructor & Destructor Documentation

gmx::Site::Site ( int  globalIndex )

inlineexplicit

Construct from global atom indices.

Parameters

globalIndex

Atom index in the global state (as input to the simulation)

gmx::Site::Site ( const Site &  site )

inline

Explicitly define copies.

Implicit definition is not possible because of the mutex member, and a copy constructor is necessary to use Site in a std::vector. Really, we should make a copy point to the same implementation object to reuse its cache.

Member Function Documentation

RVec gmx::Site::centerOfMass ( const t_commrec &  cr, size_t  nx, ArrayRef< const RVec >  x, double gmx_unused  t  )

inline

Get the position of this site at time t.

Parameters

cr	Communications record.
nx	Number of locally available atoms (size of local atom data arrays)
x	Array of locally available atom coordinates.
t	the current time.

Returns

position vector.

int gmx::Site::index ( ) const

inline

Get the global atom index of an atomic site.

Returns

global index provided at construction.

Site& gmx::Site::operator= ( const Site &  )

delete

Disallow assignment.

Assignment doesn't make sense because it implies that a site's meaning is fuzzy. If the definition of a site is changing, just make a new site. There's nothing to be gained by reusing one or by creating it uninitialized.

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

• src/gromacs/restraint/restraintmdmodule_impl.h