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.

By providing the current time, we can cache results in order to use them once per timestep. In the long term, we would prefer to also allow client code to preregister interest in a position at a given time, or issue "futures".

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