Avogadro::NeighborList Class Reference

A list container for finding spatial neighbors of atoms. More...

#include <avogadro/neighborlist.h>

List of all members.

Public Member Functions
	NeighborList (Molecule *mol, double rcut, bool periodic=false, int boxSize=1)
	NeighborList (const QList< Atom * > &atoms, double rcut, bool periodic=false, int boxSize=1)
void	update ()
QList< Atom * >	nbrs (Atom *atom, bool uniqueOnly=true)
QList< Atom * >	nbrs (const Eigen::Vector3f *pos)
double	r2 (unsigned int index) const

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Detailed Description

A list container for finding spatial neighbors of atoms.

Author:

Tim Vandermeersch

NeighborList can be used for finding non-bonded interactions between pairs of atoms. Based on: Near-neighbor calculations using a modified cell-linked list method Mattson, W.; B. M. Rice (1999). "Near-neighbor calculations using a modified cell-linked list method". Computer Physics Communications 119: 135.

http://dx.doi.org/10.1016/S0010-4655%2898%2900203-3

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Constructor & Destructor Documentation

Avogadro::NeighborList::NeighborList	(	Molecule *	mol,
		double	rcut,
		bool	periodic = false,
		int	boxSize = 1
	)

Constructor to include all atoms.

Parameters:

mol	The molecule containing the atoms
rcut	The cut-off distance.
boxSize	The number of cells per rcut distance.

References Avogadro::Molecule::atoms().

Avogadro::NeighborList::NeighborList	(	const QList< Atom * > &	atoms,
		double	rcut,
		bool	periodic = false,
		int	boxSize = 1
	)

Construcor.

Parameters:

atoms	The atoms
rcut	The cut-off distance.
periodic	Use periodic boundary conditions.
The	number of cells per rcut distance.

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Member Function Documentation

QList< Atom * > Avogadro::NeighborList::nbrs	(	Atom *	atom,
		bool	uniqueOnly = true
	)

Get the near-neighbor atoms for atom. The squared distance is checked and is cached for later use (see r2() function).

Note: Atoms in relative 1-2 and 1-3 positions are not returned. The atom itself isn't added to the list.

Parameters:

atom	The atom for which to return the near-neighbors

Returns:

The near-neighbors for atom

References QList::append(), QList::clear(), Avogadro::Primitive::index(), and Avogadro::Atom::pos().

QList< Atom * > Avogadro::NeighborList::nbrs

(

const Eigen::Vector3f *

pos

)

Get the near-neighbor atoms around pos. The squared distance is checked and is cached for later use (see r2() function).

Parameters:

pos	The position for which to return the near-neighbors

Returns:

The near-neighbors for atom

References QList::append(), and QList::clear().

double Avogadro::NeighborList::r2

(

unsigned int

index

)

const [inline]

Get the cached squared distance from the atom last used to call nbrs to the atom with index in the returned vector.

Parameters:

index

The index for the atom in the vector of atoms returned by nbrs().

Returns:

The cached squared distance.

void Avogadro::NeighborList::update

(

)

Update the cells. While minimizing or running MD simulations, atoms move and can go from on cell into the next. This function should be called every 10-20 iterations to make sure the cells stay accurate.

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

• /home/kitware/dashboards/avogadro/libavogadro/src/neighborlist.h
• /home/kitware/dashboards/avogadro/libavogadro/src/neighborlist.cpp