Faunus::ExclusionsVicinity Class Reference

Determines if two particles within a group are excluded from mutual nonbonded interactions. More...

#include <molecule.h>

Public Types
using	char_bool = unsigned char
	obs: std::vector<bool> uses packing with performance implications
using	AtomPair = std::pair< int, int >

Public Member Functions
	ExclusionsVicinity (int atoms_cnt=0, int max_difference=0)
void	add (int i, int j)
void	add (const std::vector< std::pair< int, int >> &pairs)
bool	isExcluded (int i, int j) const
bool	empty () const
	true if no excluded interactions at all

Static Public Member Functions
static ExclusionsVicinity	create (int atoms_cnt, const std::vector< AtomPair > &pairs)
	Generates memory-optimal structure from underlying pair list. More...

Friends
void	to_json (json &j, const ExclusionsVicinity &exclusions)

Detailed Description

Determines if two particles within a group are excluded from mutual nonbonded interactions.

This is a memory optimized implementation especially for linear molecules. The matrix of excluded pairs has dimensions of number of atoms × maximal distance between excluded neighbours (in terms of atom indices within the molecule).

Constructor & Destructor Documentation

ExclusionsVicinity()

Faunus::ExclusionsVicinity::ExclusionsVicinity ( int  atoms_cnt = 0, int  max_difference = 0  )

explicit

Parameters

atoms_cnt	number of atoms in the molecule
max_difference	maximal allowed distance

Member Function Documentation

add()

void Faunus::ExclusionsVicinity::add	(	int	i,
		int	j
	)

Parameters

i,j	indices of atoms within molecule with excluded nonbonded interaction

create()

ExclusionsVicinity Faunus::ExclusionsVicinity::create ( int  atoms_cnt, const std::vector< AtomPair > &  pairs  )

static

Generates memory-optimal structure from underlying pair list.

Parameters

atoms_cnt	number of atoms in the molecule
pairs	list of excluded pairs using intramolecular indices

isExcluded()

bool Faunus::ExclusionsVicinity::isExcluded ( int  i, int  j  ) const

inline

Parameters

i,j	indices of atoms within molecule with excluded nonbonded interaction

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

• src/molecule.h
• src/molecule.cpp