Neighbour list class. More...

#include <nblist.h>

Inheritance diagram for votca::csg::NBList:

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Collaboration diagram for votca::csg::NBList:

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Classes
class	Functor

class	FunctorMember
	Functor for member functions. More...

class	FunctorNonMember
	Functor for non-member functions. More...

Public Member Functions
	NBList ()

	~NBList () override

virtual void	Generate (BeadList &list1, BeadList &list2, bool do_exclusions=true)
	Generate the neighbour list based on two bead lists (e.g. bead types)

virtual void	Generate (BeadList &list, bool do_exclusions=true)
	Generate the neighbour list based on a single bead list.

void	setCutoff (double cutoff)
	set the cutoff for the neighbour search

double	getCutoff () const
	get the cutoff for the neighbour search

template<typename T >
void	SetMatchFunction (T object, bool(T::fkt)(Bead , Bead , const Eigen::Vector3d &, double dist))
	match function for class member functions

void	SetMatchFunction (bool(fkt)(Bead , Bead *, const Eigen::Vector3d &, double))
	match function for static member functions or plain functions

template<typename pair_type >
void	setPairType ()
	function to use a user defined pair type

Public Member Functions inherited from votca::csg::PairList< Bead *, BeadPair >
	PairList ()=default

virtual	~PairList ()

void	AddPair (BeadPair *p)

iterator	begin ()

const_iterator	begin () const

iterator	end ()

const_iterator	end () const

BeadPair *	front ()

BeadPair *	back ()

bool	empty () const

Index	size () const

void	Cleanup ()

BeadPair *	FindPair (Bead e1, Bead e2)

const BeadPair *	FindPair (Bead e1, Bead e2) const

partners *	FindPartners (Bead *e1)

Static Public Member Functions
static bool	match_always (Bead , Bead , const Eigen::Vector3d &, double)
	standard match function

Protected Types
using	pair_creator_t = BeadPair ()(Bead , Bead , const Eigen::Vector3d &)

Static Protected Member Functions
template<typename pair_type >
static BeadPair *	beadpair_create_policy (Bead bead1, Bead bead2, const Eigen::Vector3d &r)
	policy function to create new bead types

Protected Attributes
double	cutoff_
	cutoff

bool	do_exclusions_
	take into account exclusions from topolgoy

pair_creator_t	pair_creator_
	the current bead pair creator function

std::unique_ptr< Functor >	match_function_

Protected Attributes inherited from votca::csg::PairList< Bead *, BeadPair >
std::vector< BeadPair * >	pairs_

std::map< Bead , std::map< Bead , BeadPair * > >	pair_map_

Additional Inherited Members
Public Types inherited from votca::csg::PairList< Bead *, BeadPair >
using	iterator

using	const_iterator

typedef std::map< Bead , BeadPair >	partners

using	element_t

using	pair_t

Detailed Description

Neighbour list class.

Implements a simple N^2 neighbour search and stores neigbourlist with pair structure. User defined criteria can be added by SetMatchFunction. To only get every pair listed once, the SetMatchFunction can be used and always return that the pair is not stored.

Definition at line 39 of file nblist.h.

Member Typedef Documentation

◆ pair_creator_t

using votca::csg::NBList::pair_creator_t = BeadPair *(*)(Bead *, Bead *, const Eigen::Vector3d &)

protected

Definition at line 102 of file nblist.h.

Constructor & Destructor Documentation

◆ NBList()

votca::csg::NBList::NBList ( )

Definition at line 28 of file nblist.cc.

◆ ~NBList()

votca::csg::NBList::~NBList ( )

override

Definition at line 33 of file nblist.cc.

Member Function Documentation

◆ beadpair_create_policy()

template<typename pair_type >

static BeadPair * votca::csg::NBList::beadpair_create_policy	(	Bead *	bead1,
		Bead *	bead2,
		const Eigen::Vector3d &	r )

inlinestaticprotected

policy function to create new bead types

Definition at line 97 of file nblist.h.

◆ Generate() [1/2]

virtual void votca::csg::NBList::Generate	(	BeadList &	list,
		bool	do_exclusions = true )

inlinevirtual

Generate the neighbour list based on a single bead list.

Reimplemented in votca::csg::NBListGrid.

Definition at line 48 of file nblist.h.

◆ Generate() [2/2]

void votca::csg::NBList::Generate	(	BeadList &	list1,
		BeadList &	list2,
		bool	do_exclusions = true )

virtual

Generate the neighbour list based on two bead lists (e.g. bead types)

Reimplemented in votca::csg::NBListGrid.

Definition at line 37 of file nblist.cc.

◆ getCutoff()

double votca::csg::NBList::getCutoff ( ) const

inline

get the cutoff for the neighbour search

Definition at line 55 of file nblist.h.

◆ match_always()

static bool votca::csg::NBList::match_always	(	Bead *	,
		Bead *	,
		const Eigen::Vector3d &	,
		double	)

inlinestatic

standard match function

Definition at line 81 of file nblist.h.

◆ setCutoff()

void votca::csg::NBList::setCutoff ( double cutoff )

inline

set the cutoff for the neighbour search

Definition at line 53 of file nblist.h.

◆ SetMatchFunction() [1/2]

void votca::csg::NBList::SetMatchFunction ( bool(* fkt )(Bead *, Bead *, const Eigen::Vector3d &, double) )

inline

match function for static member functions or plain functions

Definition at line 166 of file nblist.h.

◆ SetMatchFunction() [2/2]

template<typename T >

void votca::csg::NBList::SetMatchFunction	(	T *	object,
		bool(T::*	fkt )(Bead , Bead , const Eigen::Vector3d &, double dist) )

inline

match function for class member functions

SetMatchFunction can be used to specify additional criteria, weather two beads are added to the list of pairs or not. The function gets the two two beads and the distance vector as argument. If a pair should be added, the function should return true, otherwise false.

This function can also be used, in a situation where each pair needs only to be processed once, but the total number of pairs is to big to be stored in memory, e.g. to calculate rdf for huge systems. In this case, set a match function which always returns false (->no pair is added), and do the processing in the match function.

Definition at line 159 of file nblist.h.

◆ setPairType()

template<typename pair_type >

void votca::csg::NBList::setPairType ( )

function to use a user defined pair type

Definition at line 154 of file nblist.h.

Member Data Documentation

◆ cutoff_

double votca::csg::NBList::cutoff_

protected

cutoff

Definition at line 91 of file nblist.h.

◆ do_exclusions_

bool votca::csg::NBList::do_exclusions_

protected

take into account exclusions from topolgoy

Definition at line 93 of file nblist.h.

◆ match_function_

std::unique_ptr<Functor> votca::csg::NBList::match_function_

protected

Definition at line 150 of file nblist.h.

◆ pair_creator_

pair_creator_t votca::csg::NBList::pair_creator_

protected

the current bead pair creator function

Definition at line 104 of file nblist.h.

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

csg/include/votca/csg/nblist.h
csg/src/libcsg/nblist.cc

Classes

Public Member Functions

Static Public Member Functions

Protected Types

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ pair_creator_t

Constructor & Destructor Documentation

◆ NBList()

◆ ~NBList()

Member Function Documentation

◆ beadpair_create_policy()

◆ Generate() [1/2]

◆ Generate() [2/2]

◆ getCutoff()

◆ match_always()

◆ setCutoff()

◆ SetMatchFunction() [1/2]

◆ SetMatchFunction() [2/2]

◆ setPairType()

Member Data Documentation

◆ cutoff_

◆ do_exclusions_

◆ match_function_

◆ pair_creator_