gmx::AtomPairlist Class Reference

#include <gromacs/nbnxm/atompairlist.h>

Description

A plain atom pair list, used only for perturbed non-bonded interactions.

A list of atom pairs stored as list of so-called j-atoms for each i-atom in the list. The list is constructed by calling addIEntry() and specifying a maximum number of j-entries that can be added. Then addJEntry() can be called to add j-atoms. For performance it can be good to call popIEntryWhenEmpty() after potentially adding j-atoms, to remove empty i-entries.

Classes
struct	IEntry
	An i-entry. More...
struct	JEntry
	A j-entry. More...

Public Member Functions
void	addIEntry (const IEntry &iEntry, int maxJEntries)
	Adds a new i-entry with space for at most maxJEntries j-entries. More...
void	addJEntry (const JEntry &jEntry)
	Adds a j-entry for the last i-entry.
void	popIEntryWhenEmpty ()
	Checks whether the last i-entry has no j-entries and if so removes it.
void	clear ()
	Clears the pair list.
gmx::ArrayRef< const IEntry >	iList () const
	Returns the list of i-entries.
gmx::ArrayRef< const JEntry >	jList (gmx::Index iEntry) const
	Returns the list of j-entries for i-entry iEntry.
gmx::ArrayRef< const JEntry >	flatJList () const
	Returns a concatenated list of all j-entries for all i-entries.
int	numExclusionsWithinRlist () const
	Returns the number of excluded pairs within rlist at list creation.

Member Function Documentation

void gmx::AtomPairlist::addIEntry ( const IEntry &  iEntry, int  maxJEntries  )

inline

Adds a new i-entry with space for at most maxJEntries j-entries.

Note that this will replace the last entry instead when that is empty, i.e. has an empty list of j-entries.

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

• src/gromacs/nbnxm/atompairlist.h