Package etomica.nbr.cell

Provides classes for organizing boxs into subcells and collecting atoms in them for cell-based neighbor iteration.

See:
Description

Interface Summary

AtomsetIteratorCellular

Interface for atomset iterators that use cell-based neighbor lists for iteration.

Class Summary

Api1ACell	Generates pairs that are cell-based neighbors of a specific Atom.
ApiAACell	Returns iterates formed from all cell-based neighbor pairs.
AtomIteratorCell	Returns occupants of all cells as iterates.
BoxAgentSourceCellManager	BoxAgentSource responsible for creating a NeighborCellManager.
Cell	Site used to form array of cells for cell-based neighbor listing.
Cell.CellFactory
NeighborCellManager	Class that defines and manages construction and use of lattice of cells for cell-based neighbor listing.
PotentialMasterCell	A PotentialMaster for use with a Simulation where cell-listing of atoms and their neighbors is appropriate.

Package etomica.nbr.cell Description

Provides classes for organizing boxs into subcells and collecting atoms in them for cell-based neighbor iteration. Each instance of Box holds a class that implements BoxCellManager, which holds the lattice of cells and provides methods for placing the atoms in the cells. Each cell in the lattice has a linked list of atoms that are contained within it, usually based on its coordinate position in the box. Atoms being listed this way should be constructed with an AtomSequencerCell for its sequencer (the type of sequencer held by an atom is determined by the sequencer factory given to the constructor, which in turns is identified by the IteratorFactory that is held by the PotentialMaster). PotentialMasterCell is a PotentialMaster that performs energy calculations using cell-based neighbor identification. It automatically uses an instance of IteratorFactoryCell for its IteratorFactory.