Package etomica.config

Provides classes for specifying the arrangement of atoms and molecules in space.

See:
Description

Interface Summary

Configuration	General class for assignment of molecules to positions in a box.
IConformation

Class Summary

ConfigurationFile	reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationLattice	Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationLattice.MyLattice	Used to store the state of a lattice.
ConfigurationLatticeSimple	Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationLatticeWithPlane	Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationOrientedFile	ConfigurationFile subclass capable of handling oriented atoms.
ConfigurationZincblende	Sets the configuration to the zincblende structure, which consists of two fcc lattices, with one shifted in each direction by one-quarter of the lattice constant.
ConformationChain	General class for a collection of linearly linked atoms.
ConformationChain2D
ConformationChain3D
ConformationChainLinear	Places atoms in a straight line.
ConformationChainZigZag	Takes two vectors, and returns them in repeating order to form a zig-zag chain molecule.
ConformationChainZigZag2
ConformationLinear	Places atoms in a straight line.
ConformationWater
GrainBoundaryConfiguration
GrainBoundaryTiltConfiguration

Package etomica.config Description

Provides classes for specifying the arrangement of atoms and molecules in space. Two general categories of classes are defined:

• classes extending <@link etomica.config.Configuration Configuration> define arrangements of molecules a Box. A Configuration acts on all molecules in the box, and their placement takes into account the dimensions of the Box's Boundary.
• classes extending <@link etomica.config.Conformation Conformation> define arrangements of Atoms in an atom group. These classes act on the atoms in an AtomList, and they put the atoms in some specified arrangement that typically is centered on or near the origin.

Each AtomFactory holds a Conformation class that it uses to place in a standard arrangement the Atoms in the atom group it builds.

The molecules initially populating a Box have the coordinates given to them by their AtomFactory. Thus most molecules initially lie on top of one another. A Configuration must be instantiated and applied (using its initializeCoordinates method) to the Box before simulation commences.