Package etomica.space

Specifies abstract classes and interfaces that define the nature of the physical space in which a simulation is performed.

See:
Description

Interface Summary

IOrientation	Interface for a class that specifies an orientation in space.
ISpace
IVectorRandom	Vector interface for vectors having random number methods
RotationTensor	A tensor intended for use to define rotations in space.
Tensor

Class Summary

Boundary	Parent class of boundary objects that describe the size and periodic nature of the box boundaries.
BoundaryDeformableLattice	Deformable boundary that takes the shape of a primitive with some number of cells in each dimension.
BoundaryDeformablePeriodic	Boundary shaped as an arbitrary parallelepiped.
BoundaryEvent
BoundaryEventManager
BoundaryRectangular	Boundary that is in the shape of a rectangular parallelepiped.
BoundaryRectangularNonperiodic	Boundary that is not periodic in any direction.
BoundaryRectangularPeriodic	Rectangular boundary that is periodic in every dimension.
BoundaryRectangularPore	Class for implementing pore periodic boundary conditions, in which one dimension is periodic.
BoundaryRectangularSlit	Class for implementing slit periodic boundary conditions, in which one dimension is not periodic.
Space

Package etomica.space Description

Specifies abstract classes and interfaces that define the nature of the physical space in which a simulation is performed. Implementations are given in the packages etomica.space3d, etomica.space2d, and etomica.space1d, for 3-, 2-, and 1-dimensional spaces, respectively. The key elements are:

• Space, which serves primarily as a factory for the other classes. Subclasses of Space make vectors, etc. appropriate to the space it represents.
• Vector, which for a D-dimensional space is a set of D fields of type double, with methods used the perform vector operations on them.
• Tensor, which defines a 2nd-rank tensor in the D-dimensional space. It hold D^2 fields of type double, and defines methods used to perform tensor operations on them.
• Orientation, which provides fields and operations define and manipulate the orientation of a rigid body.
• Boundary, which is held by a Box instance to define the size of the space and to specify what happens as atoms cross the boundary of the space (e.g., periodic boundaries).

All of the classes above (except perhaps Boundary) are implemented in the space subpackages in a manner specific to the space being defined. Additionally, this package defines several Coordinate interface, classes and factories that don't require spatially-dependent implementations (instead they are formed from fields that are specific to the space). Coordinates may be just a position/orientation, or additionally include momentum components. An instance of Coordinate is held by every Atom.

Coordinate interfaces are named beginning with "I", and indicate the number and type of fields as follows

• ICoordinate has just a vector position
• ICoordinateAngular has just a vector orientation
• IcoordinateKinetic has a vector position and vector velocity
• IcoordinateAngularKinetic has position, orientation, and velocities for each

Implementations of these interfaces are given in the like-named classes obtained by removing the initial "I".

CoordinateFactory classes make each type of coordinate, using vectors, etc. made from a given Space. The coordinate factory is used by an AtomFactory to give each constructed Atom its Coordinate instance.

The CoordinatePair class is an important tool for classes that perform calculations based on pairs of atoms.