Package etomica.atom

Interface Summary

Interface	Description
AtomLeafAgentManager.AgentSource<E>	Interface for an object that wants an agent associated with each Atom in a Box.
AtomSource	Interface for objects when return atoms (meeting some specification) from a box.
AtomTest	Interface for a class that determines if an atom satisfies a test.
AtomTestCollective	AtomTest that needs to be informed whenever something has changed and the status of atoms should be redetermined.
AtomToAtomLeafList	Interface for class that determines an AtomArrayList given an atom.
AtomToIndex	Interface for class that associates an integer with an atom.
AtomTypeAgentManager.AgentSource<E>	Interface for an object that wants an agent associated with each AtomType in a Simulation.
DiameterHash	This provides an interface for a class that acts like a hashmap for atomic diameters.
IAtom	IAtom is an interface for atoms in the simulation.
IAtomKinetic	Interface for an atom that holds vectors for velocity.
IAtomList	Interface for a list of IAtoms.
IAtomOriented	Interface for a IAtom that includes an IVector that defines the atom's orientation.
IAtomOrientedKinetic	Interface for an Atom that has a position, orientation, velocity and angular velocity.

Class Summary

Class	Description
Atom	Atom that represents a physical atom with a position.
AtomArrayList
AtomGroupVelocityAverage	Calculates the mass average velocity over a set of atoms.
AtomHydrogen
AtomLeafAgentManager<E>	AtomAgentManager acts on behalf of client classes (an AgentSource) to manage agents for every leaf Atom in a box.
AtomLeafDynamic
AtomListFromArray	AtomSet formed by wrapping an Atom array.
AtomOriented
AtomOrientedDynamic
AtomOrientedQuaternion
AtomPair	Data structure that contains two mutable atom instances.
AtomSetSinglet	Data structure that contains a single mutable atom instance.
AtomSourceRandomLeaf	AtomSource that returns a completely random leaf atom.
AtomSourceRandomSpecies	AtomSource that returns a completely random leaf atom.
AtomToAtomSetFixed
AtomToIndexChild	Defines the index as the Atom's node's index.
AtomToParentChildList
AtomType	Identifies a set of atoms and defines properties of those atoms.
AtomTypeAgentManager<E>	AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to manage agents for every AtomType in a box.
AtomTypeOriented	Atom type for a sphere that has some feature depending upon an orientation coordinate.
AtomTypeSpheroPolyhedron
DiameterHashByElement	This class hashes atomic diameters based on the element.
DiameterHashByElementType	This class hashes atomic diameters based on both element and atom type.
DiameterHashByType	This class hashes atomic diameters based on the atom type.