Package etomica.atom

Provides classes that define and organize atoms and the information related to them.

See:
Description

Interface Summary

AtomFilter	Interface for a class that screens atoms according to some criterion.
AtomFilterCollective	Filter that needs to be informed whenever something has changed and the filtered status of atoms should be redetermined.
AtomLeafAgentManager.AgentSource	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.
AtomToAtomLeafList	Interface for class that determines an AtomArrayList given an atom.
AtomToIndex	Interface for class that associates an integer with an atom.
AtomTypeAgentManager.AgentSource	Interface for an object that wants an agent associated with each AtomType in a Simulation.
DipoleSource	Interface for something that can calculate the dipole of a molecule.
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.
IAtomPositionDefinition	Returns a vector given an atom, thereby defining the position of the atom or atom group.
IAtomTypeOriented
IMoleculeKinetic	Interface for an molecule that holds vectors for velocity.
IMoleculeOriented	Interface for a IAtom that includes an IVector that defines the atom's position.
IMoleculeOrientedKinetic	Interface for an Atom that has a position, orientation, velocity and angular velocity.
IMoleculePositioned
MoleculeAgentManager.MoleculeAgentSource	Interface for an object that wants an agent associated with each IMolecule an IBox.
MoleculeSource	Interface for objects when return atoms (meeting some specification) from a box.
MoleculeToIndex	Interface for class that associates an integer with an atom.
MoleculeToMoleculeList	Interface for class that determines an AtomArrayList given an atom.
OrientationCalc	Interface for a class that can calculate the orientation of a molecule or to set the orientation of a molecule.
OrientationCalcQuaternion	OrientationCalc interface that handles quaternions (as a a double array) instead of an Orientation object.
SpeciesAgentManager.AgentSource	Interface for an object that wants an agent associated with each AtomType in a Simulation.

Class Summary

Atom	Atom that represents a physical atom with a position.
AtomArrayList
AtomFilterInShape	Filter that accepts atom if it is inside a specified Shape instance.
AtomFilterStatic
AtomGroupVelocityAverage	Calculates the mass average velocity over a set of atoms.
AtomLeafAgentManager	AtomAgentManager acts on behalf of client classes (an AgentSource) to manage agents for every leaf Atom in a box.
AtomLeafAgentManager.AgentIterator	Iterator that loops over the agents, skipping null elements
AtomLeafDynamic
AtomListWrapper	AtomSet formed by wrapping an AtomArrayList.
AtomOriented
AtomOrientedDynamic
AtomPair	Data structure that contains two mutable atom instances.
AtomPositionCOM	Calculates the center of mass (COM) over a set of atoms.
AtomPositionFirstAtom	Returns the position of the first child leaf atom.
AtomPositionGeometricCenter	Calculates the geometric center over a set of atoms.
AtomPositionGeometricCenterPBC	Calculates the geometric center over a set of atoms.
AtomsetArray	AtomSet formed by wrapping an Atom array.
AtomSetSinglet	Data structure that contains a single mutable atom instance.
AtomSourceRandomLeaf	AtomSource that returns a completely random leaf atom.
AtomToAtomSetFixed
AtomToIndexChild	Defines the index as the Atom's node's index.
AtomToParentChildList
AtomTypeAgentManager	AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to manage agents in every AtomType in a box.
AtomTypeAgentManager.AgentIterator	Iterator that loops over the agents, skipping null elements
AtomTypeLeaf	Type for an atom that is a leaf in the species hierarchy.
AtomTypeOrientedSphere	Atom type for a sphere that has some feature depending upon an orientation coordinate.
AtomTypeSphere	Atom type for a simple monatomic atom that has a length scale associated with its size.
AtomTypeWell
Molecule
MoleculeAgentManager	MoleculeAgentManager acts on behalf of client classes (an AgentSource) to manage agents in every IMolecule in a box.
MoleculeAgentManager.AgentIterator	Iterator that loops over the agents, skipping null elements
MoleculeArrayList
MoleculeListWrapper	AtomSet formed by wrapping an AtomArrayList.
MoleculeOriented	Molecule class appropriate for a rigid molecule.
MoleculeOrientedDynamic	Molecule class appropriate for a rigid molecule in a dynamic context.
MoleculePair	Data structure that contains two mutable atom instances.
MoleculesetArray	AtomSet formed by wrapping an Atom array.
MoleculeSetSinglet	Data structure that contains a single mutable atom instance.
MoleculeSourceRandomMolecule	AtomSource that returns a completely random molecule.
MoleculeToMoleculeListSpecies
OrientationCalcAtom	OrientationCalc implementation that handles a monotomic oriented molecule.
SpeciesAgentManager	AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to manage agents in every AtomType in a box.
SpeciesAgentManager.AgentIterator	Iterator that loops over the agents, skipping null elements

Package etomica.atom Description

Provides classes that define and organize atoms and the information related to them. The physical atoms that are manipulated in a simulation are represented by instances of the class Atom. Atom plays a larger role than this, however. Instances of Atom are arranged into a tree structure, through which they organize atoms into molecules, species, and boxs.

This "Atom tree" may be understood as follows:

• At the top of the tree is an instance of SpeciesRoot, which serves as a single point of reference for all Atom instances in the simulation.
• At the bottom of the tree are the "leaf Atoms", which correspond the physical atoms being simulated.
• Below the SpeciesRoot atom are instances of SpeciesMaster, which correspond to the boxs being simulated. All Atoms in the tree below a given SpeciesMaster belong to a single Box, and are subject to interaction with each other (Atoms in different Boxs have no mutual interactions). Every instance of a Box has a single SpeciesMaster field.
• Below each SpeciesMaster in the tree are one or more SpeciesAgent instances. There is a SpeciesAgent for each Species that has been instantiated by the Simulation.
• SpeciesRoot, SpeciesMaster, and SpeciesAgent are all subclasses of Atom.
• Below each SpeciesAgent are Atom instances that represent the molecules of the corresponding Species. This is the "molecule layer" of the tree. If the molecules are monatomic, this branch of the tree terminates here, and the molecules are the physical "leaf" atoms of that species. Note that there is no Molecule class; these and all other nodes of the tree are (logically) Atom instances.
• For multiatomic species, below the molecules will be one or more levels that represent molecule subgroups (e.g., methyl groups), and finally the physical atoms themselves (which often are directly below the molecule layer).

The tree structure is implemented by the etomica.atom.AtomTreeNode AtomTreeNode class, which is held as a field by each Atom. AtomTreeNode is subclassed into AtomTreeNodeLeaf and AtomTreeNodeGroup, respectively, for Atoms that are leaf atoms in the species hierarchy, and atom groups, which include everything else.

Information about an Atom's position in the atom hierarchy is coded in an integer index, which can be interpreted using the methods of AtomIndexManger. The appropriate instance of AtomIndexManager for this purpose is held by the Atom's AtomType instance (discussed below).

The state of an Atom -- usually its position and perhaps velocity (but more general definitions are possible) -- is held by a Coordinate field (defined in etomica.space) which is made by the governing Space and which is provided to the Atom at construction. The conduct of the simulation primarily entails the manipulation of the fields of the Atom Coordinates.

The AtomType class is used to hold information that is common to many Atom instances. Each Atom has a final AtomType field that is specifed at construction. Atoms that that are group atoms (having AtomTreeNodeGroup as their node field) have types that are (or extend) AtomTypeGroup. Leaf atoms have types that extend AtomTypeLeaf. Instances of AtomType are arranged in a hierarchy that parallels that Atom hierarchy. Important features are as follows:

• At the top of the type hierarchy is AtomTypeRoot, which is the AtomType held by SpeciesRoot.
• Below AtomTypeRoot is a single instance of AtomTypeGroup, which is the AtomType held by all SpeciesMaster instances. The Box an atom is in has no significance to its AtomType.
• Below the SpeciesMaster AtomType is an AtomType instance corresponding to each Species. All SpeciesAgents for a given Species reference the same AtomType.
• Likewise, on down the tree all similarly formed Atoms will reference the same AtomType instance. The AtomType tree is a condensed version of the Atom tree; it has the same number of layers, but each layer in general has fewer nodes.

AtomTypes are very important in defining the interactions between Atoms, as developed in the etomica.potential package.

Each Atom instance at or below the molecule layer is constructed by an AtomFactory. Complicated molecules are constructed by piecing together groups of atoms constructed by subfactories. Thus the AtomFactories can be viewed in a hierarchy that mimicks the AtomType hierarchy; accordingly there is a one-to-one correspondence between the AtomTypes and the AtomFactories. The key AtomFactories are:

• AtomFactoryMono, which produces a leaf atom.
• AtomFactoryHomo, which produces an Atom that groups identically-formed child atoms (made by a single subfactory).
• AtomFactoryHetero, which produces an Atom that groups heterogeneous child atoms (made by more than one subfactory).

This package also defines data structures used to collect Atom instances. These include:

• AtomSet, an interface for a collection of an arbitrary (but usually small) number of atoms.
• AtomPair, an AtomSet formed from exactly two Atoms.
• AtomList, a linked list of Atoms; good for making mutable collections (atoms easily added and removed) for which random access is not often demanded
• AtomArrayList, a collection of Atoms which provides fast access at the expense of slower mutability

AtomSet, and AtomPair in particular, are the expected arguments of Potential classes when calculating interatomic interactions. Iteration over Atoms, AtomPairs and AtomSets is provided by the classes of etomica.atom.iterator.

Atom groups hold their child Atoms in an AtomList. The AtomLinkers used to form this list are referable directly as fields of their corresponding Atoms; access to this linker is needed for iterations that begin with a specific Atom.

The Parameter classes are not carefully developed are subject to substantial change or elimination in the near future.