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Packages 
Package Description
etomica.action
Provides interfaces and classes that define elementary actions that can be performed on simulation elements.
etomica.action.activity
Collects classes that extend etomica.action.Activity, which implements Action and is an abstract class appropriate to encapsulate complex, time-consuming tasks.
etomica.api  
etomica.atom
Provides classes that define and organize atoms and the information related to them.
etomica.atom.iterator
Provides interfaces and classes for iteration of Atoms.
etomica.box  
etomica.chem.electrostatics
Under development; subject to significant change or removal.
etomica.chem.elements
Under development; subject to significant change or removal.
etomica.chem.models
Under development; subject to significant change or removal.
etomica.compatibility
Provides infrastructure that enables classes to specify restrictions on their use with other classes.
etomica.config
Provides classes for specifying the arrangement of atoms and molecules in space.
etomica.data
Defines structures that represent, generate, process, and output data from a simulation.
etomica.data.meter
DataSources that act on a Box.
etomica.data.types
Defines classes that encapsulate various types of data and enable casting between them.
etomica.exception
Defines exceptions for use in the etomica framework.
etomica.graphics  
etomica.integrator
Provides Integrator classes that implement different molecular simulation algorithms.
etomica.integrator.mcmove
Defines Monte Carlo trial moves that are used by the IntegratorMC class.
etomica.junit
Provides classes that define or support unit tests to check for the correct functioning of some etomica classes.
etomica.junit.atom  
etomica.junit.atom.iterator
Provides classes that define or support unit tests to check for the correct functioning of the atom iterators.
etomica.junit.data  
etomica.junit.data.types  
etomica.junit.simulation  
etomica.junit.space  
etomica.lattice
Provides classes for defining regular arrays of objects (sites), typically points in space.
etomica.lattice.crystal
Defines primitives and basis points for construction of various Bravais lattices.
etomica.listener  
etomica.math
Provides classes implementing some selected mathematical utilities.
etomica.math.discrete
Defines classes that provide some discrete mathematics utilities, particularly the generation of permutations and combinations.
etomica.math.geometry
Provides classes that define points, planes, and geometric shapes.
etomica.math.geometry.coordinate  
etomica.math.linearalgebra
Defines classes that provide linear algebra utilities, such as eigensystem analysis and solution of linear algebraic equations.
etomica.models.aceticAcid  
etomica.models.co2  
etomica.models.water
Under development; subject to significant change or removal.
etomica.modifier
Provides classes that define adapters to permit modification of arbitrary fields in arbitrary classes.
etomica.nbr
Provides classes that implement neighbor-listing capabilities.
etomica.nbr.cell
Provides classes for organizing boxs into subcells and collecting atoms in them for cell-based neighbor iteration.
etomica.nbr.cell.molecule
Provides classes for organizing boxs into subcells and collecting atoms in them for cell-based neighbor iteration.
etomica.nbr.list
Provides classes that implement neighbor-listing capabilities.
etomica.nbr.list.molecule
Provides classes that implement neighbor-listing capabilities.
etomica.nbr.molecule
Provides classes that implement neighbor-listing capabilities.
etomica.nbr.site  
etomica.parser  
etomica.potential  
etomica.simulation  
etomica.simulation.prototypes  
etomica.space
Specifies abstract classes and interfaces that define the nature of the physical space in which a simulation is performed.
etomica.space1d
Implementation of space classes for a 1-dimensional space.
etomica.space2d
Implementation of space classes for a 2-dimensional space.
etomica.space3d
Implementation of space classes for a 3-dimensional space.
etomica.spaceNd  
etomica.species  
etomica.statmech  
etomica.tests  
etomica.units
Defines units and dimensions that are used for conversions during input or output.
etomica.units.systems
Provides classes that specify a system of units, such as SI, English, etc.
etomica.util
Collects miscellaneous utility classes that serve a variety of purposes.
etomica.util.numerical  
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