Package etomica.parser

Class ParmedStructure

java.lang.Object

etomica.parser.ParmedStructure

public class ParmedStructure
extends java.lang.Object

Class that contains the data from a ParmEd Structure, and has methods to load this data into various etomica components.

This class should not be instantiated directly, but instead created by the ParmedParser static methods which invoke the Python library.

See Also:

ParmedParser

Method Summary

Modifier and Type	Method	Description
Box	getBox()	Gets the (single, rectangular) box found in this Structure.
PotentialGroup	getIntermolecularPotential()	Gets the intermolecular PotentialGroup for the atom types found in this Structure.
java.util.List<IMolecule>	getMolecules()	Gets the list of all molecules in the Structure, initialized with their coordinates in space.
SpeciesGeneral	getSpecies()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getBox

public Box getBox()

Gets the (single, rectangular) box found in this Structure.

Returns:

a Box object with the same boundary coordinates as the box in the Structure.

getSpecies

public SpeciesGeneral getSpecies()

getIntermolecularPotential

public PotentialGroup getIntermolecularPotential()

Gets the intermolecular PotentialGroup for the atom types found in this Structure. Constructs all unique unordered pairs of atom types and creates P2LennardJones potentials using Lorentz-Berthelot combining rules.

Returns:

the PotentialGroup for potentials between molecules in this Structure.

getMolecules

public java.util.List<IMolecule> getMolecules()

Gets the list of all molecules in the Structure, initialized with their coordinates in space.

Returns:

a List containing all the molecules of a species in the structure.