gov.nasa.javaGenes.forceFields
Class MultiBodiesForOneEnergy
java.lang.Object
gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
- All Implemented Interfaces:
- java.lang.Cloneable, java.io.Serializable
- Direct Known Subclasses:
- Bodies
- public class MultiBodiesForOneEnergy
- extends java.lang.Object
- implements java.lang.Cloneable, java.io.Serializable
- See Also:
- Serialized Form
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
multiBodies
protected java.util.Vector multiBodies
molecule
protected Molecule molecule
MultiBodiesForOneEnergy
public MultiBodiesForOneEnergy()
MultiBodiesForOneEnergy
public MultiBodiesForOneEnergy(Molecule inMolecule)
MultiBodiesForOneEnergy
public MultiBodiesForOneEnergy(Molecule inMolecule,
Potential potential)
MultiBodiesForOneEnergy
public MultiBodiesForOneEnergy(Molecule inMolecule,
double cutoff)
deepCopyMultiBodiesForOneEnergy
public MultiBodiesForOneEnergy deepCopyMultiBodiesForOneEnergy()
- copy the graph and make copies of all edges and vertices
clone
public java.lang.Object clone()
throws java.lang.CloneNotSupportedException
- copy the MultiBodiesForOneEnergy and make copies molecule and the multiBodies
- Throws:
java.lang.CloneNotSupportedException
getNumberOfAtoms
public int getNumberOfAtoms()
createArrays
public void createArrays()
getBodiesNames
public java.util.Vector getBodiesNames()
add
public void add(MultiBody m)
getMolecule
public Molecule getMolecule()
size
public int size()
get
public MultiBody get(int index)
scaleLengthsBy
public void scaleLengthsBy(double scaleFactor)
scaleLengthsByAndReturnThis
public MultiBodiesForOneEnergy scaleLengthsByAndReturnThis(double scaleFactor)
removeBodiesAboveCutoff
public void removeBodiesAboveCutoff(Potential form)
makeMoleculeAndBodiesFiles
public void makeMoleculeAndBodiesFiles(java.lang.String baseName)
writeTwoBodiesToTsdFile
public void writeTwoBodiesToTsdFile(java.lang.String filename)
writeThreeBodiesToTsdFile
public void writeThreeBodiesToTsdFile(java.lang.String filename)