JavaGenes, NASA Ames. Written largely by Al Globus

gov.nasa.javaGenes.forceFields
Class MultiBodiesForOneEnergy

java.lang.Object
  extended bygov.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

Field Summary
protected  Molecule molecule
           
protected  java.util.Vector multiBodies
           
 
Constructor Summary
MultiBodiesForOneEnergy()
           
MultiBodiesForOneEnergy(Molecule inMolecule)
           
MultiBodiesForOneEnergy(Molecule inMolecule, double cutoff)
           
MultiBodiesForOneEnergy(Molecule inMolecule, Potential potential)
           
 
Method Summary
 void add(MultiBody m)
           
 java.lang.Object clone()
          copy the MultiBodiesForOneEnergy and make copies molecule and the multiBodies
 void createArrays()
           
 MultiBodiesForOneEnergy deepCopyMultiBodiesForOneEnergy()
          copy the graph and make copies of all edges and vertices
 MultiBody get(int index)
           
 java.util.Vector getBodiesNames()
           
 Molecule getMolecule()
           
 int getNumberOfAtoms()
           
 void makeMoleculeAndBodiesFiles(java.lang.String baseName)
           
 void removeBodiesAboveCutoff(Potential form)
           
 void scaleLengthsBy(double scaleFactor)
           
 MultiBodiesForOneEnergy scaleLengthsByAndReturnThis(double scaleFactor)
           
 int size()
           
 void writeThreeBodiesToTsdFile(java.lang.String filename)
           
 void writeTwoBodiesToTsdFile(java.lang.String filename)
           
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

multiBodies

protected java.util.Vector multiBodies

molecule

protected Molecule molecule
Constructor Detail

MultiBodiesForOneEnergy

public MultiBodiesForOneEnergy()

MultiBodiesForOneEnergy

public MultiBodiesForOneEnergy(Molecule inMolecule)

MultiBodiesForOneEnergy

public MultiBodiesForOneEnergy(Molecule inMolecule,
                               Potential potential)

MultiBodiesForOneEnergy

public MultiBodiesForOneEnergy(Molecule inMolecule,
                               double cutoff)
Method Detail

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)

JavaGenes, NASA Ames. Written largely by Al Globus