core.pbc
Class PBC

java.lang.Object
  core.pbc.PBC

Direct Known Subclasses:

PBC_RectBox, PBC_TruncOct

public class PBC

extends java.lang.Object

PBC (Periodic Boundary Condition).

Utilities for handling periodic boundary conditions, such as nearest images and gathering procedures.

Currently supported boundary conditions are:

• vacuum ("v")
• rectangular ("r")
• truncated octahedral ("t")

Often-used gather methods are:

• default GROMOS gathering: gather with respect to first atom ("g")
• center-of-geometry gathering: gather with respect to the center of geometry of the ungathered molecule ("cog")

Since:

0.1

Version:

0.1, January 2005

Author:

Mika Kastenholz, Vincent Kraeutler

See Also:

PBC_RectBox, PBC_TruncOct

Nested Class Summary

(package private) class	PBC.ByMoleculeGatherer
(package private) class	PBC.CoGGatherer
(package private) class	PBC.G96Gatherer
(package private) static interface	PBC.Gatherer
(package private) class	PBC.InBoxGatherer gathers all molecules first individually and moves them afterwards into the central box.

Field Summary

PBC.Gatherer

gatherMethod Comment for gatherMethod

Constructor Summary

PBC(java.lang.String gatherName)
Vacuum is he vanilla periodic boundary condition.

Method Summary

static void	boxCheck(double[] box)
double[][]	gather(double[][] pos, int[] boundaryatoms, double[] box)
static PBC	getPbc(java.lang.String pbc, java.lang.String gatherMethod) simple pbc selector.
double[]	nearestImage(double[] v1, double[] v2, double[] box) Return the nearest image of v2 with respect to v1.

Methods inherited from class java.lang.Object

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

Field Detail

gatherMethod

public final PBC.Gatherer gatherMethod

Comment for gatherMethod

Constructor Detail

PBC

public PBC(java.lang.String gatherName)
    throws java.lang.IllegalArgumentException

Vacuum is he vanilla periodic boundary condition.

Parameters:

gatherName -

Throws:

java.lang.IllegalArgumentException

Method Detail

getPbc

public static PBC getPbc(java.lang.String pbc,
                         java.lang.String gatherMethod)

simple pbc selector.

returns the PBC subclass and Gatherer appropriate for its arguments. mostly because jython and mathematica seem to have a bit of an issue with nested classes.

Parameters:

pbc - pbc-specifier

gatherMethod - gather method specifier

Returns:

the appropriate periodic boundary condition

nearestImage

public double[] nearestImage(double[] v1,
                             double[] v2,
                             double[] box)

Return the nearest image of v2 with respect to v1.

Parameters:

v1 -

v2 -

box -

Returns:

the position of the nearest image of v2

boxCheck

public static void boxCheck(double[] box)

gather

public double[][] gather(double[][] pos,
                         int[] boundaryatoms,
                         double[] box)