xzli.jecp.unitcell
Class NiggliMatrix

java.lang.Object
  |
  +--xzli.jecp.unitcell.NiggliMatrix

public class NiggliMatrix

extends java.lang.Object

Implemention of Niggli reduction and lattice symmetry search alogrithms. This is the core of JECP/UNITCELL.

See Also:

ReducedCellGUI.java, LatticeSymmetryGUI.java

Field Summary

double	a The lattice parameter of a primitive cell
double	A The component of Niggli matrix
double	alpha The lattice parameter of a primitive cell
double	b The lattice parameter of a primitive cell
double	B The component of Niggli matrix
double	beta The lattice parameter of a primitive cell
double	c The lattice parameter of a primitive cell
double	C The component of Niggli matrix
double	D The component of Niggli matrix
double	E The component of Niggli matrix
double	F The component of Niggli matrix
double	gamma The lattice parameter of a primitive cell

Constructor Summary

NiggliMatrix()

Method Summary

static void	main(java.lang.String[] args) Main function for testing
void	NiggliMatrix() Constructor: It should be used together with setNiggliMatrix method
void	NiggliMatrix(double s11, double s22, double s33, double s12, double s23, double s31) Constructor: To create an instrance with the components of a Niggli matrix
boolean	reduce() Niggli cell reduction algorithm: A Unified Algorithm for Determining the Reduced (Niggli) Cell.
java.util.ArrayList	searchLatticeSymmetry() Procedure for identification of lattice symmetry: Cell Reduction and Lattice Symmetry Determination.
java.util.ArrayList	searchLatticeSymmetry(java.io.PrintWriter pw) Procedure for identification of lattice symmetry: Cell Reduction and Lattice Symmetry Determination.
void	setCellParameters() Get cell paramters from Niggli Matrix
void	setNiggliMatrix(double a, double b, double c, double aphla, double beta, double gamma) To set up a NiggliMatrix instance with lattice parameters.
void	setTolerance(double t) A tolerance parameter t means if|A-B|
void	showConventionalCell(java.util.ArrayList list, int v1, int v2, int v3) To transform conventional cell of Bravais lattice and print the conventional cell on monitor.
void	showConventionalCell(java.io.PrintWriter pw, java.util.ArrayList list, int v1, int v2, int v3) To transform conventional cell of Bravais lattice and write to a given output stream.
void	showNiggliMatrix() To print Niggli matrix on monitor.
void	showPrimitiveCell() To print lattice parameters on monitor.

Methods inherited from class java.lang.Object

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

Field Detail

A

public double A

The component of Niggli matrix

B

public double B

The component of Niggli matrix

C

public double C

The component of Niggli matrix

D

public double D

The component of Niggli matrix

E

public double E

The component of Niggli matrix

F

public double F

The component of Niggli matrix

a

public double a

The lattice parameter of a primitive cell

b

public double b

The lattice parameter of a primitive cell

c

public double c

The lattice parameter of a primitive cell

alpha

public double alpha

The lattice parameter of a primitive cell

beta

public double beta

The lattice parameter of a primitive cell

gamma

public double gamma

The lattice parameter of a primitive cell

Constructor Detail

NiggliMatrix

public NiggliMatrix()

Method Detail

NiggliMatrix

public void NiggliMatrix()

Constructor: It should be used together with setNiggliMatrix method

NiggliMatrix

public void NiggliMatrix(double s11,
                         double s22,
                         double s33,
                         double s12,
                         double s23,
                         double s31)

Constructor: To create an instrance with the components of a Niggli matrix

setNiggliMatrix

public void setNiggliMatrix(double a,
                            double b,
                            double c,
                            double aphla,
                            double beta,
                            double gamma)

To set up a NiggliMatrix instance with lattice parameters.

Parameters:

a - in Angstrom or 1/Angstrom

b - in Angstrom or 1/Angstrom

c - in Angstrom or 1/Angstrom

beta - in Degree

gamma - in Degree

setTolerance

public void setTolerance(double t)

A tolerance parameter t means if|A-B|

setCellParameters

public void setCellParameters()

Get cell paramters from Niggli Matrix

reduce

public boolean reduce()

Niggli cell reduction algorithm: A Unified Algorithm for Determining the Reduced (Niggli) Cell. I. Krivy and B. Gruber. Acta Cryst. (1976) A32, 297-298. An appropriate tolerance value is needed (default 0.01)

showNiggliMatrix

public void showNiggliMatrix()

To print Niggli matrix on monitor.

showPrimitiveCell

public void showPrimitiveCell()

To print lattice parameters on monitor.

searchLatticeSymmetry

public java.util.ArrayList searchLatticeSymmetry()

Procedure for identification of lattice symmetry: Cell Reduction and Lattice Symmetry Determination. William Clegg. Acta Cryst. (1981) A37, 913-915. output on monitor.

Returns:

a list of vectors with lengths and angles.

searchLatticeSymmetry

public java.util.ArrayList searchLatticeSymmetry(java.io.PrintWriter pw)

Procedure for identification of lattice symmetry: Cell Reduction and Lattice Symmetry Determination. William Clegg. Acta Cryst. (1981) A37, 913-915. output into a given ouput stream.

Parameters:

pw - a output stream

Returns:

a list of vectors with lengths and angles

showConventionalCell

public void showConventionalCell(java.util.ArrayList list,
                                 int v1,
                                 int v2,
                                 int v3)

To transform conventional cell of Bravais lattice and print the conventional cell on monitor.

Parameters:

list - a list of vectors generated using the Clegg's algorithm

v1 - the number of the 1st selected vector

v2 - the number of the 2nd selected vector

v3 - the number of the 3rd selected vector

showConventionalCell

public void showConventionalCell(java.io.PrintWriter pw,
                                 java.util.ArrayList list,
                                 int v1,
                                 int v2,
                                 int v3)

To transform conventional cell of Bravais lattice and write to a given output stream.

Parameters:

list - a list of vectors generated using the Clegg's algorithm

v1 - the number of the 1st selected vector

v2 - the number of the 2nd selected vector

v3 - the number of the 3rd selected vector

main

public static void main(java.lang.String[] args)

Main function for testing