LaueX

Alain Soyer
Laboratoire de Minéralogie-Cristallographie associé au CNRS
Universités P. et M. Curie et D. Diderot
4, place Jussieu - tour 16
Case 115
F-75252 PARIS CEDEX 05

Fax: 33-1-44.27.37.85
E-mail: soyer@lmcp.jussieu.fr
URL: http://www.lmcp.jussieu.fr/~soyer/

Version française

Introduction:

laueX is an easy to used interactive program, with a MacIntosh like graphical user interface. It allows to:

simulate a Laue diagram, giving the orientation of the crystal and the cell parameters. When the structure of the crystal is known, the program may evaluate the intensities of the Laue spots and shows the result as spots whose size is proportional to the intensity.

index an experimental Laue diagram, by the knowledge of the cell parameters and the position of a number of spots of low indexes. It determines the orientation of the crystal.

align or rotate the crystal.

print the simulation diagram as a Postscript file or to a printer.

laueX is written in C language, and designed for UNIX workstations. It requires X-Window and OSF-Motif libraries.

Getting the software:

The program laueX is available via ftp (File Transfert Protocol) on the Internet. To get it, it is necessary to follow the following steps:

connect to the ftp server of the laboratory:
"ftp ftp.lmcp.jussieu.fr"
Name: "anonymous"
Password: "your_name@your_address"

move to the laueX directory:
ftp> "cd pub/sincris/software/general/laueX"

transfert the archive file:
ftp> "bin"
ftp> "get laueX.tar.Z"
.....
ftp> "quit"

extract the files:
"uncompress laueX.tar.Z"
"tar -xvf laueX.tar"

This notice is available on the Web, in the software section of the crystallographic server:
URL: http://www.lmcp.jussieu.fr/sincris/logiciel/

Installation:

The directory laueX has the following structure:

         laueX
           |
 .---------+-----------.
 |         |           |
 |         |           |
doc     sources     samples

sources contains the source code, doc the documentation and samples examples.

Move to the "sources" directory:
"cd laueX/sources"

Edit the makefile. You must add the correct options for compilation and link, as well as the libraries names which depend on your system (variables CC, CFLAGS, LFLAGS and XLIBS).
Default options are for IBM AIX. Replace them by the correct options. Note that values are given in comment for certain systems.
Modify also the value of variable DIR witch indicates the directory where the executable module will be stored.

Edit the include file laue.h. You must give the correct full filenames in the variables GEN_FILENAME and SF_FILENAME. These variable indicate to the program the location of the files spgrp.gen and scat_fact.dat respectively. If a WEB browser is available on your system, update the variable G_HELP, giving the command to be used to look at the html notice.

Run the makefile. If you get some error messages or warnings please send them to the author of the program. This will help him to correct and improve the portability of the program.

If all the previous steps are sucessfull, you are now ready to run laueX.

The set of axes:

LaueX uses the usual crystallographic axes, in direct and reciprocal spaces. You must understand the use of two other sets of axes:

The apparatus axes:

It is an orthonormal set of fixed axes linked to the apparatus, and defined as:
O origin in the crystal,
X vector pointing toward the X ray source,
Y horizontal direction,
Z vertical direction.

The detector axes:

It is an orthonormal set of axes linked to the flat detector, and defined as:
Od origin at the center of the detector,
Xd vector along the "horizontal" axis of the detector,
Yd vector along the "vertical" axis of the detector,
Zd perpendicular to the surface of the detector.
For example, in the particular case of a Laue diagram in the transmission case, Zd is parallel to X, Xd parallel to Y and Yd parallel to Z.

Running the program:

You must use an X-window compatible terminal. After starting the program, the main menu is displayed on your screen:

A menu bar gives access to a number of sub-menus.

The "File" pulldown menu opens sub-menus used to read, create, modify or save two kinds of data files:
-a file storing informations about the asymetric unit of the crystal;
-a file storing other informations needed for the simulation or the indexation.

The "Data" pulldown menu is used to input or modify the crystal data, the detector data, the experimental spots data if needed, and the X-ray source data.

The "Orientation" button is used to give or modify the orientation of the crystal.

The "Indexation" button is used to search for the indexation of an experimental diagram, and to choose one of the possible solutions.

The simulation of a diagram is computed in the "Simulation" pulldown menu. It also allows to choose for various options and to print the simulated diagram.

On line help is available by clicking the "Help" button.

Format of the data files:

The file xxx.asy (see for example quartz.asy) contains the information about the atoms of the asymetric unit. One line is written for each atom, and must look as:

-unit coordinates of the atom (3 real numbers): these cell coordinates must be given with the origin choice as indicated in the International tables, volume A (1983).
-kind of the atom: a string of character (up to 4 characters, for example Si for silicon or Fe3+ for an iron ion); see the scat-fact.dat file for the symbols used for the elements.
For large structures, this file may be created by another program.

The file xxx.dat must be used (created, read or written) only through the menus of the program laueX. Do not try to modify it with an editor. Its format is not described here, because it may be subject to modification in the future.

A file containing the spectrum of an X ray source has the following format:
on the first line, the number of data lines, the minimum wavelenght (in Angstrom) and the wavelenght step.
On each subsequent line, the value of the intensity (in arbitrary units) for the corresponding wavelenght.

Bibliography:

J.P.Riquet et R.Bonnet
Dépouillement par ordinateur des clichés de diffraction obtenus par la méthode de Laue
J.Appl.Crys. 12 (1979) 39-41

E.Preus
Plot program for Laue patterns and stereographic projections
Comp.Physics Commun. 18 (1979) 261-275

C.A.Cornelius
A simple computer method for the orientation of single crystals of any structure using Laue back-reflection X-ray photographs
Acta Cryst. A37 (1981) 430-436

J.Laugier and A.Filhol
An interactive program for the interpretation and simulation of Laue patterns
J.Appl.Crys. 16 (1983) 281-283

C.Marin and E.Dieguez
Development of the computational procedures for the simulation and indexing of back-reflection Laue patterns
J.Appl.Crys. 27 (1994) 846-852

J.W.Campbell
LAUEGEN, an X-windows-based program for the processing of Laue X-ray diffraction data
J.Appl.Crys. 28 (1995) 228-236

Annex:

For each space group, the "International Tables for Crystallography" (1983) Vol.I gives the recommanded symetry generators. All these generators are described in chapter 11, table 11.2 and 11.3 on pages 791 and 792.
The file spgrp.gen contains the generators for all the space groups (including the different possible choices for the axes and the origin).

Table I:

Generator symbol ! Indices           ! Generator ! Subroutine name
                 !                   ! number    ! 
-----------------+-------------------+-----------+----------------
  1              ! 0, 0, 0           !  1        ! TRANSL
-----------------+-------------------+-----------+----------------
 -1      0,0,0   ! 0, 0, 0           ! -1        ! CENTRE
 -1      0,0,0   ! 0, 0, 0 Hexagonal !           !
-----------------+-------------------+-----------+----------------
  2      0,0,z   ! 0, 0, 1           !  2        ! AXE2N
  2      0,y,0   ! 0, 1, 0           !           !
  2      x,0,0   ! 1, 0, 0           !           !
  2      x,x,0   ! 1, 1, 0           !           !
  2      x,0,x   ! 1, 0, 1           !           !
  2      0,y,y   ! 0, 1, 1           !           !
  2      x,-x,0  ! 1,-1, 0           !           !
  2      -x,0,x  !-1, 0, 1           !           !
  2      0,y,-y  ! 0, 1,-1           !           !
  2      0,0,z   ! 0, 0, 1 Hexagonal !           !
  2      x,x,0   ! 1, 1, 0 Hexagonal !           !
  2      x,-x,0  ! 1,-1, 0 Hexagonal !           !
-----------------+-------------------+-----------+----------------
  m      x,y,0   ! 0, 0, 1           ! -2        ! MIRORN
  m      x,0,z   ! 0, 1, 0           !           !
  m      0,y,z   ! 1, 0, 0           !           !
  m      x,-x,z  ! 1, 1, 0           !           !
  m      -x,y,x  ! 1, 0, 1           !           !
  m      x,y,-y  ! 0, 1, 1           !           !
  m      x,x,z   ! 1,-1, 0           !           !
  m      x,y,x   !-1, 0, 1           !           !
  m      x,y,y   ! 0, 1,-1           !           !
  m      x,y,0   ! 0, 0, 1 Hexagonal !           !
  m      x,-x,z  ! 1, 1, 0 Hexagonal !           !
  m      x,x,z   ! 1,-1, 0 Hexagonal !           !
-----------------+-------------------+-----------+----------------
  3(+)   x,x,x   ! 1, 1, 1           !  3        ! AXE3N
  3(+)   x,-x,-x ! 1,-1,-1           !           !
  3(+)   -x,x,-x !-1, 1,-1           !           !
  3(+)   -x,-x,x !-1,-1, 1           !           !
  3(-)   x,x,x   ! 1, 1, 1           !           !
  3(-)   x,-x,-x ! 1,-1,-1           !           !
  3(-)   -x,x,-x !-1, 1,-1           !           !
  3(-)   -x,-x,x !-1,-1, 1           !           !
-----------------+-------------------+-----------+----------------
 -3(+)   x,x,x   ! 1, 1, 1           ! -3        ! AXE3IN
 -3(+)   x,-x,-x ! 1,-1,-1           !           !
 -3(+)   -x,x,-x !-1, 1,-1           !           !
 -3(+)   -x,-x,x !-1,-1, 1           !           !
 -3(-)   x,x,x   ! 1, 1, 1           !           !
 -3(-)   x,-x,-x ! 1,-1,-1           !           !
 -3(-)   -x,x,-x !-1, 1,-1           !           !
 -3(-)   -x,-x,x !-1,-1, 1           !           !
-----------------+-------------------+-----------+----------------
  4(+)   0,0,z   ! 0, 0, 1           !  4        ! AXE4N
  4(+)   0,y,0   ! 0, 1, 0           !           !
  4(+)   x,0,0   ! 1, 0, 0           !           !
  4(-)   0,0,z   ! 0, 0, 1           !           !
  4(-)   0,y,0   ! 0, 1, 0           !           !
  4(-)   x,0,0   ! 1, 0, 0           !           !
-----------------+-------------------+-----------+----------------
 -4(+)   0,0,z   ! 0, 0, 1           ! -4        ! AXE4IN
 -4(+)   0,y,0   ! 0, 1, 0           !           !
 -4(+)   x,0,0   ! 1, 0, 0           !           !
 -4(-)   0,0,z   ! 0, 0, 1           !           !
 -4(-)   0,y,0   ! 0, 1, 0           !           !
 -4(-)   x,0,0   ! 1, 0, 0           !           !
-----------------+-------------------+-----------+----------------
  2      x,0,0   ! 1, 0, 0 Hexagonal !  5        ! AXE2H
  2      0,y,0   ! 0, 1, 0 Hexagonal !           !
  2      x,2x,0  ! 1, 2, 0 Hexagonal !           !
  2      2x,x,0  ! 2, 1, 0 Hexagonal !           !
-----------------+-------------------+-----------+----------------
  m      x,2x,z  ! 1, 0, 0 Hexagonal ! -5        ! MIRORH
  m      2x,x,z  ! 0, 1, 0 Hexagonal !           !
  m      x,0,z   ! 1, 2, 0 Hexagonal !           !
  m      0,y,z   ! 2, 1, 0 Hexagonal !           !
-----------------+-------------------+-----------+----------------
  6(+)   0,0,z   ! 0, 0, 1 Hexagonal !  6        ! AXE6H
  6(-)   0,0,z   ! 0, 0, 1 Hexagonal !           !
-----------------+-------------------+-----------+----------------
 -6(+)   0,0,z   ! 0, 0, 1 Hexagonal ! -6        ! AXE6IH
 -6(-)   0,0,z   ! 0, 0, 1 Hexagonal !           !
-----------------+-------------------+-----------+----------------
  3(+)   0,0,z   ! 0, 0, 1 Hexagonal !  7        ! AXE3H
  3(-)   0,0,z   ! 0, 0, 1 Hexagonal !           !
-----------------+-------------------+-----------+----------------
 -3(+)   0,0,z   ! 0, 0, 1 Hexagonal ! -7        ! AXE3IH
 -3(-)   0,0,z   ! 0, 0, 1 Hexagonal !           !
-----------------+-------------------+-----------+----------------

Comments:

Please fill in the next lines and send them back to the author by electronic mail (soyer@lmcp.jussieu.fr) or fax. This is only a model: you may add as many lines and comments as you want. Thanks for your help.

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LaueX

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