JOR

Reciprocal Space Visualizer

  © Steffen Weber, 1998

Introduction

JOR is a software for the 3D-visualization of the reciprocal lattice points for crystals/quasicrystals.

purpose for diffractometer data:

When collecting X-ray diffraction data  on a four-circle diffractometer, one starts with an automated peak searching process. The found peaks then shall help in establishing the orientation matrix so that the diffractometer control software can find & scan all the peaks which are given in a peak input list.
Since the diffractometer accepts 3D coordinates only  we have to convert the five or six integer indices of the quasicrystal (h1 h2 h3 h4 h5 h6  in contrast to h k l for crystals)  into cartesian non-integer values by some section algorithm.
After some peaks have been found by the peak search process we need to identify those reflections in terms of the higher-dimensional integer indices.
Now this can be a very tedious exercise. JOR's task is to simulate a 3D diffraction patterns and then overlay the peaks from the peak search and rotate/scale each set until they coincide. Then we obtain the indices for the found peaks and then we can calculate the orientation matrix so we may proceed with the actual data collection.
The calculated diffraction pattern can be modified in realtime (varying slider settings for the maximum internal space component, range of interplanar spacings, 2Theta range and lattice parameters.

purpose for pseudo Weissenberg data:

JOR has been extended to import full sets of reconstructed 3D data (reciprocal space points reconstructed from pseudo Weissenberg data). One can then select a number of basis vectors and try to index all spots. A least squares refinement routine refines those basis vectors and the origin. Then the lattice parameters and the orientation matrix are determined.
An absorbtion correction routine for general convex polyhedral crystal shapes has been implemented. This uses the Gauss integration for usually 10 divisions along each axis (x,y,z). This Java-coded routine corrects about ten reflections/second on a 300 MHz machine for 10x10x10 divisions. The crystal shapes can easily be defined using my program JSHAPE.

Main Features

• for octagonal, decagonal, dodecagonal and icosahedral quasicrystals
• real time modification of simulation
• stereo pairs
• real time rotations by mouse drags
• image shifting and zooming by mouse drag
• measuring distances and angles by clicking reflections
• display of labels/indices
• independent rotation/scaling of two data sets (simulation & peak search positions)
• output of GIF and PPM (routines by Jef Poskanzer)
• least squares refinement of basis vectors
• absorption correction for polyhedral shapes

Screen Shot