Automatic indexing of area-detector data of periodic and aperiodic crystals

Abstract

An autoindexing procedure is described that produces the indexing of diffraction data of aperiodic crystals. The procedure has been designed for indexing the data obtained with an area detector, but it can also be applied to data obtained with a single‐point detector. The essential step in the indexing process is the ability to discriminate between reflections that fit to a reciprocal lattice, the satellite reflections and possible reflections that do not belong to this indexing. To achieve this goal, the refinement of the orientation matrix and the diffractometer parameters is made an intrinsic part of the process of indexing. The proposed autoindexing procedure has been implemented in a computer program called BAYINDEX. Successful application to data sets of three different one‐dimensionally modulated structures, one two‐dimensionally modulated structure and a periodic crystal is presented. Very good agreement between experimental and theoretical reflection positions is found. The indexing produced by BAYINDEX can serve as the basis for integration routines.

Determination of crystal orientation by an area-detector image for surface X-ray diffraction

“…In practice, two series of CTRs should be used for more precise determination of the direction of the surface normal. It should be noted that, when the lattice parameters of the surface layers are unknown, some automatic indexing algorithms for oscillation photographs in the 'still approximation' should be used with some modifications (Duisenberg, 1992;Steller et al, 1997;Pilz et al, 2002). Remember that the method presented here provides the direction of the surface normal without its lattice parameters.…”

“…Correction of misalignment of the area detector with refinement of the U matrix should also be made in a similar manner as for oscillation photographs (Pilz et al, 2002). Once the U matrix is calculated using at least three two-dimensional diffraction spots, indices of all two-dimensional spots recorded on the area detector can be calculated.…”

Ind_X: program for indexing single-crystal diffraction patterns

“…Pflugrath, 1999;Otwinowski & Minor, 2001;Leslie et al, 2002;Kabsch, 2010), but also a number of standalone indexing tools have been reported (e.g. Klein, 1975;Duisenberg, 1992;Pilz et al, 2002;Sauter et al, 2004). Ind_X is a program for indexing diffraction data given in the form of reciprocal lattice nodes.…”

The software packageANAELUfor X-ray diffraction analysis using two-dimensional patterns

“…Among the facilities where two-dimensional detectors are installed, one finds commercial X-ray systems, synchrotrons and neutron sources (Smilgies, 2009;Jones et al, 2005;Koizumi et al, 2007). This has motivated the development of computational tools for aiding the interpretation and quantitative analysis of twodimensional patterns, of which a few are (i) FIT2D (Hammersley et al, 1996), (ii) BLU-ICE (McPhillips et al, 2002), (iii) XRD2DSCAN (Rodriguez-Navarro, 2006), (iv) BAYINDEX (Pilz et al, 2002), (v) BEARTEX (Wenk et al, 1998) and (vi) MAUD (Ischia et al, 2005). This has motivated the development of computational tools for aiding the interpretation and quantitative analysis of twodimensional patterns, of which a few are (i) FIT2D (Hammersley et al, 1996), (ii) BLU-ICE (McPhillips et al, 2002), (iii) XRD2DSCAN (Rodriguez-Navarro, 2006), (iv) BAYINDEX (Pilz et al, 2002), (v) BEARTEX (Wenk et al, 1998) and (vi) MAUD (Ischia et al, 2005).…”

“…The investigation of reciprocal-space maps, strain, texture and general order-disorder phenomena is greatly facilitated by the use of two-dimensional detectors (Xu et al, 2006;Chapman et al, 2005;Fong et al, 2005Fong et al, , 2004Smilgies, 2009;He, 2003;Stapleton et al, 2008;Mü ller-Buschbaum, 2003;Wenk & Grigull, 2003). This has motivated the development of computational tools for aiding the interpretation and quantitative analysis of twodimensional patterns, of which a few are (i) FIT2D (Hammersley et al, 1996), (ii) BLU-ICE (McPhillips et al, 2002), (iii) XRD2DSCAN (Rodriguez-Navarro, 2006), (iv) BAYINDEX (Pilz et al, 2002), (v) BEARTEX (Wenk et al, 1998) and (vi) MAUD (Ischia et al, 2005). The investigation of thin films by grazing-incidence diffraction is currently a subject of great interest.…”