CRYSFIRE - Automatic Powder Indexing for Non-Specialists.
Robin Shirley, School of Human Sciences, University of Surrey, Guildford, Surrey GU2 5XH, UK.

Increasingly the principal barrier to the ab initio determination of structures from powder data is the initial determination of the unknown unit cell - indexing the powder pattern. Without this, none of the observed intensities can be assigned to their correct locations in reciprocal space, so that further progress is impossible.

CRYSFIRE (the new name for CRYS2RUN release II) is a unified system of programs and scripts running under MSDOS (or in a DOS box under Windows) that attempts to make indexing more accessible for non-specialists, as well as faster and more manageable for all users. Data are used in the form of peak positions rather than profiles - these can be typed or pasted in very easily, and facilities are also provided to import peaks-files generated by programs such as WinFit and XFIT.

The new name CRYSFIRE indicates that the user can employ CRYS to fire off indexing runs in a sort of shotgun approach, in which different indexing programs are deployed to make a combined assault on the dataset in question. The two principal new features are:

  1. The ability to make targeted calls to different indexing programs without changing the dataset name, because all file in the runs are kept distinct by system naming of file extensions (so that .LZS is a short [S} output file from LZON [LZ], etc.). This applies particularly to the intermediate files used by QDAT, etc., which would previously have conflicted.
  2. The cumulative indexing history for each dataset is now collected in both a log file and a line-per-solution summary file, in which the solutions are kept sorted according to probability (i.e. lines indexed and figure of merit). This was achieved by modifying the source code of the new programs to generate these files, and providing post-processors for the classic trio of ITO, TREOR and DICVOL, for which it was considered safer not to mess with the executables distributed by the respective authors.

Other enhancements include:

  1. The addition of a further three target indexing programs (or program variants) - TAUP, KOHL and FJZN, to bring the total available up to eight..
  2. The provision of two new translator programs WF2CRYS and XF2CRYS to import data from the peaks files written by WinFit and XFIT respectively.
  3. Considerably more expertise built into CRYS to enhance its role as indexing wizard, such as a comprehensive set of defaults which can often launch a multi-program indexing process without the need for user intervention. For those not taking the all-default route, CRYS now supports more of the main steering parameters used by indexing programs, providing advice and a default in each case.
  4. A new MERGESUM script to merge the summary files for two different dataset names, leaving the merged summary optionally in a third file. V/V1 ratios are recalculated, based on the volume for the solution now at the top of the sorted list.

Like the original CRYS2RUN, CRYSFIRE is a script-based system for non-specialists that runs under DOS and calls the major indexing programs using CRYS as a front end, feeding data to the indexing programs via the format-translator QDAT. CRYS is now at v9.33e. While continuing to provide data-grooming facilities such as self-calibration for detecting and correcting 2theta-zero errors, CRYS has been extended in its role as indexing wizard, and now provides extensive advice and assistance in launching indexing programs, including an all-default route.

Different datasets present problems to different programs, and the chances of success increase if a variety of programs using quite different methods can be deployed. The number of indexing programs supported in the new release has thus been increased from 3 to 8. The classic trio of ITO, TREOR and DICVOL in the original CRYS2RUN are now augmented by new versions of the other programs, to give the following list (typical run times are shown in square brackets and refer to a 200MHz Pentium):

1) Jan Visser's ITO v12 [a few seconds]

2) Per-Eric Werner's TREOR90 [under a minute]

3) Daniel Louër's DICVOL91 [a few seconds down to orthorhombic, 5-30 minutes for monoclinic, depending on cell volume]

4) TAUP (based on Daniel Taupin's 1974 POWDER program for exhaustive searches in index space [a few seconds down do orthorhombic, hours or days to monoclinic]

5) KOHL (based on Franz Kohlbeck's TMO program for rapid heuristic searches in index space [under a minute]

6) FJZN6 (a powerful ITO variant that uses the Ishida & Watanabe PM criterion for evaluating zones) [15 seconds]

7) LZON (a new PC version of the Shirley, Louër & Visser combined-strategy program, which uses zone-finding, the dominant-zone heuristic and dichotomy) [up to 15 minutes]

8) LOSHFZRF (a manually-aimed version of LZON, requiring the user to specify a basis set) [under a minute]

CRYSFIRE runs under DOS (or in a DOS box under Windows) on any PC-compatible machine offering c.550K base memory for DOS programs, and enough environment space (typically 1K-2K) for the environment variables used to communicate between the different components of the CRYSFIRE system.

Real-mode under DOS might be dismissed as a primitive environment, but it is computationally very efficient and well suited to these compact but computationally intensive programs. A protected mode Windows version of LZON turned out to run 3 times slower than the otherwise-identical DOS version running in a DOS box under Windows on the same machine.

Unfortunately no Unix or Linux versions are available, since the tricky and antique FORTRAN used by some of the indexing programs is unacceptable to modern Unix compilers.

CRYSFIRE and its supported indexing programs are distributed free for non-profit use via the CCP14 website (www.ccp14.ac.uk), where Lachlan Cranswick has provided several detailed tutorials demonstrating its use - for example, see http://www.ccp14.ac.uk/tutorial/crys/index.html.

References

ITO:
Visser, J. W. (1969), A Fully Automatic Program for Finding the Unit Cell from Powder Data, J. Appl. Cryst., 2, 89­95.
DICVOL:
Boultif, A. & Louër, D. (1991), Indexing of powder diffraction patterns for low-symmetry lattices by the successive dichotomy method, J. Appl. Cryst., 24, 987-993.
Louër, D. & Vargas, R. (1982), Indexation Automatique des Diagrammes de Poudre par Dichotomies Successives, J. Appl. Cryst., 15, 542­545.
TREOR:
Werner, P.-E., Eriksson, L. & Westdahl, M. (1985), TREOR, a Semi-Exhaustive Trial-and-Error Powder Indexing Program for All Symmetries, J. Appl. Cryst., 18, 367-370.
TAUP:
Taupin, D. (1973), A Powder­Diagram Automatic­Indexing Routine, J. Appl. Cryst., 6, 380­385.
(A later paper exists, but it does not refer to the base version used in the CRYSFIRE system.)
KOHL:
Kohlbeck, F. & Hörl, E. M. (1976), Indexing Program for Powder Patterns Especially Suitable for Triclinic, Monoclinic and Orthorhombic Lattices, J. Appl. Cryst., 9, 28­33.
Kohlbeck, F. & Hörl, E. M. (1978), Trial and error indexing program for powder patterns of monoclinic substances, J. Appl. Cryst., 11, 60­61.
FJZN6:
Shirley, R. (1999), A modified version of Visser's ITO zone-indexing program, using the Ishida & Watanabe PM criterion for zone evaluation, (not yet published). See also Visser (1969) for the ITO6 base version, and Ishida & Watanabe (1982) for the PM criterion.
LZON, LOSHFZRF:
Shirley, R. & Louër, D. (1978), New powder indexing programs for any symmetry which combine grid­search with successive dichotomy, Acta Cryst., A34, S382.
PM Criterion (used in FJZN6 and LZON):
Ishida, T & Watanabe, Y. (1982), A criterion method for indexing unknown powder diffraction patterns, Z. Krist., 160, 19­32.
AUTOX:
Zlokazov, V. B. (1995), AUTOX - A Program for Autoindexing Reflections from Multiphase Polycrystals, Computer Physics Comm., 85, 415-422.
Page last updated 17 Oct 1999
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