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COMPUTER PROGRAM ABSTRACTS
Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/. Lists of software presented and/or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
J. Appl. Cryst. (1998). 31, 826
POWDIS and POWUTL ± PC programs for the display and simulation of X-ray powder patterns P. MC ARDLE * AND D. CUNNINGHAM Department of Chemistry, University College, Galway, Ireland. E-mail:
[email protected] (Received 16 May 1997; accepted 29 September 1997 )
The crystallographic problem: X-ray powder patterns can provide a useful check on the relationship between the phase of a crystal chosen for singlecrystal work and the phase of the bulk sample. This software allows the direct comparison of single-crystal and powder data and provides facilities for display, plotting and simulation of powder patterns.
Method of solution: Two programs POWDIS and POWUTL are provided for the display of powder data and for the manipulation of data ®les. POWDIS can display and plot powder spectra. The spectra may be marked, integrated and plotted. A zoom facility is provided and spectra may be displayed together for comparison (Fig. 1). The display may be in d space or 2 units and the displayed radiation wavelength can be altered. One useful application of this facility is that spectra obtained with Co radiation ( = 1.79 AÊ) which show excellent resolution on organic pharmaceutical samples can be replotted for comparison with more conventional Cu data. The powder patterns in Fig. 1 are, in the upper trace, the observed pattern for a nickel salicylaldimene complex cocrystallized with CsNO3 in a supramolecular assembly and, in the lower pattern, that computed for the Cs and Ni atoms only. This arrangement of metal atoms was easily detected in powder patterns of related assemblies. The POWUTL program can: (i) convert SHELX .hkl ®les to powder patterns; (ii) perform simple digital ®ltering (to increase or decrease resolution); (iii) convert to and from Crystallographic Information File (CIF) format; (iv) change wavelength and maintain digitization; and (v) generate powder data from SHELX .ins ®les. Option (v) requires the use of SHELX-93 (Sheldrick, 1993). Hardware environment: The program requires at least a 386/387, DOS5 and 4 Mbytes of RAM. Availability: The programs and test data are available via the WWW (http:// balor.ucg.ie/cryst/software.htm) or on ¯oppy disk from the authors.
Fig. 1. Top: observed pattern for a nickel salicylaldimene complex co-crystallized with CsNO3 in a supramolecular assembly. Bottom: computed pattern for the Cs and Ni atoms only.
# 1998 International Union of Crystallography Printed in Great Britain ± all rights reserved
Keywords: SHELX; powder diffraction.
single
crystal;
References Sheldrick, G. M. (1993). SHELXL-93: A Computer Program for Crystal Structure Determination, University of GoÈttingen, Germany.
J. Appl. Cryst. (1998). 31, 826±827
VALMAP 1.0 ± a program for the calculation and visualization of contour maps of bond-valence sums JAVIER GONZAÂ LEZ- PLATAS * AND CRISTINA GONZAÂ LEZ- SILGO FõÂsica Fundamental y Experimental, Grupo de Rayos X, Universidad de La Laguna, E-38204 ± La Laguna, Tenerife, Spain. E-mail:
[email protected] (Received 19 September 1997; accepted 15 December 1997 )
The crystallographic problem: Many programs have been written to help in crystal chemical analysis, in the case of inorganic crystal structures, where the co-ordination polyhedra are greatly distorted or ill de®ned as a result of ionic or electronic effects (Burdett, 1980): large polarizable ions, lone electron pairs or unusual oxidation states. Also, in some isomorphous series of structures, certain sites are found to be consistently under- or overbonded (the bondvalence sum is too small or too large), indicating the presence of tensile or comprehensive bond strain as a result of steric effects (Brown, 1992). The present program provides a special valence-sum technique [developed by Walterson (1978)] in order to visualize these electronic and steric anomalies, often around any atom, revealing the shape of its potential site in the structure. Many physical properties (ferroelectricity, superconductivity, etc.) can be explained with this type of map because it is possible to show the path along which the electrons or ions might diffuse, changing the oxidation state or to create a spontaneous polarization, for example. Method of solution: The program reads an input ASCII ®le or from the standard input. As a minimum, it must include the unit-cell parameters, the space-group symbol, the atomic coordinates, the occupation factor and the Journal of Applied Crystallography ISSN 0021-8898 # 1998
COMPUTER PROGRAM ABSTRACTS particular type of atom related to the search (normally a cation or a light atom in the structure). The aim of VALMAPPis to calculate the bond-valence sum s that a particular atom would have if it was placed at any arbitrary point in the crystal. The bond valence s is evaluated from the relation to the bond length r of the nearest atom (with r < rmax): s exp
r0 ÿ r =0:37 (Brown & Alttermat, 1985). The rmax value is ®tted evaluating the in¯uence from the second, third etc. coordination spheres. `Moving' this atom systematically through all points of a selected cubic grid gives its valence-sum map. Then, a contour map is displayed in the screen, showing sharp peaks at the maximum corresponding to the atoms of the structure; smooth cavities corresponding to the ideal atom P sites have atomic valence equal to s. It is possible to choose the plane and its limits to plot the map. Software environment: The source code is written in Fortran77. The executable ®le is compiled for the protected DOS mode (32 bits), Windows 3.1x (using Win32S), Windows 95 and Windows NT. The program offers a user-friendly graphical user interface (GUI) that is fully mouse-controlled. The graphical interface is based on the INTERACTER Library version 4.0. Hardware environment: The program runs on PC-compatible computers under DOS 6.0 or higher, Windows 3.1x (with Win32S), Windows 95 and Windows NT. The DOS version needs about 2.0 Mbytes of disk space (the program is bounded with the DOS-Extender) and 1.2 Mbytes for the other versions. The program uses VGA/SVGA graphics and needs an IBM-compatible mouse. Program speci®cation: Up to about 100 atoms in the asymmetric unit can be used to calculate the contour maps of the bond-valence sum. The program found the higher graphics resolution for DOS and for Windows it needs a Windows video driver with colours 32 k/65 k/ 16 M. There are two forms of output ®le: HPGL and PostScript. In DOS one can choose a Laserjet or Deskjet printer. Documentation: The program is very easy to use, but a manual is provided in the form of a MS-Word document, with some examples. Availability: VALMAP 1.0 can be freely obtained from the authors by e-mail (
[email protected]). Keywords: bond valence; contour maps; graphical user interface. # 1998 International Union of Crystallography Printed in Great Britain ± all rights reserved
References Brown, I. D. (1992). Acta Cryst. B48, 553±572. Brown, I. D. & Alttermat, D. (1985). Acta Cryst. B41, 244±247. Burdett, J. K. (1980). Molecular Shapes. New York: John Wiley. Walterson, K. (1978). Acta Cryst. A34, 901±905.
J. Appl. Cryst. (1998). 31, 827±828
CARAT ± a package for mathematical crystallography W. PLESKEN ,* J. OPGENORTH T. SCHULZ
AND
RWTH-Aachen, Lehrstuhl B fuÈr Mathematik, Templergraben 64, D-52062 Aachen, Germany. E-mail:
[email protected] (Received 25 August 1997; accepted 15 December 1997 )
The crystallographic problem: CARAT handles enumeration and construction problems, as well as recognition and comparison problems, for crystallographic groups up to dimension 6. The enumeration part is already beyond the the scope of a book such as International Tables for Crystallography, Vol. A, (Hahn, 1995) or Crystallographic Groups of Four-Dimensional Space (Brown et al., 1977). Enumeration problems include (a) splitting arithmetic crystal classes (Z classes of ®nite unimodular groups) into space-group types (af®ne classes of space groups), (b) splitting geometric crystal classes (Q classes of ®nite unimodular groups) into arithmetic crystal classes, (c) splitting Bravais types (Bravais ¯ocks) into arithmetic crystal classes, (d ) splitting crystal families into Bravais types, (e) splitting crystal families into geometric classes and (f ) enumerating inclusions between Bravais groups. Recognition problems include (a) deciding af®ne equivalence (isomorphism) of space groups, (b) deciding arithmetic equivalence [Z equivalence, which is conjugacy under GLn
Z] of point groups, (c) deciding geometric equivalence [Q equivalence, which is conjugacy under GLn
Q] of point groups, (d ) ®nding the Bravais type of a point group and (e) computing the family symbol, cf. Plesken & Hanrath (1984) for point groups.
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Most of the tasks described above can already be handled by CARAT; the few remaining items will soon be added. Method of solution: CARAT contains tables and implementations of various algorithms. The tables include representations of the arithmetic classes of the Bravais groups up to degree 6 together with their normalizers and inclusions. It is planned for the future to provide tables of the geometric classes also up to degree 6. The main algorithms implemented include a centering (sublattice) algorithm, a lattice automorphism and isometry algorithm, and the Zassenhaus algorithm to compute vector systems. It is also possible to calculate generators for normalizers of point groups via perfect forms in the Bravais manifold. Software environment: CARAT is a compilation of about 60 programs, all of which are written in C. It uses a normal Unix environment on user-de®ned ®les, which are basically of two types. Together with the system comes a library of C functions which makes it possible to develop programs for special purposes. Great care is taken that the enumeration problems (a)±(f ) and recognition problems (a)±(e) can easily be performed even by inexperienced users. The software is running successfully on various Unix machines, including those running Linux, HP-UX and Solaris. It should be easily portable to any Unix machine. Documentation and availability: There is a short LATEX ®le giving the basic details for handling the package. Each program comes with short online help. A skeleton of the mathematical background is described by Opgenorth et al. (1998), where further references are given. CARAT is available at http://samuel. math.rwth-aachen.de/LBFM/carat/. Keywords: Higher-dimensional space groups; dimension-independent concepts; space-group classi®cation; pointgroup classi®cation. References Brown, H., BuÈlow, R., NeubuÈser, J., Wondratschek, H. & Zassenhaus, H. (1977). Crystallographic Groups of Four-Dimensional Space. New York: John Wiley. Hahn, Th. (1995). Editor. International Tables for Crystallography, Vol. A, 4th ed. Dordrecht: Kluwer Academic Publishers. Opgenorth, J., Plesken, W. & Schulz, T. (1998). Acta. Cryst. A 54, 517±531. Journal of Applied Crystallography ISSN 0021-8898 # 1998
