Free crystallographic software for DOS and Java

Steffen Weber, NIRIM, Namiki 1-1, Tsukuba, 305 Japan

A selection of computer programs covering various crystallographic aspects may be downloaded from my website [1] . Programs are available for the DOS platform (also running in the DOS mode of Windows95/98) and for the Java platform. Except for one, all programs offer a mouse-controlled graphical user interface. Java programs are available in two forms, namely as applets which may be run directly in a webbrowser, such as Netscape and Microsoft Internet Explorer or as stand-alone applications, which require a Java interpreter in form of the JDK [2] by SunMicrosystems^©. Below the programs are listed by category. Programs are listed more than once if they cover several categories. The superscripts indicate the type of program: DOS program ^(D), Java applets ^(j) and Java applications ^(J). Most programs (except applets) allow the user to save the generated graphics as PostScript files. My latest software project is the Java structure viewer JSV, which also includes diffraction pattern calculations, stereographic projections, a periodic table and a unit cell visualizer.

structure display: XRSV ^(D), JAtom ^(j), JSV ^(J);
diffraction pattern simulations (Laue, precession, powder, Kossel): XRDIFF ^(D),
KOQUA ^(D), QREFGEN ^(D), DECA-ZONAX ^(D), JLauegram ^(j), JSV ^(J);
stereographic projections: STEREOGRAMS ^(D), JStereogram ^(j), JWulff ^(J);
3D reciprocal space visualization: VSV ^(D), XRDL ^(J)- 3D/2D reciprocal lattice, Laue;
point groups: POLYHEDRA ^(D), JPoly ^(j);
wallpaper patterns: Plane Groups ^(D);
quasiperiodic tessellations: TILING ^(D), JTiling ^(j);
polyhedra and crystal shapes: POLYHEDRA ^(D), XRSHAPE ^(D), JPoly ^(j), JShape ^(j,J);
vector visualization: VSV ^(D); Jcell ^(j), JSV ^(J);
periodic tables: PT^(D), Jpt ^(j);
Fourier transforms (FT): FOURIER ^(D) -FT of point sets, JFourier ^(ja)-FT of poinsets, JFmap ^(J)- 3D Fourier maps;
difference plot: RSDP ^(D), JRSDP ^(j);

Furthermore there are Java applets for plotting atomic form factor curves, for calculating linear absorption coefficients and others.

[1]http://www.nirim.go.jp/~weber

[2] http://www.javasoft.com/products/jdk/1.2/download-windows.html

Editor's Note: Steffen asks you to make a contribution to UNICEF if you like his programs and continue to use them. This collection is well worth looking at.

XD - A Computer Program Package for Multipole Refinement
and Analysis of Charge Densities from Diffraction Data.

Characteristic of recent advances in X-ray diffraction is the increase in speed, resolution and accuracy which makes it possible to study macromolecular structures on the one hand, and to gain information on small molecules at the electronic level, on the other hand. In the latter context, quantum mechanics provides a link between energy, structure, and chemical behaviour of molecules through the wavefunction. Development of the molecular orbital theory has led to modern computational techniques for approximating molecular wavefunctions, but the standard ab initio procedures rapidly become unmanageable with increasing size of the system considered (Veillard 1991). Density functional theory promises an approximate treatment of electron correlation effects with a relatively modest computational cost, and is being applied to chemical problems (Labonowski and Andzelm 1991; Ziegler 1991; Kohn, Becke and Parr 1996), but there still exists an upper limit to the size of the system which can bestudied by this method. Explicit in density functional theory is an approach that can bypass the calculation of the wavefunction. The corresponding Hohenberg-Kohn theorem (Hohenberg and Kohn 1964) shows that the ground state energy is a unique functional of the electron density. It gives a theoretical basis for inter-relating chemical properties through an observable property - the charge distribution.

Modern single-crystal X-ray diffraction analysis is a technique for experimental determination of the electron, hence charge density (CD) distribution rho(r) in molecules and crystals (Jeffrey and Piniela 1991; Coppens1992, 1997). An analytical representation of the continuous electrondensity of the unit cell as a sum over pseudoatom densities centred at nuclear sites is exemplified by the multipole model of Stewart (1973), which explicitly accounts for the asphericity of the atomic electron density in crystals, caused by chemical bonding and intermolecular interactions. Fitting such a model to high-resolution X-ray diffraction data leads to an CD distribution which is by definition correlated, being a representation of the true density. This density may be interpreted subsequently using the theory of Atoms in Molecules (AIM) (Bader 1990). Indeed, application of the AIM theory to experimental X-ray crystallographic results both requires and greatly enhances the value of the multipole model.

Various computer implementations of this scheme developed from the early 1970s onwards, first for least squares refinement of the multipole model with diffraction data, later for derivation of direct-space properties of the density distribution and its analysis by AIM methods. The principal programs or packages in common use are MOLLY (Hansen and Coppens 1978), POP (Epstein, Ruble and Craven 1982), VALRAY (Stewart 1976), and LSEXP (Hirshfeld 1971, 1977). LSEXP differs somewhat from the others in using cosine functions which can be expressed as combinations of the spherical harmonic functions employed in Stewart's original multipole model (Stewart 1973).

In 1993 the IUCr Commission on Charge, Spin and Momentum Densities adopted as a project the writing of an integrated package, to be distributed, supported, documented and maintained centrally, with the objective of promoting a wide application of X-ray charge density methods to chemical problems. The outcome is the package now known as XD. Further information from the web site www.chem.gla.ac.uk/~paul/xd.html.

References - for program XD

• Bader, R.F.W. (1990). Atoms in Molecules - A Quantum Theory. Oxford University Press.
• Coppens, P. (1992). Ann. Rev. Phys. Chem. 43, 663.
• Coppens, P. (1997). X-Ray Charge Densities and Chemical Bonding. Oxford University Press: IUCr Texts on Crystallography No. 4.
• Epstein, J., Ruble, J.R. and Craven, B.M. (1982). Acta Cryst. B38, 140.
• Hansen, N.K. and Coppens, P. (1978). Acta Cryst. A34, 909.
• Hirshfeld, F.L. (1971). Acta Cryst. B27, 769.
• Hirshfeld, F.L. (1977). Isr. J. Chem. 16, 198.
• Hohenberg, P. and Kohn, W. (1964). Phys. Rev. B 136, 864.
• Jeffrey, G.A. and Piniela, J.F. (1991). Eds. The Application of Charge Density Research to Chemistry and Drug Design. NATO ASI Series B Vol. 250, Plenum Press: New York.
• Kohn, W., Becke, A.D. and Parr, R.G. (1996). J. Phys. Chem. 100}, 12974.
• Labonowski, J.K. and Andzelm, J.W. (1991). Density-Functional Methods in Chemistry. Springer-Verlag: New York.
• Stewart, R.F. (1973). J. Chem. Phys. 58, 1668.
• Stewart, R.F. (1976). Acta Cryst. A32, 565; Stewart, R.F. and Spackman, M.A. VALRAY System, Department of Chemistry, Carnegie-Mellon University, Pittsburgh PA 15213, USA
• Veillard, A. (1991). Chem. Rev. 91, 743.
• Ziegler,T. (1991). Chem. Rev. 91, 651.

Click here to return to BCA homepage