Fox Wiki

Welcome to the Fox wiki ! Fox, 'Free Objects for Crystallography' is a free, open-source program for the ab initio structure determination from powder diffraction.

Nota Bene: this is a wiki, which means that you can (and are encouraged to) modify or add pages to the wiki. This is particularly true for the tutorials and feature requests pages. To learn more about how to modify or add pages to the wiki, look at the HelpContents page, and experiment on the WikiSandBox page.

• Tip: the Dynamical Occupancy Correction can automatically correct atoms overlapping due to special positions or shraed atoms between polyhedra. It is activated by default as an option in the Crystal object. However, if no overlap or special position is expected, do not activate it as it slows down a lot the computation.

Beginning with Fox

Introduction

The FOX program (for Linux, MacOS X and windows) was made for the ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Its most interesting features for ab initio structure determination are:

• a versatile description of the crystal contents: either isolated atoms , molecules described using a bond length, bond angles and dihedral angles, and polyhedra for inorganic compounds. You can describe your structure by using any combination of groups of atoms, using a chemist's or crystallographer knowledge about the connectivity in your sample to constrain possible solutions..

• an automatic correction for special positions and shared atoms between polyhedra, suitable for global optimization algorithms.

• the ability to use simultaneously multiple powder patterns (X-rays, neutrons), as well as single crystal data (e.g. extracted from a powder pattern)

• smart global optimization algorithms which can get out of false minima.

• a graphical interface (see the screenshots) with a 3D crystal structure view, with live updates during the optimization process.

So, if you:

• have an unknown compound but with (approximately) known composition.

• have a powder pattern (X-Ray or neutron or both), which you have already indexed (with the refined unit cell), and for which you have some idea of the possible spacegroup(s) (using systematic extinctions).

• would like to solve the structure (i.e. find the atom -or group of atoms- positions, before refining them with another package).

Then Fox can help you.

This program can be used also for educational purposes, to show a 3D display of Crystal structures, and the associated powder pattern(s) (see how adding atoms, changing the lattice, or changing the spacegroup affects the powder spectrum and the 3D structure).

If you would also like to choose your own criterion and algorithm to solve the structure, then it will be even better : FOX is built on a very customizable and expandable library (ObjCryst++), which allows you to evaluate your Crystal structure following a combination of criteria: currently available are the diffraction data Chi², an anti-bump and a bond-valence cost function, but it would be very easy to write a new criterion using (say) interatomic distances (energy of the configuration, analysis of the coordination). This, with a versatile way to describe the unit cell's contents, is what makes the algorithms used interesting. For example you can combine several datasets (X-Ray, Neutron...) for the same structure,...

Getting Fox

• About Fox: authors, references, bibliography...

• List of crystal structures solved using Fox (very incomplete ! Please add yours with links to the online article, if available)

Using Fox to solve Crystal structures

• Read the Fox Changelog, or the more detailed SVN Changelog

• Fox Development Information

  • Current development

  • Feature requests (add your own requests !) Here are also described the long-term Fox projects.

• Compiling Fox:

  • Compiling Fox under Linux

  • Compiling Fox under MacOS X

  • Compiling Fox under windows