F.O.X. Home Page

The ObjCryst++/FOX webpage can be found at http://objcryst.sourceforge.net, and is mirrored on CCP14 web sites ( UK mirror , Canadian Mirror, US Mirror). There are mailing lists to which you can subscribe to get announcements about the FOX program and/or the Object-Oriented Crystallographic Computing library.

Author: Vincent Favre-Nicolin (more about the author here) in collaboration with Radovan Cerny.
The program was written at the Laboratory of Crystallography, in Geneva (Switzerland), with support from the Swiss National Science Foundation. (project #21-53847.98)). See the ObjCryst++ homepage for more details about the source code.

NEWS

Latest version is 1.1 (january 7th, 2002). It features speed improvements, use of integrated R(w)-factors (for a better handling of patterns with badly defined), the possibility to use single crystal data (eg extracted intensities), overall temperature factor, and is more user-friendly (eg no need to hit 'return' after each input). See the full changelog.

The FOX program was mainly made for the structure solution from powder diffraction data. Its most interesting features for ab initio structure determination are :

• the ability to use multiple patterns (X-rays, neutrons)
• a versatile description of scatterers: either isolated atoms , molecules described using a bond length, bond angles and dihedral angles, and polyhedra for inorganic compounds.
• An automatic and dynamic correction for special positions and shared atoms between polyhedra, suitable for a global optimization algorithms.
• Global optimization algorithms which can get out of false minima.
  

So, if you have:

• 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 systametic extinctions).
• would like to solve the structure (ie find the atom 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, which allows you to evaluate your Crystal structure following a combination of criteria: currently there are only R, Rw factors and an Anti-bump 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 is what makes this program different from other available programs.

For example currently you can combine several Powder patterns (X-Ray, Neutron,...) for the same structure,...

FOX is available in precompiled form for Windows (98, NT) and Linux-x86 (the source code is available along the ObjCryst++ code-see the ObjCryst++ home page for info). You can download from several sites:

• University of Geneva
• Sourceforge
• CCP14 (UK)
• CCP14 (Canada)
• CCP14 (USA)

For Windows, download the Fox-Windows-20011015.zip file.

For Linux, download the Fox-Linux-x86-20011015-glibc213.tar.gz or  Fox-Linux-x86-20011015-glibc22.tar.gz file, depending on the glibc version (2.1.3 or 2.2) version that you have on your computer (the 2.1.3 should alsowork on 2.2). If you cannot resolve dependencies problems, contact me to compile Fox from source (or see the ObjCryst++ home page).

• For Linux, simply uncompress the .tar.gz archive. This will create a directory with the Fox program, example  files, and the documentation.
• For Windows, unzip the file, which will also create a folder with the Fox program. This program uses the glut library, you do not need to move the glut32.dll to your System directory, as long as the 'FOX.exe' application remains along the glut32.dll file.

Using FOX

• As a demonstration (even if you are not a crystallographer you can try that), you can launch fox, then use the top menu File->Load and open the example file example/pbso4-joint.xml. This is a file showing the global optimization of a very simple and well-known structure, PbSO4. Then
• Click on the 'Crystal' tab, and in the window, choose the menu Display->3D Display. This opens a window with the crystal structure. You can click& drag with the mouse to rotate the structure (on Windows 95 this may crash)
• Click on the 'Powder Diffraction' tab, and for the two PowderPattern objects, choose the menu Pattern->Show Graph. This will show you the current observed (blue) and calculated (red) patterns.
• Click on the 'Crystal' tab, and choose Parameters->Randomize Structure (it would be too easy to start from the solution)
• Click on the 'Global Optimization' tab. Then choose Optimize->Run. This will launch the global optimization running. You will see the structure eveolve, as well as the Cost functions (the two Rws in that case)
• To do your own global optimization, follow the step-by-step Howto.

Known Bugs

• In windows 95 and NT SP1 (not 98 or NT with SP4), the 3D Crystal view (using OpenGL) leads quickly to a crash when you rotate the structure. Otherwise it runs fine on win'95 and win'NT4-SP1.
• Under Linux, sometimes the refreshing of the interface stops during refinement. Solution: save using the top window menu (everything is still functionnal), quit and restart/reload.


Note1: If you have remarks about what could be done to significantly improve the program (or the documentation), feel free to send me an email , especially if something in this documentqtion does not work.
The program is currently not very forgiving for improper or unexpected input (hence follow closely the above step-by-step howto).

Note2: This is an open-source project. If there is something that you would like to see in it, you can contribute to it by submiting code. See the ObjCryst++/FOX Web Site for details.

Note3: if the program encounters an error, it will sometime manage to save the complete environment in a file which should be in the Fox directory, named "ObjCryst-date-time.xml" , which you can reload.
 
Reference for Fox
The reference for Fox is: V.Favre-Nicolin and R. Cerny, in preparation for J. Appl. Cryst (2002).

The FOX Program is copyright (2000-2001) Vincent FAVRE-NICOLIN, Radovan Cerny, and the University of Geneva.

The FOX program can be used free of charge by every one. You can redistribute the program provided that (1) it is not modified and (2) it is accompanied by its full (unchanged) documentation and (3) you clearly indicate in your distribution where newer versions can be found.

Disclaimer of Warranty and Limitation of Liability. THE SOFTWARE IS PROVIDED ON AN"AS IS" BASIS. THE AUTHORS DO NOT WARRANT THAT OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED, ERROR FREE, OR VIRUS-FREE, OR THAT ANY DEFECT IN THE SOFTWARE WILL BE CORRECTED. THE AUTHORS EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, AND ANY WARRANTY OF NON-INFRINGEMENT. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS AGREEMENT, AND NO USE OF THE SOFTWARE IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, YOU AGREE THAT IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY THEREOF, AND REGARDLESS OF THE LEGAL OR EQUITABLE THEORY (CONTRACT, TORT OR OTHERWISE) UPON WHICH THE CLAIM IS BASED. YOU ALSO AGREE THAT THE AUTHORS ENTIRE LIABILITY TO YOU OR ANY THIRD PARTY FOR ANY CLAIM OR DEMAND ARISING FROM OR RELATED TO THIS AGREEMENT SHALL NOT EXCEED, IN THE AGGREGATE, THE SUM OF THE FEE YOU PAID FOR THE PRODUCT (IF ANY).

This page & project is hosted on  and mirrored on CCP14 ( UK mirror, Canadian Mirror, US Mirror)