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 (http://v.favrenicolin.free.fr
)
This program was developped in collaboration with Radovan
Cerny, and was written at the Laboratory
of Crystallography, in Geneva (Switzerland), with support from the
Swiss
National Science Foundation. (project #21-53847.98)). The development
still goes on as a personal research project after my move to the ESRF.
See the ObjCryst++ homepage for more details about the source code.
Reference for Fox
The reference for Fox is: V.Favre-Nicolin and R. Cerny, in preparation
for J. Appl. Cryst (2002), http://objcryst.sourceforge.net
NEWS
Latest version is 1.1.1 (january 17th, 2002). A few bugs only occuring under windows were removed (crash of the examples after a number of tests, or when clicking in a powder pattern graph window). Version 1.1 features speed improvements, use of integrated R(w)-factors (for a better handling of patterns with badly defined profiles), the possibility to use single crystal data (eg extracted intensities), overall temperature factor, a better handling of molecules (importing zmatrices and therefore pdb), and is more user-friendly (eg no need to hit 'return' after each input). See the full changelog.Introduction
The FOX program was made for the ab initio structure solution from powder diffraction data. Its most interesting features for ab initio structure determination are :DownloadSo, if you have:
- the ability to use multiple patterns (X-rays, neutrons), as well as single crystal data (eg extracted from a powder pattern)
- a versatile description of scatterers: 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 .
- 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.
- A graphical interface with a 3D crystal structure view, live updated during the optimization process.
Then FOX can help 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 systemetic extinctions).
- would like to solve the structure (ie find the atom -or group of atoms- positions, before refining them with another package).
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, with a versatile way to describe the unit cell's contents, is what makes the algorithms used interesting.
For example you can combine several Powder patterns (X-Ray, Neutron,...) for the same structure,...
FOX is available in precompiled form for Windows (tested on 98, NT SP4, 2000) 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: For Windows, download the Fox-20020117.zip file (precompiled).InstallationFor Linux, download the Fox-20020117.tar.bz2 (source).
Please send me an email. to tell me how the linux install went: I have had troubles to find a suitable and simple way to install Fox under Linux, so I need some feedback.
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 where you launched Fox, named "ObjCryst-date-time .xml" , which you can try to reload.
The FOX Program is copyright (2000-2002) 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).
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