Help fight Software Patents !
You who enjoy the use of free software, please take some
time to think about Software Patents! If these are made legal in Europe
too, that could eventually lead to the extinction of free software. Please
see more information on the main ObjCryst++/Fox
web page (UK,
Canada,
US Mirror)
for a scientific approach of the problem, and on FFII
and EuroLinux.
I will not be able to distribute Fox anymore if/when Software Patents exist in Europe...
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 1.1.2 (march 2nd, 2002). A few bugs only occuring under windows were removed (when changing space group or unit cell), and it is now possible to limit the extent in sin(theta)/lambda of the calculated diffracted data. The threshold below which the dynamical occupancy correction was applied has been corrected to 1 Angstroem.Introduction
Version 1.1 featured 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.Molecules imported from a z-matrix file with Fox 1.1 or 1.1.1 must be reimported in 1.1.2 if the 3rd and 4th atom are of the same type (they have not been properly saved in the xml file).
The license has been changed to the General Public License. Note that people wishing to use ObjCryst++ without the constraint of releasing their source code may contact me for the right to use a different license (academic, free software particularly).
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 if you have trouble with the linux install.
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, (2000-2001) Radovan CERNY, and the University of Geneva.This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
This page & project is hosted on
and mirrored on CCP14 ( UK mirror, Canadian Mirror, US Mirror)