[Objcryst-foxx] Fox v.1.5 Beta test
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From: Favre-Nicolin V. <vi...@us...> - 2003-06-25 23:14:51
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Hi all, After spending a good day writing letters to european representatives (h= ope=20 some of you did the same, hum ?), I have put the last touch to the next maj= or=20 version of Fox. This version really needs serious testing before release, as there are a= =20 number of major changes, as you can see below. I'd very much like to see=20 tested: - your xml files, to see if there is no problem switching to the new globa= l=20 optimization algorithm - any organic sample, as this should be much better handled by the new=20 Molecule object. You can convert any ZScatterer to the new Molecule object= =20 using the import/export menu of the ZScatterer object. This rellay needs=20 testing - and of course the supplied Fox examples for the new Molecule format (see= =20 the file below) This version is roughly 50% faster on powder patterns, and the number of= =20 trials has also diminished by a factor 2 for the cimetidine and potassium=20 tartrate examples. I hope it can be used to solve more complex samples,=20 especially organic ones. Many thanks go to Brian Toby for its help on the 3D display of crystal=20 structure & fourier maps, as well as polishing the CIF output function. The beta version of Fox can be obtained: =2D for people compiling it, by updating to the latest CVS and re-compiling. =2D for people under windows and no compiler, get it from the usual places: ftp://ftp.unige.ch/pub/soft/crystal/fox/test ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/test http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/objcryst/test/ http://ccp14.semo.edu/ccp/ccp14/ftp-mirror/objcryst/test/ You should get the Fox-20030625CVS.zip, and put the .exe in the same=20 directory as your old Fox.exe. You can also get the updated examples in examples-molecule.zip. Note that the new documentation should appear by friday on the Fox websit= e=20 (delay due to sourceforge), at http://objcryst.sf.net/Fox/ Report to me any success or failure, I intend to do the official release= =20 sometime next week if everything goes all right. Cheers, Vincent Changelog: NEW FEATURES-MAJOR CHANGES * The optimization will now use log(likelihood) as a criterion: in practice, this means that the Chi^2 statistics are used rather than the user-chosen cost functions. The likelihood can sometimes be parametrized in the objects (crystal, pattern), but not any more in the Global Optimization objects. * Added a Molecule class, which suprsedes the ZScatterer approach The scatterer is defined by a list of atoms, and restraints (bond lengths, angles and dihedral angles) to specify the geometry. This gives more flexibility, allows a better=20 convergence and allows to correctly define cyclic molecules. * Added the ability to define a statistical positionnal error for atoms, which will be taken into account following Maximum Likelihood principles (ML field in ScatteringPowers), of course with a significant amount of approximations to be computationnaly friendly. * CIF output (with the help of Brian Toby). OTHER NEW FEATURES * Faster computation when using integrated profiles for powder pattern objects * Error bars are now displayed on the Powder Pattern graphical=20 display. * Further improvements of the Fourier maps display (mostly from Brian Toby) * A cursor can be displayed in the center of the 3D Crystal view, its coordinates are displayed at the bottom of the window, with the value of Fourier maps (if any) * Added atom labels in 3D Crystal view (right-click menu to deactivate) * In OpenGL view of a Crystal structure, shift-dragging with left mouse button now correctly changes the center of the view without changing the rotation center. * Changed lighting model in 3D Crystal view * Added the ability to save structure factors from a DiffractionSingleCrystal object, including detailed contributions from different elements (useful for anomalous diffraction experiments) =20 BUG FIXES * Fixed bug when exporting to a Fenske-Hall z-matrix, the 4th atom was always repeated twice * Overall ZScatterer occupancy is now correctly taken into account. * Auto-save of xml files will now use local time rather than gmt. =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |