Sweeping a little dust. Reworked the documentation to use CSS,
DocBook Website and XML based dtds. Can embed manuals in the ToC.
The technology is
Released Gnu Xtal System 3.7.2.
Probably it should have been 3.8, but the theory was that by
4.0 the system would have been irreversibly reworked.
The facilities offered by sourceforge.net may offer a stable
and accessible environment for stimulating collaborative new
development work in Xtal (or not, as the case may be).
March 1 2001:
Minor fixes to several programs are included in this release. Most
of which you won't notice. The biggest change for unix platforms is
that the PIG and PREVUE graphics interface text entry modes are now
implemented as Tcl/Tk widgets. These have complex key bindings
which are documented under the tcl entry man page ( man 3
Feb 1 2001:
A bug was detected in the reporting of sigma values in the
structure factor factor listings for Frel, F2rel and
Irel. Unfortunately instead of reporting sigma in each case it is
sigma2, appropriately scaled. A bug fix wil be made
- March 1 2000:
The download page for Xtal version 3.7 has been installed. The
executable modules for other platforms will be added as they become
available. Users are also able to do their own installations using
the supplied source codes.
- February 2000:
As Announced at the Society of Crystallographers in Australia
(SCA) Crystal XXI meeting in Threadbo, 1st-4th Feb, The Xtal System
is going the Free Software route!
It is envisaged that by March 2000 Xtal3.7 will be ready for
distribution in the form of binary executables for a range of
architectures. Hopefully soon thereafter, the sources will also be
Xtal3.7 is progressing more and more along the free software
path, with interfaces to XFIG added in PLOTX , POV-Ray and RasMol
in PIG, and with the adoption of Tcl/Tk based graphics for all
graphical programs. The new graphics interface has greatly
facilitated development of a new Powder diffraction pattern
calculating routine, POWGEN and an associated new program ADDPAT
for reading various Powder diffractometer files.
August 99: Improvements to Xtal3.6.1
ADDATM reads LINK lines for adding H atom calculation constraints
to the archive for the CRILSQ "riding atom" refinements. PLINK can
be used to purge link lines from archive in update mode.
Generation of LINK lines by BONDAT (for CRILSQ)
BONDAT may be used to generate LINK lines for calculated sites for
addition to the archive file for the CRILSQ "riding atom"
Improvement to the filled-contour facility in CONTRS
The filled contour facility in CONTRS has been improved by sorting
all contours by area to place the smallest areas on top - instead
of being overwritten by larger contours in Xtal3.6. There remains a
fundamental flaw in the algorithm in that re-entrant contours have
the wrong colour by one shade, and if the zero contour is not a
good baseline (inflection point), the contours may appear
incorrect. By and large, filled contours are intended for glossy
slide shows rather than the precision requirements of publications.
New least squares refinement program CRILSQ
A new Least squares program CRILSQ has been added to 3.6. CRILSQ is
a full-matrix F**2 refinement program which permits linked-atom
sites as a "riding-atom" model. Details of this are given in the
writeup but suffice it to say that the initial geometry constrained
(i.e. "linked") sites may be generated using the PIG "build/auto
H-atom" option. This step generated the required LINK information
which is stored in the archive for subsequent ADDATM and CRILSQ
calculations. The same LINK information can be generated using
BONDAT. The current version of CRILSQ does not refine or apply
Restraints. It does however refine the Flack parameter.
Improvements to the speed and versatility of CRISP
Modifications to CRISP have led to some improvements in speed of
solution, more stable block-diagonal least squares refinement for
peak elimination, improved random phase generator and assorted bug
Improvements to PIG
An auto-hydrogen building feature has been added to PIG which auto-
matically adds H-atom sites to the atom list where this can deduced
from the chemistry and the geometry. *Caution* may need to be
exercised when when parent C-atom geometries are unusual.
H-atom sites generated with this option are accompanied by LINK
line information which is loaded into the archive file via ADDATM
(intended for the CRILSQ "riding atom" model).
Note that LINK information is NOT generated if H atoms are assigned
directly from peak sites.
The addition of LINK information may be switched off if the riding
atom features of CRILSQ are not being used via the 'PIG nolink'
PIG can now generate a POV-Ray control file (.pov) and
automatically spawn a background POV-Ray process to display the
file on UNIX platforms at least. The POV-Ray program needs to
installed as per the implementation instructions. Users have some
control over the image size and type generated, with mean squared
displacements represented by ellipsoids at various probability
levels. Read the PIG manual pages for an explanation of how to
use/configure this feature.
New CIF validation program PREPUB
A program has been added to 3.6 which applies a subset of the IUCr
CIF data validation tests (as per CIFCHECK) to all data blocks in a
user supplied CIF. The tests applied are:
Xtal3.6 is released but with the new least squares routine CRILSQ
ommitted. It is intended to distribute a free upgrade (3.6.1) to
existing 3.6 users early in June of 1999.
Xtal makes no use of file access times whatsoever. Nucleus routines
do get the current time and date for storing as auxilliary
information in certain files, so if your operating system supplies
this incorrectly, it will certainly be recorded. However, the time
stamp is purely for users information, and is not used by xtal to
control archive updates or file read/writes. Xtal output listings
continue to record the year as a 2 digit number.
- December 98:
Xtal3.6 will be released starting in January 1999.