Sections

25/Sep/2004: News - It's been awhile, eh? The author has been enjoying writing chemistry software at work, but now there's an update. The targetted platform is now Mandrake 10, for which everything should hopefully work without modification.

24/Sep/2004: Xortoth - Xortoth is temporarily decommissioned, pending an overhaul.

15/May/2004: News - CRK has had a bit of an interior code remodelling. It has also been updated to compile with GCC 3.4, Qt 3.3 and MPQC 2.2.2. GCC precompiled headers are now used.

9/Nov/2003: Xortoth - A whole new phase of the Xortoth middleware has been introduced: the Question/Answer server is being rewritten in Java. The protocol is completely equivalent to the original PHP implementation, and is being tested alongside it. The PHP version will soon be deprecated, though it will probably remain current for a long time as far as the basic functionality is concerned. The Java implementation does not yet implement the task or permission features, but that is next.
  The new implementation is run as a Java servlet, and is targetted at the Tomcat/Jakarta application server stack. Presently there is no guidance for installing the necessary pieces, but that will change once it is feature complete.

17/Aug/2003: Xykron - Display of predicted electronic spectra now offers additional levels of control (wavelength range and whether to include only ground state excitations). The eigenvalue viewer is also scalable now.

20/Jul/2003: Xentark - Xentark has been modified to submit results while the calculation is still in progress; this can alleviate some frustrating delays.

5/Jul/2003: Xentark - Xentark now calculates partial charges properly, using the natural atomic orbital populations much are made available by MPQC. Hydrogen charges are not standardised as zero, however.

4/Jul/2003: News - The Help section on this site has been extended, and is slightly closer to completion. Also, the current package versioning has been upgraded to 2.1.0, since the feature set of the interface has stabilised somewhat lately.

28/Jun/2003: Xentark - Minor tweak to increase the combinations of oscillator strengths determined. Some numbers have been compared with results from Gaussian98, and they appear to be reasonably consistent.

22/Jun/2003: Xentark - A very significant new feature has been added to Xentark: it now calculates oscillator strengths for particular electronic excitations (which are said to be qualitatively proportional to the intensity of the absorption), after determining the eigenvalues. The method used could be described as ZDO (zero differential overlap; also ignores p & d overlap), and is quite simple and fast. The transition electric dipole moments for the excitations are also stored. The significance of this is that it is the author's first direct use of the underlying wavefunction matrix, rather than using the MPQC libraries as a "black box" and overlaying high-level functionality. This is also partly why there have not been very many mundane improvements to CRK lately. Note that although the results of this new calculation feature do seem to make sense, only rather preliminary verification has taken place thus far.

26/May/2003: Xykron - An additional "when to stop" clause added to the OptiClean algorithm, which should improve results in many cases. Graphical glyphs are now used to denote particular symmetry elements in 3D structure display.

3/May/2003: News - As of 2.0.6, user authentication is implemented in Xortoth and is honoured by Xykron/Xentark/Xuru. The management protocol is implemented, and Xykron now has an operational interface for adding users, groups, members etc. Authentication of users and permission handling for the user-management features is nominally fully operational, although has undergone only cursory testing.
  Object-level permissions constitute the next feature along these lines, and although the table structure now supports it, the necessary protocol/interface enhancements have yet to be made.

3/May/2003: Xortoth - User-login security and user-management implementation is complete. Also, fields have been added to the Tree table to facilitate Unix-like permissions on parts of the hierarchy; these are, however, not yet used.

26/Apr/2003: Xortoth - Xortoth has been rewired to include security, and the other CRK packages updated accordingly to make use of it. There is a new database table, Perms, which manages users and groups. Presently security is only implemented as far as gaining access to being able to use Xortoth, or not. Actual permission granularity is next, and will be Unix-like (owner/group/all).
  On a general note, Xortoth security will not likely be "hardened" in the immediate future. Although there are some common sense precautions, like using MD5 hashes through the webservice interface and for passing passwords as parameters, there are still plenty of ways a hacker could take advantage of a naive admin.

23/Apr/2003: Xortoth - Improved configurability for Xortoth: now a file 'datasources' is read to ascertain a list of MySQL databases, and their appropriate connection parameters. The webservice page, FatClient.php, takes an optional form parameter, as '?db=' which may be used to indicate which database is to be used for the connection. If omitted, the first valid line in the 'datasources' file will be used.
  Further improvements to Xortoth's installability will ensue.

22/Apr/2003: News - Packages have undergone some minor fixes in order to be comfortably included in Mandrake 9.2. Expect to see Xykron, Xentark and DrawMol make a show; Xortoth then Xuru will follow. Many thanks to Austin Acton (www.groundstate.ca) for putting in the time to do this.

12/Apr/2003: Xykron - A minor glitch fixed which prevents overly-long summary enumerations of collections from blocking the user interface.

5/Apr/2003: Xentark - Minor improvement which allows "minimal records" to be kept during a Xentark computation: if set in the CompParams panel, will cause only the last cycle to record a CompResults property. This is useful for some long calculations running under low basis sets, which can operate through hundreds of cycles, which aren't necessarily very interesting.

30/Mar/2003: Xykron - Eigenvalue (orbital energy level) viewing now shows transition probabilities, when available. Also, the CompResults panel has a viewer for electronic excitations, which it presents as a simulated UV-Vis spectrum.

29/Mar/2003: Xuru - Xuru has been augmented to be able to be able to run external scripts, which are provided with an input file (CompParams+Structure3D) and expected to generate an output file (CompResults), which will be integrated into the CRK hierarchy after successful completion.