[seul-sci] Announcement/Introduction to GDIS

[s.fleming@wbmt.tudelft.nl]

Greetings,

I apologise for the length of this email, but as it is an
announcement and (at the end) an introduction I hope you'll
forgive me.

I've been working on little GTK based molecular display project
(GDIS) for a couple of years now, but have only just publicly
released it (http://gdis.seul.org). I work in the field of
molecular modelling, and so it's kind of tailored to the stuff
I'm interested in, but probably has enough features to be of
more general interest to some chemistry and physics people.
GDIS can load a few different files types, perhaps the most
common being the MSI (company formerly known as BIOSYM)
.car/.arc, the .xyz, and the .xtl formats.

If you're into crystals (like I mostly am), you can load up
asymmetric cells in GULP format, or (less well supported) XTL
format, and GDIS should automatically build a full cell. Plus,
you can bring up a periodicity dialog that shows the space group
information and allows you to toggle the asymmetric/full cell
display and generate periodic images as desired. Further, if
you're interested in crystal morphology, you can display the
resulting polyhedron that arises from a bunch of input (hkl)
planes and normal lengths. The only file format that allows this
is the GDIS Morphology File (.gmf) and there are a few examples
in the .tgz package. At present, GDIS can't take advantage of
the crystal point group for morphology generation, but this may
be introduced in the future.

GDIS also has a very rudimentary dialog for constructing and
editing molecular compounds, and, if you have GULP installed, you
can even do energy calculations geometry optimization. Bear in
mind that this will most likely be rubbish, unless you supply a
system specific empirical potential library, rather than go with
the crappy default one I whipped up for demonstration purposes
(see the GDIS and/or the GULP home page for more details).

There is also a dialog for measuring bonds, distances, bond
angles, and dihedral angles. A pretty periodic table (GPeriodic)
also pops up when you want to edit element colours in order to
generate nice rendered POVRay images. A rendering dialog gives
you a few nice options (eg ball&stick, antialias etc.) so that
you can generate some beautiful images to decorate your walls.

There is an initializer for generating starting configurations
for molecular dynamics (MD) simulations, if you have loaded up
a solvent followed by solute molecules. Sadly, you cannot do MD
runs yet, but the author of the GULP program (which can) is a
friend of mine and so this may become possible in the future.

Finally, there is a feature for generating van der Waal surfaces
by rolling a probe ion over an input structure. It is primarily
intended for scanning planar surfaces (eg results from a MARVIN
run) and NOT for isolated molecules.

Anyway, I hope it's of use to some of you, and please feel free
to offer comments, suggestions, and/or bug notifications. A
mailing list will be set up soon, so keep your eyes peeled for
details.

PS: if you're curious, I'm a 28 year old Aussie currently working
as a post-doc in the Netherlands. I finished my PhD about a year
& a half ago at Curtin University (Perth, Western Australia) on
computer modelling of gibbsite crystallization. So, I've kind of
migrated to chemistry, even though I did my under-grad degree in
physics - which was when I first got into C programming by writing
some very simple QM and planetary orbit calculation programs. I got
involved with linux during my PhD when my supervisor (one of the
authors of MARVIN) suggested that I install linux & learn to use
Perl for scanning & processing my data. I never looked back. In
fact, I used LyX to write my thesis and had many a laugh at
colleagues who were complaining how painful it was to use MS-Word
for large documents, such as a thesis.

Cheers

-- 
Sean Fleming
--------------------------------
Laboratory for Process Equipment
Leeghwaterstraat 44 
2628 CA Delft
The Netherlands
--------------------------------
Phone:  +31 (0)15 278 6661  
  Fax:  +31 (0)15 278 6975