[Ifeffit] A few questions...

Matt Newville newville at cars.uchicago.edu
Fri Jan 23 09:45:31 CST 2004


On Fri, 23 Jan 2004, Bruce Ravel wrote:
> On Friday 23 January 2004 01:32 am, Peter Southon wrote:
> > Atoms: Has there been any thought of allowing Atoms to open up standard
> > crystallographic data files, even CIF files? (I know CIF can be quite
> > complicated) Some crystallographer colleagues are hand-typing quite a few
> > structures from cif files into Atoms, and I suspect many others might do
> > the same.
> You are not the first to suggest this.  Perhaps I should move it a bit
> higher up the list of things to do.
> > Alternately, is there a friendly programmer out there who can write a
> > script to extract the relevant details out of cif and write an atoms input
> > file?
> If someone does this, please forward it to me so I can adapt it for
> use in Atoms.

If I might make a suggestion for a project related to this that 
someone other than Bruce or myself might be willing to take on:

A considerable amount of the data in the Atoms.inp database of
crystal structures does not produce correct output.  Describing
crystal structures is not always trivial, and conventions change, 
so I wouldn't want to blame atoms, the literature sources, or the 
translation of those sources, but it's not too unusual for the 
result to be bad.
A simple test would be to run atoms on every atoms.inp file and
check the results for such 'obvious mistakes' as atoms closer than
0.5 Ang, and coordination numbers>20.  Since there are many nearly
equivalent atoms.inp for many similar structures, paring these down
to 'known to work' inputs would be helpful.

> > And while I'm about it ... it occurred to me that these questions above
> > could well have been asked before, but as a newcomer to this list it is
> > quite difficult to trawl through the archives to find relevant answers. Is
> > there any possibility and/or interest in some kind of index of these
> > discussions?
> Yay!  Excellent suggestion.  In fact, in one of my recent rants about
> all the ways that people could contribute to the ifeffit family
> without actually writing code for ifeffit, athena, or artemis, I
> mentioned precisely this.
> I have been with the ifeffit list from the beginning and I have many
> times wished their were an index.
> So... any takers?  Here's a place to start:  http://www.htdig.org/

I was just looking at the Ifeffit FAQ and noticing how out-of-date 
and thin it is.  Then again, all the documentation needs work!

It would be nice if the mailing list archive had a built-in search.
This is not a standard feature of the Mailman program, but a quick
search tells me that it is possible in principle to combine htdig
and Mailman.  I'll look into this possibility.

A discussion in November mentioned the possibility of having web
pages authored by outside users (such as a wiki).  Such a system
would allow 'the interested community' to help with some of the web
pages and information.  This seems like a good idea, but setting up
the basic system to allow this would be work too, and the size of
'the interested community' is not clear ;).  Another possibility
would be to move the Ifeffit web pages (possibly including
Ravelware) to someplace like Sourceforge where multiple authors
could get access.  All of this is still open for discussion, and if
anyone has suggestions along these lines or would like to help out,
please let us know.


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