Hello all, Just a couple of questions for Bruce. Artemis: I've tried using the "Sum of paths" feature, which I assume is the equivalent of ifeffit's ff2chi command. For some reason it doesn't work if no data file has been opened, even though the operation does not refer to any data. Its easy to work around, but perhaps something to be fixed? 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. 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? 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? Peter
On Friday 23 January 2004 01:32 am, Peter Southon wrote:
Artemis: I've tried using the "Sum of paths" feature, which I assume is the equivalent of ifeffit's ff2chi command. For some reason it doesn't work if no data file has been opened, even though the operation does not refer to any data. Its easy to work around, but perhaps something to be fixed?
I have already fixed this bug and it will be available in the next release of Artemis. Also in the next release will be the ability to do a sum of paths only using the selected (highlighted in orange) paths, i.e. a sum of a subset of paths. And, yes, "Sum of paths" uses ifeffit's ff2chi() command.
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.
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/ Oh, to my memory, neither of those topics has come up on the list yet. So, you're blazin' new ground, Peter ;-) B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Peter,Bruce, 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. --Matt
On Friday 23 January 2004 10:45 am, Matt Newville wrote:
Since there are many nearly equivalent atoms.inp for many similar structures, paring these down to 'known to work' inputs would be helpful.
I should point out, since it is not obvious to the casual observer, that a large number of the input files in Matt's database are derived from a database of structures from American Minerologist maintained by a fellow at University of Arizona. http://www.geo.arizona.edu/AMS/amcsd.php It's not the case that either Matt or I one day got super interested in minerology. rather, I stumbled across that web site and realized it would only be about a days work to convert it all into atoms.inp form. So one day a couple years ago I wrote a perl script which attempted to convert the entire database. My script worked on about 95% of the files. I spot checked much less than 1% of converted files. There are many nearly equivalent files because there were many such files in the AM database. There are many that may not work well because I spot checked very few. If anyone is interested in seeing the script that I used to do the conversion, I'd be happy to pack up the whole kit 'n' kaboodle and put it on my web site. B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
participants (3)
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Bruce Ravel -
Matt Newville -
Peter Southon