Hi everybody, I would like to draw your attention to the following postdoc position:
https://www.pse.kit.edu/karriere/joboffer.php?id=85889&language=en It will be great if you forward it to suitable candidates. Thank you in advance and best from me, Tonya -----Ursprüngliche Nachricht----- Von: Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> Im Auftrag von ifeffit-requ...@millenia.cars.aps.anl.gov Gesendet: Montag, 16. August 2021 23:46 An: ifeffit@millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 222, Issue 2 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Problem Importing CIF files into Larch (Matt Newville) 2. Re: Problem Importing CIF files into Larch (Vincent Wu) 3. Re: Problem Importing CIF files into Larch (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Mon, 16 Aug 2021 15:21:13 -0500 From: Matt Newville <newvi...@cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem Importing CIF files into Larch Message-ID: <ca+7esbrwmtgyta+t+2u+++qz92jqytjfdqsfkhvzccqmqfi...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Amol, Sorry for the delay, I was offline most of last week. Thanks for posting these CIF files. I think these should be usable -- the basic "cif2feffinp()" function works on these to generate a valid Feff.inp, but the GUI CIF Browser is currently expecting additional fields such as publication information. I guess those fields should be optional. I think there is another issue with using multi-site CIF structures that I want to look into. So, I hope to get this fixed soon, but I also want to tackle a few other issues before posting a completely new version. --Matt On Tue, Aug 10, 2021 at 4:12 PM <amolagarwal2...@u.northwestern.edu> wrote: > Hi, > > I hope you are doing well. I am writing regarding some issues that I > am having with opening my CIF files in Larch. I have used these same > CIF files in the past in Artemis to run feff calculations. When I open > these files in the Larch open feff tab, it shows a dialog box saying > that there is an error opening the CIF file. This is happening with > all my CIF files and I am not sure why. I am attaching a couple of > these CIF files. I would really appreciate some help on this. > > > > Amol Agarwal > > PhD Student > > Materials Science & Engineering | Northwestern University > > > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20210816/35726498/attachment-0001.htm> ------------------------------ Message: 2 Date: Mon, 16 Aug 2021 13:30:44 -0700 From: Vincent Wu <vincen...@ucsb.edu> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem Importing CIF files into Larch Message-ID: <CAHd9kXoSNt15f0P5c5P9wjTDKRfGjW6nqFOQngcdm7dFm=x...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I've found that if I have cif files that don't work with Larch, I use Pymatgen to read the CIF and output a Pymatgen generated CIF, which would then work with Larch. I believe that Pymatgen cleans up cifs in a way, so that they become compatible. Vincent On Mon, Aug 16, 2021 at 1:22 PM Matt Newville <newvi...@cars.uchicago.edu> wrote: > Hi Amol, > > Sorry for the delay, I was offline most of last week. Thanks for posting > these CIF files. > I think these should be usable -- the basic "cif2feffinp()" function > works on these to generate a valid Feff.inp, but the GUI CIF Browser > is currently expecting additional fields such as publication information. I > guess those fields should be optional. I think there is another issue > with using multi-site CIF structures that I want to look into. > So, I hope to get this fixed soon, but I also want to tackle a few > other issues before posting a completely new version. > > --Matt > > > On Tue, Aug 10, 2021 at 4:12 PM <amolagarwal2...@u.northwestern.edu> > wrote: > >> Hi, >> >> I hope you are doing well. I am writing regarding some issues that I >> am having with opening my CIF files in Larch. I have used these same >> CIF files in the past in Artemis to run feff calculations. When I >> open these files in the Larch open feff tab, it shows a dialog box >> saying that there is an error opening the CIF file. This is happening >> with all my CIF files and I am not sure why. I am attaching a couple >> of these CIF files. I would really appreciate some help on this. >> >> >> >> Amol Agarwal >> >> PhD Student >> >> Materials Science & Engineering | Northwestern University >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> > > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20210816/850a997c/attachment-0001.htm> ------------------------------ Message: 3 Date: Mon, 16 Aug 2021 16:45:20 -0500 From: Matt Newville <newvi...@cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem Importing CIF files into Larch Message-ID: <ca+7esbpjyp3+6gs_5gdr1mls5vwhbk06kpohutbaz3zdjpc...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Vincent, Yeah - we are using pymatgen to do the actual CIF parsing, and I think that part is working fine. Well, except that it isn't great at identifying equivalent positions and so tends to give at least 2x more sites than actually necessary. In itself, that isn't a huge problem. The problem that Amol (and, I'm guessing you saw too) was that structures generated by pymatgen or CrystalMaker, etc won't have some of the fields currently expected. I started with a restricted set from the AmMin Database, and was focused on searching through these, so just assumed that each structure would have a publication -- that is also true for structures from COD, but won't be true for structures from CrystalMaker or ShelXL. And right now, the CIF Browser wants to take any CIF you read in and add it to the database (so you'll have it next time). But, it should not assume the CIF file will have all that information.... That's all to say that I think this is fixable.... On Mon, Aug 16, 2021 at 3:31 PM Vincent Wu <vincen...@ucsb.edu> wrote: > Hello, > > I've found that if I have cif files that don't work with Larch, I use > Pymatgen to read the CIF and output a Pymatgen generated CIF, which > would then work with Larch. I believe that Pymatgen cleans up cifs in > a way, so that they become compatible. > > Vincent > > On Mon, Aug 16, 2021 at 1:22 PM Matt Newville > <newvi...@cars.uchicago.edu> > wrote: > >> Hi Amol, >> >> Sorry for the delay, I was offline most of last week. Thanks for >> posting these CIF files. >> I think these should be usable -- the basic "cif2feffinp()" function >> works on these to generate a valid Feff.inp, but the GUI CIF Browser >> is currently expecting additional fields such as publication information. I >> guess those fields should be optional. I think there is another issue >> with using multi-site CIF structures that I want to look into. >> So, I hope to get this fixed soon, but I also want to tackle a few >> other issues before posting a completely new version. >> >> --Matt >> >> >> On Tue, Aug 10, 2021 at 4:12 PM <amolagarwal2...@u.northwestern.edu> >> wrote: >> >>> Hi, >>> >>> I hope you are doing well. I am writing regarding some issues that I >>> am having with opening my CIF files in Larch. I have used these same >>> CIF files in the past in Artemis to run feff calculations. When I >>> open these files in the Larch open feff tab, it shows a dialog box >>> saying that there is an error opening the CIF file. This is >>> happening with all my CIF files and I am not sure why. I am >>> attaching a couple of these CIF files. I would really appreciate some help >>> on this. >>> >>> >>> >>> Amol Agarwal >>> >>> PhD Student >>> >>> Materials Science & Engineering | Northwestern University >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit@millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: >>> http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >>> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411 -------------- next part -------------- An HTML attachment was scrubbed... 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