- Ifeffit - millenia.cars.aps.anl.gov

RE: [Ifeffit] Solution flow cells
by Jensen, Mark P. 22 Jul '04

22 Jul '04

And just to add to Matt, Shelly, and Tsu-Chien's responses. Matt mentioned Mark Antonio's electrochemical cell. It is not a flow cell, though we did design a closely related, but unpublished, cell design for in the beam titrations. ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: Newville, Matthew G. > Sent: Thursday, July 22, 2004 2:55 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Solution flow cells > > Just to follow up on and add to Shelly's and Tsu-Chien's > responses: > > There's a paper by M. Hoffmann, et al (J. Fulton, and others > from PNNL) on a flow-cell, especially for high pressure fluids. > I believe it's in J Phys Chem (1999), but don't have the > exact citation. This might be the one Shelly saw at PNC CAT. > > Mark Antonio has a nice electrochemical cell in which he can > change both potential, but can't remember if he can flow in a > changed solution... is that "flow"? > > I believe the catalyst people who run at ESRF (esp. the DXAFS > line) have some nice flow cells too, but don't know if or > where it's published. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Solution flow cells
by Kelly, Shelly D. 22 Jul '04

22 Jul '04

Hi Scott, See below: > Hi all, > > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an XAS > flow cell desgined for liquids. Sealed cells for liquids, > yes; flow cells for passing gases over solids, yes; but no > solution-chemistry flow cell. I feel like someone must have > published work in that area before, but I can't seem to find it. > > So, does anyone know of any work done using a liquid-phase > XAS flow cell? Simon Bare uses a flow cell for passing liquids/gasses over a sample. This one is a glass container with kapton windows with ports for input and output. Also I have seen something like that at PNC cat. I think that Ed Stern et. al. was using it. The one at PNC cat circulated the liquid through a boron carbide section that is x-ray transparent. Shelly

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using atoms and feff
by Bruce Ravel 21 Jul '04

21 Jul '04

Hi folks, I suppose I should preface this message by saying that I will not say anything new and profound. Indeed, this email is something of a rant -- so some of you may want to click ahead to the next email right now and avoid the whole darn thing! Today I was asked a Frequently Asked Question about using atoms and feff and getting started with some fits. This particular question is pretty common, but it's one that kind of bugs me. It's been rattling around in my brain for the remainder of the evening. To get it out of my brain, I figured I would write a message to the mailing list. A colleague showed me some data and explained a bit about the sample. This person had the lattice constants and space group for the oxide form of the absorbing element but expressed a confusion about how to proceed. I asked to see the rest of the crystallographic data -- specifically the atomic positions. I was shown a printout of some stuff from webelements.com or some similar web compilation of information about the elements. Sure enough, the lattice constants were given for the oxide form, but neither complete crystallographic data nor a crystallographic reference were listed. As everyone here should know, feff requires a list of atomic coordinates as its input data. To get a feff calculation, you must tell feff where the atoms are. Ifeffit and Artemis rely upon feff to provide theoretical fitting standards, thus to start fitting you need somehow to run feff. It is a syllogism, then, that you need some kind of list of atomic coordinates before you can begin fitting with Ifeffit and Artemis. With but a passing understanding of crystallography, it should be clear that you cannot generate a list of atomic coordinates given *only* the space group and lattice constants of a crystal. The space group and lattice constants tell you the shape and size of the unit cell, but, by themselves, do not tell you what is inside the unit cell. You see, a unit cell is just like a birthday present. The box might be big and pretty, but it's not a very good present until you open it up and find out what's inside. So........ if you intend to start your analysis by using Atoms, you have to find the COMPLETE crystallographic data. Often, this is one of the more difficult parts of the analysis problem. Sometimes crystallography data is hard to find. Matt keeps a big pile of atoms.inp files on one of his web sites and that helps a lot. Many libraries have copies of Wyckoff -- that also helps a lot. Google can be awfully handy -- indeed I ended up finding the missing crystallographic data earlier today with the help of Google. Often times you will be reduced to an exhausting search through the crystallography journals looking for the data you need. Other times you will never find what you are looking for and will just have to use something similar (but not the same) as your starting point. I presume it was already abundantly clear to everyone reading this message that the space group and lattice constants by themselves are not enough to use Atoms. But I needed to vent and so availed myself of this public forum. B P.S. The question of what to do when your sample is different from its crystalline form or when your sample is not a crystal at all has been discussed several times recently. If, after reading this little rant, that's your concern, you should read and respond to one of those threads rather than to this one. P.P.S. The next time you dig through the literature to find some obscure crystal structure, save someone else the effort. Be a hero, donate the atoms.inp file to Matt's database. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 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/

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Artemis on Mac OSX
by POGER David 202545 21 Jul '04

21 Jul '04

Hi all I am quite new in the 'EXAFS community' and I have a problem with Artemis (v 0.7.007) on my Mac (OS X, v 10.3). When I try to load a FEFF path file (feffxxxx.dat), the program simply crashes and there's nothing I can do then, but killing the program. It creates the file 'ARTEMIS.TRAP' that I have attached. Could anyone help me? I would really appreciate your help. Thanks. David __________________________________________ POGER David Département de Réponse et Dynamique Cellulaires Laboratoire de Biophysique Moléculaire et Cellulaire Bat. K - P 215A - CEA Grenoble 17 rue des Martyrs 38054 GRENOBLE Cedex 9 FRANCE Tel: +33 (0)4 38 78 48 48 Fax: +33 (0)4 38 78 54 87 Email : david. <mailto:david.poger@cea.fr> poger(a)cea.fr

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New Comer
by jawad shah 21 Jul '04

21 Jul '04

Hi friends! I am the new commer in this field.I hope that all of you will guide and wellcome me.I am a person having no PC, With a brilliant academic record. DEar friends i hope that all of you will help me in this field. Best Regards to all friends Jawad __________________________________ Do you Yahoo!? Vote for the stars of Yahoo!'s next ad campaign! http://advision.webevents.yahoo.com/yahoo/votelifeengine/

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Re: Artemis Question
by Bruce Ravel 20 Jul '04

20 Jul '04

On Sunday 18 July 2004 11:38 pm, John Butler wrote: > Basically, the problem that I'm having is that the system I'm working > on is a solution (to start I'm trying to look at a solution of Zinc > Sulfate and then look at data with other components we're interested > in). Unfortunately, the part of the manual dealing with solution > analysis hasn't been written yet, and the people I know who use EXAFS > don't do anything with solutions. > > I was hoping that you could point me in the right direction for how to > proceed with the analysis (e.g. is there anywhere I'm likely to find > the FEFF files ... is there a 'standard' way to attack this kind of > problem). Of course I assume you're a pretty busy guy and have > neither the time nor inclination to give me a detailed step by step > guide or anything ... I was just hoping you could point me in the > right direction, give me a couple of tips, and/or show me where to > look. John, As you can see, I have forwarded you question along with my answer to the Ifeffit mailing list. You are correct to assume that I'm a busy guy. This week (like each of the other weeks this month) I am at NSLS collecting some data and helping our users. Fortunately, the mailing list is a solution to the "busy expert" problem. Enough people read and respond to the mailing list that someone should be available to answer just about every question. I doubt, actually, that you problem is really so hard to get started with. Lots of problems in XAFS do not fall into nice little pigeon holes. One knows how to deal with data on an iron foil because one knows what the structure of iron metal is. Most real research problems, obviously enough, are problems precisely because the structure is not perfectly well known. In the case of a solvated complex, there is probably some sort of analogue which can be used as a starting place. Perhaps there is some similar compound whose structure *is* known. Perhaps your solvated complex has a crystalline form that is similar, at least in the local environment, to the solvated form. In any case, find something that is similar to your real material. Run feff and compare to the data. Perhaps your analogue structure will be close to your data. In that case, you should be able to parameterize the feff calculation in such a way that you can begin to understand the ways in which your complex differs from your analogue. Perhaps the analogue structure is a very poor match for the data. That in itself is information, in that it tells you to go look for a different analogue. The common theme to what I have said here (and indeed to any analysis problem) is that you make some educated guesses as to what you real sample looks like. You test those guesses. If they seem to be leading you in the right direction, super. If not, make new (and newly educated!) guesses. My other piece of advice would be to spend some time fitting known spectra. If you are new to XAFS, then you are learning two things at the same time: how to interpret XAFS data and how to use my and Matt's screw-ball analysis programs! I consider it a good idea to spend some time fitting data for which you know the answer so that you can learn how to use the codes before plunging into the harder but more interesting problem of your own research. Good luck and join the mailing list, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 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/

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Re: Athena & artemis download
by Scott Calvin 17 Jul '04

17 Jul '04

Hi Sabyasachi, It is best to address questions like this to the Ifeffit mailing list, since others may also be interested. If you are not yet a subscriber to that list, you can join at http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I have forwarded your question to this list. I recall seeing the problem you describe before, and I think it had something to do with the updater. Try going in to your ifeffit directory and finding updater.exe. If you run that directly, you may find the updater kicks in and after grabbing about half a dozen updates, has your Artemis up to speed. --Scott Calvin Sarah Lawrence College >Scott, >I was one of the participants of this year's EXAFS short course at >BNL last month. It was a great course and I have learnt a lot about >the latest of what's happening in the field. > > I am having trouble downloading the correct version of Artemis from >the website. I have downloaded Ifeffit 1.2.5a.exe from the website >(I have Windows 2000) and when I am trying to open Artemis it opens >the 0.6 version instead of the latest 0.7 version. Could you please >let me know what's the best way to download the suite of EXAFS >software ? > >Many thanks in advance. > >Sabyasachi

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ParseCIF added to web page
by Kelly, Shelly D. 16 Jul '04

16 Jul '04

Hi Dave, I added your program to my little web page. Take a look see. http://146.137.194.45/exafs.html Thanks for contributing! Shelly ****************************************************************** Shelly Kelly EMAIL: skelly(a)anl.gov Argonne National Laboratory PHONE: 630-252-7376 9700 South Cass Ave. FAX: 630-252-9793 Argonne, IL 60439

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CIF to Atoms.inp-v2
by Barton, David (DG) 16 Jul '04

16 Jul '04

Users, Sorry about the resend of my previous message, but the file wasn't attached correctly so I am trying alternate mail settings to attach the file..... There have been several instances of Artemis users asking Bruce for the ability to input CIF crystallographic files directly into Artemis. In my attempt to learn Perl and produce something of value to more than one person, I wrote a program that converts CIF crystallographic files into Atoms.inp files. Bruce may implement this sometime directly into Artemis, but in the meantime I will offer the standalone, command-line conversion program to anyone who can use it. Attached is a zip file with my first version of the Perl CIF->atoms.inp file converter. The main program was snarfed from Bruce's amc2inp.pl program which converts mineral files to atoms input files. <<ParseCIF.zip>> cif2inp.pl ---main Perl program. Converts .CIF files to atoms.inp file usage: perl cif2inp.pl aucl.cif parser.pm ---parser module written by Wolfgang Bluhm of PDB at UCSD, parses CIF file into an array of hash arrays. This should be put into the STAR:: subdirectory in the perl library directory. datablock.pm ---reads the hash dictionary.pm ---dictionary of CIF terms (not used) AuCl.cif ---example CIF file from ICSD database with two records in it. The converter currently imports a single CIF file (which may have multiple CIF records) located in the \CIF directory and outputs a *.inp file for each CIF record into the \inp directory. This program has been tested with hundreds of CIF files from the ICSD and CSD databases. I cannot claim if they will work with CIFs from other sources, but I attempted to trap as many errors as I could. This program could easily be expanded to work on multiple CIF files (similar to amc2inp.pl) or...preferably....included directly in Artemis and/or ATOMS as a direct CIF file importer into these programs. I am sure there are many people that would benefit from the ability to directly open CIF files in ATOMS/Artemis and not have to worry about running a standalone application to convert their CIF files to atoms.inp files. Feel free to use any of the code that I have attached. The parser.pm and datablock.pm modules are copyrighted by UCSD (http://pdb.sdsc.edu/STAR/ <http://pdb.sdsc.edu/S! TAR/> ) but they are given away fr ee for any non-commercial use. Matt or Shelly--feel free to post the files on your websites if you see the value in sharing them. Regards, Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-9350 Email: dgbarton(a)dow.com

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CIF to ATOMS.inp
by Barton, David (DG) 16 Jul '04

16 Jul '04

Users, There have been several instances of Artemis users asking Bruce for the ability to input CIF crystallographic files directly into Artemis. In my attempt to learn Perl and produce something of value to more than one person, I wrote a program that converts CIF crystallographic files into Atoms.inp files. Bruce may implement this sometime directly into Artemis, but in the meantime I will offer the standalone, command-line conversion program to anyone who can use it. Attached is a zip file with my first version of the Perl CIF->atoms.inp file converter. The main program was snarfed from Bruce's amc2inp.pl program which converts mineral files to atoms input files. cif2inp.pl ---main Perl program. Converts .CIF files to atoms.inp file usage: perl cif2inp.pl aucl.cif parser.pm ---parser module written by Wolfgang Bluhm of PDB at UCSD, parses CIF file into an array of hash arrays. This should be put into the STAR:: subdirectory in the perl library directory. datablock.pm ---reads the hash dictionary.pm ---dictionary of CIF terms (not used) AuCl.cif ---example CIF file from ICSD database with two records in it. The converter currently imports a single CIF file (which may have multiple CIF records) located in the \CIF directory and outputs a *.inp file for each CIF record into the \inp directory. This program has been tested with hundreds of CIF files from the ICSD and CSD databases. I cannot claim if they will work with CIFs from other sources, but I attempted to trap as many errors as I could. This program could easily be expanded to work on multiple CIF files (similar to amc2inp.pl) or...preferably....included directly in Artemis and/or ATOMS as a direct CIF file importer into these programs. I am sure there are many people that would benefit from the ability to directly open CIF files in ATOMS/Artemis and not have to worry about running a standalone application to convert their CIF files to atoms.inp files. Feel free to use any of the code that I have attached. The parser.pm and datablock.pm modules are copyrighted by UCSD (http://pdb.sdsc.edu/STAR/) but they are given aw! ay free for any non-commercial use

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