July 2004 - Ifeffit - millenia.cars.aps.anl.gov

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 18 Jul '04

18 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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Atoms restraints
by Massimiliano Stola 15 Jul '04

15 Jul '04

Thank you for all the explanations about constraints for the histidine ring within Artemis. Well, I think that it will be easier, but boring, building several reasonable structures and test them one by one... I think I'll finally follow this way. I'll be interested as well in the possibility to simulate exafs data for several structures at once, like Stefano asked. It would be a nice feature for the next releases of the program! Regards Max

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Chi^2 and R-factor reporting requirements
by Stanislav Stoupin 12 Jul '04

12 Jul '04

Hello all, I would like to hear your opinion about reporting Chi^2 and R-factor values in EXAFS studies. I found that Chi^2 and R-factor values are not provided by many EXAFS papers. However, according to standards of The International XAFS Society (http://ixs.iit.edu/) both these values should be reported. My understanding is that the reduced Chi^2 should be close to 1 in ideal case. In practice however, the value is always greater than 1 because of systematic errors. For example, my reduced Chi^2 values are around 300. However, the R-factor values are about 3% which doesn't look as "ugly" as Chi^2 reduced. On the other hand, ifeffit overestimates uncertainties using reduced Chi^2 value. Thus, all errors are taken into account. The final question: Is it appropriate to report just R-factor calculated by ifeffit and the obtained uncertainties (which look reasonable) without reporting the "ugly" Chi^2/reduced Chi^2 values? Stanislav Stanislav Stoupin ----------------------------------- Research Assistant/PhD student BCPS department Illinois Institute of Technology email: stousta(a)iit.edu voice: 312-567-7983

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RE: [Ifeffit] multiple fits
by Kelly, Shelly D. 12 Jul '04

12 Jul '04

Hi Stefano, > > I have the following question: let's say I have a data set for which > I would like to try a long series of possible models and monitor the > result of the fits. The models are geometric variations of a > starting structure.I have all related feff.inp files for each model > ready. Is there a way to process the data so that I can get out the > related fits? I do not think I can do this using artemis, but maybe > there is a set of commands to be given from the command line? > > Thanks > Stefano The short answer is no. The long answer is sure. But the script that you need to write is long and complicated. You have to teach the computer how to model the structure for all the variations so that it will make the appropriate variables to determine in the fit, and also how to handle the output. These tools are not incorporated into ifeffit. I am responding to your request, because I did this as a graduate student. Back in the old days, I was using atoms, feff, and feffit. The program that I wrote moves the atoms in a unit cell, writes out a atoms.inp file, runs atoms, runs feff, makes a feffit.inp file and runs a fit, and then makes a spread sheet to compare the answers. If you are interested, I wrote is a small EXAFS paper about this script, and would be happy to share. S.D. Kelly, R. Ingalls, and E. A. Stern, "Determining crystalline atomic positions using XAFS, a new addition to the UWXAFS analysis package," Journal of Synchrotron Radiation. 8 311-313, 2001. In the end, I think that you will agree that you have a lot of work ahead of you. HTH Shelly

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multiple fits
by Stefano Ciurli 12 Jul '04

12 Jul '04

Hello, I have the following question: let's say I have a data set for which I would like to try a long series of possible models and monitor the result of the fits. The models are geometric variations of a starting structure.I have all related feff.inp files for each model ready. Is there a way to process the data so that I can get out the related fits? I do not think I can do this using artemis, but maybe there is a set of commands to be given from the command line? Thanks Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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