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

a cautionary tale
by Peter Southon 21 May '04

21 May '04

Hello fellow Ifeffiters This a story about making feff.inp input files for FEFF. The more experienced readers of this list will probably be well aware of the issues involved, but I thought that relative newcomers such as myself might not know (which is why I'm posting this on the Ifefft list rather than the Feff list). In a nutshell, it is wise to create a large cluster of atoms to put into Feff (ie use a large Rmax in Atoms), but limit the number of paths with a reduced Rmax in Feff. I used Artemis/Atoms to make up a Feff input file (feff.inp) from crystallographic parameters, setting Rmax in Atoms to a relatively large value of 7.5 Å to create quite a large cluster of atoms. I then used FEFF to calculate scattering paths within the cluster, but first reduced the Rmax in feff.inp to 5.5 Å to limit the number of paths. So far so good. I then (for reasons too involved to discuss here) edited the feff.inp file to delete all atoms more than 5.5 Å from the centre, and ran Feff again. The results (judging from the relative amplitude values) were different, and in the case of some paths very different. Some intense paths changed in amplitude by a factor of 2 or greater, although I haven't looked at the finer details of the Feff results. The paths that changed the most were high-order multiple scattering paths, and surprisingly those paths did not involve atoms at the edges of the 5.5 Å radius. Now I'm sure that someone else can explain the reasons for this much better than I can, but I assume that the potentials for the atoms outside the 5.5 Å radius (which were neglected in the second calculations) significantly affect those inside the radius. I know that its always been my practice to perform the Feff calculation using only those atoms that I think are contributing to my spectrum, and I'm sure that others do the same. My advice is to use a larger cluster of atoms in Feff if you can - but as to how large I might leave that to someone else to comment. Regards, Peter PS - and four cheers to Bruce for improvements to Artemis, I can't wait for the Windows update. Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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horae 034 Debian packages
by Carlo U. Segre 21 May '04

21 May '04

Packages of the new horae are available for the unstable and stable distributions of Debian at # stable deb http://fermi.phys.iit.edu/debian/woody binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ # unstable deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ Please contact me if you have any problems installing them. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)agni.phys.iit.edu http://www.iit.edu/~segre

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cloning feff calculations
by Bruce Ravel 20 May '04

20 May '04

Hi! Artemis now allows you to easily reuse entire feff calculations within a project. This is something you might want to do in a variety of situations. Here is one example: You have data at several temperatures. After spending some time working on your fitting model for a single data set and at one temperature, you decide to convert your project to a multiple data set, multiple temperature model. You would like to use the same feff calculation and all the same paths to fit each data set, changing only those parameters related to the changing temperature. This is now easy. In the Data menu is an option for "Clone a FEFF calculation". Here is how it works: 1. Select the data set for which you wish to use an already-defined feff calcultion. In my example, you would select the most recetly imported data set. 2. Choose the Clone option from the Data menu. This will pop up a dialog box listing all feff calculations used throughout the project. (If there is only one, it will be a short list!) 3. Choose a feff calculation and click OK. That calculation, all its paths, and all path parameters associated with the paths will be copied to the new data set. You may need to play around with it to see how it works. Once you see, it's quite simple: you select a data set and apply an existing feff calculation to the selected data set. There are two options for cloning a feff calculation. They are called "linking" and "copying". The difference between them is how the files from the feff calculation are handled. A linked clone points at the same set of files, a copied clone makes its own copies of all the files from the feff calculation. You should link when you want to be 100% sure that the exact same feffNNNN.dat files will be used each time the calculation is used. Also, the project file will be significantly smaller when you link compared to when you copy. You should copy if you think you might need to alter the feff calculation in one case separately from the other. Since this is a brand new feature, I suspect that people will find ways to break it. Let me know when that happens. Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 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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the new GDS page
by Bruce Ravel 20 May '04

20 May '04

Hi! The biggest new feature of Artemis in today's release is the new page for setting the Guess, Def, and Set parameters. Here is a screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/ar… The document has been updated to describe the new format of the GDS page. http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/artemis.pdf See section 5.7.9. As you can see, the parameters are now displayed in a list structure rather than as a stack of entry boxes. This allows many more parameters to be displayed at one time in the same space. The new layout also allocates more horizontal space to the display of the math expressions. The different kinds of parameters are displayed according to their type. The color of the text and the content of the second column indicate the parameter type. Guess parameters are in purple text and have the "g:" tag in the second column. Set parameters are in black text and have the "s:" tag. Defs are green and have "d:". Skip parameters are grey and have no tag. Not shown in the screenshot are restrains, which are pink and have the "r:" tag in the second column. To edit a parameter, click on its entry in the list. This highlights that parameter in grey, as shown for the "fee0" parameter in the screenshot. The name, type, and math expression for that parameter are entered in the space at the bottom of the page and are ready to be edited. Click the "New" button to create a brand new parameter. The neatest new feaure is what I call parameter annotation. An annotation is a short text string which says something useful about the parameter. An example of this is seen in the screen shot. The selected parameter was annotated after the fit with its best fit value and error bar. Whenever you click on a parameter, its annotation is shown in the echo area. If you double-click on a parameter, you will be prompted to supply an annotation for that parameter. This provides a nice way of documenting the role each parameter plays in the fit. There are lots of other neat features of the new GDS page. For instance, Artemis does not allow you to define a parameter more than once. And there is a very useful context menu that gets posted when you right-click on a parameter. It may take a bit of getting used to, but I suspect that you will enjoy the new GDS page. I find it to be both more powerful and easier to use than the previous format. Enjoy, B P.S. Thanks go to Scott, who I hope does not mind that I used his project file for the screenshot. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 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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Starting out with Artemis 0.7.003
by m.bondin＠pgrad.unimelb.edu.au 19 May '04

19 May '04

Hi all - I am starting out with the latest release of Artemis on Win XP (thought I would give the new and improved version a go since I like the idea of incorporating atoms in the fitting interface). I read in my data file and atoms file, got my feff.inp then attempted to generate my feff paths - Artemis asked me to pick an option (first ten, all etc) and gave me a new window with no paths listed and the message "Artemis trapped a warning! Message dumped to C:\Program Files\Ifeffit\horae\ARTEMIS.TRAP" Is Atoms now able to claculate feff paths and display them within Artemis or does it not yet have this capability? Many thanks, -- Mark Bondin PhD student School of Chemistry, University of Melbourne

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[HOWTO] converting experimental mu(E) in cm^-1
by mauro＠rulp.org 14 May '04

14 May '04

Hi, I would like your opinion on the procedure to convert the experimental mu_exp(E) in arbitrary units (counts) to mu(E) in cm^-1. This is my "student" procedure: 1. take mu_exp(E) - with EXAFS - spectrum in counts 2. take mu_th(E) - without EXAFS - spectrum in cm^-1 (from MacMaster or XOP software) 3. plot 1+2 4. while mu_exp(E) != mu_th(E) do (by hand!) 4a. mu(E) = A * mu_exp(E) + B When the two spectra coincide (more or less) I assume that the mu(E) is converted in cm^-1 units. Is this right? Does it already exist a software that makes this work automatically? Could be interesting to implement it in Athena? Thanks, M. -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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RE: RE: [Ifeffit] graphics and fit
by Kelly, Shelly D. 13 May '04

13 May '04

Hi Mark and Jeff, Here is a copy of the program. I tried to document the script well. If you have trouble, let me know. You can e-mail me off of the list. skelly(a)anl.gov. Shelly > -----Original Message----- > From: Jensen, Mark P. > Sent: Thursday, May 13, 2004 1:33 PM > To: Kelly, Shelly D. > Subject: RE: [Ifeffit] graphics and fit > > > Shelly, > > I can see several metal-ligand complexes that I have looked > at recently where your program for manipulating groups of > atoms would probably have been very useful. If you really are > willing to share, I would sure appreciate having a chance to > try it out. > > Mark Jensen > > > ------------------------------ > 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 >

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RE: [Ifeffit] graphics and fit
by Kelly, Shelly D. 13 May '04

13 May '04

Hi Stefano, Another free program that can read the output from atoms is ghemical. http://www.uku.fi/~thassine/ghemical/ I have written a rather specialized code that allows you to rotate a group of atoms until one of those atoms is at a determined distance from the original atom. Here let me explain for the specific example that I used it for. Say you have a Uranium atom and attached to it through an oxygen atom you have a PO4 group. One of the oxygen atoms of the PO4 group is shared with the uranium atom. Now from your exafs data you know that the U-P distance should be some number call it Rp. This program will leave the shared oxygen atom at the same spot, but move the PO3 atoms until the distance for U-P matches Rp. There are lots of ways that you can move the PO3 atom. The program is written to try to bend the PO3 group first and then translate the PO3 group to make the distance match. Then the program writes out the coordinates for all the atoms. This code is written in perl and doesn't have a gui interface, but I would be happy to share. Shelly > -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Thursday, May 13, 2004 5:31 AM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] graphics and fit > > > Hello, > > just a thought: wouldn't it be nice to be able to read the feff.inp > file directly into a simple molecular graphics program in order to > see if the used coordinates contain any error? Maybe it is possible > already and I am not aware of it. I understand that the program is > mainly used by material scientists, but for us working with > biological samples of metalloproteins it would be nice. > Another suggestion: I know that Excurve is able to treat the > histidine rings as a unity, and when performing the fit that program > is able to maintain the ring rigid while fitting the distance between > the metal and the imidazole ring of the histidine. How can I do that > simply using your suite? > > 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 > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Re: [Ifeffit] newcomer's simple trouble
by Stefano Ciurli 13 May '04

13 May '04

Problem solved! Textedit (the program I used this morning and that I thought was like vi, instead...) messes up the file format. Now I have a working feff.inp file and can start to work. Sorry for bothering. 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

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newcomer's simple trouble
by Stefano Ciurli 12 May '04

12 May '04

Hello, this is a more intelligent input file which still gives the same error: Stefano TITLE Ni(H2O)6 HOLE 1 1.0 * Ni K edge (8333.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 6.0 POTENTIALS * ipot Z element 0 28 Ni 1 8 O ATOMS * this list contains 7 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ni1 0.00000 1.91860 0.00000 0.00000 1 O1_1 1.91860 0.00000 1.91860 0.00000 1 O1_1 1.91860 0.00000 0.00000 1.91860 1 O1_1 1.91860 -1.91860 0.00000 0.00000 1 O1_1 1.91860 0.00000 -1.91860 0.00000 1 O1_1 1.91860 0.00000 0.00000 -1.91860 1 O1_1 1.91860 END

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