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

integrating difference spectra
by Bruce Ravel 16 Sep '03

16 Sep '03

Hi folks, In response to a request from an Athena user, I am incorporating a feature that will allow the user to integrate difference spectra. I suspect that this will prove most useful for XANES studies and for XMCD studies. I was wondering if someone on the mailing list would be so kind as to send me some sample XMCD data, either in the form of raw data or as an Athena project file, so I can test this. The most useful example at this stage would be a model system -- i.e. something that demonstrates a large dichroic effect. It would also be useful if your data set has a well known value for the integral of the difference spectrum. That way I'll have a bit of confidence that my algorithm is working. Thanks in advance! B -- Bruce Ravel ----------------------------------- ravel(a)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/

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path-sensitive math expressions
by Bruce Ravel 05 Sep '03

05 Sep '03

Hi Matt, I have some questions about a subtle detail in ifeffit. It is possible to make a def parameter which is path sensitive in the sense that it will evaluate differently for different paths. Any def parameter which includes reff, eins(), or debye() in its math expression will be that way. Here is a simple, if slightly silly, example: def rrr = reff/10 path(1, feff=feff0001.dat, dr=rrr) path(2, feff=feff0002.dat, dr=rrr) Then show rrr will report 1/10 the R_eff of the *second* path. So here are my questions: 1. Are all def parameters reevaluated every time a new path is evaluated? Or only if the path uses the def parameter in one of its math expressions? (I think the answer is the former.) 2. Is it possible to ask ifeffit which def parameters are path sensitive? Of course, I can scan the def parameters at the level of perl to see if any of them obviously are, but ifeffit might already know that. 3. If you do show ss the value is the value of the last path evaluated. Doing show @path N show ss will indeed display the value of the def parameter appropriate to the Nth path. Is there another way of forcing ss to be evaluated appropriate to a desired path? Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)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, X24c, U4b 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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how Atoms builds clusters
by Bruce Ravel 04 Sep '03

04 Sep '03

Hi everyone, I have twice recently been asked about how Atoms converts from its input data, which is the minimal set of positions necessary to describe the crystal, to the cluster that gets reported in the feff.inp file. Since there seems to be some interest in this question, I thought I would send a message to the mailing list with the answer. That way it'll be archived and anyone can go back and look at the answer. If you've ever wondered about this, read on. If the thought never crossed your mind, this is a good moment to go on to your next email message ;-) Here is the broad outline: 1. Atoms fills out the unit cell in the first octant. By "first octant" I mean that all fractional coordinates of all positions are non-negative and less than 1. 2. Enough unit cells are stacked up like blocks to make a rhomboid large enough to entirely encompass a sphere of the radius specified by the Rmax parameter. (If you poke hard enough at Atoms, you will find a situation where it fails to create a large enough rhomboid. It's an odd situation, though, and you won't run into it if your space group is orthogonal.) 3. The fractional coordinates are converted to their Cartesian equivalents. 4. All the atoms within the rhomboid but outside the sphere are tossed. 5. The atoms are translated such that the absorber is at the origin and the list is sorted by distance from the absorber. The non-obvious part of this algorithm is the first step. To fill out the unit cell, these steps are taken: a. For each atomic position given to Atoms, apply the symmetry operations associated with the point group. These are the operations reported in the symmetry.dat output file. They are also given in the International Tables of Crystallography for each space group. b. For each position found from the point group, apply the Bravais translations, if any. c. Some of the coordinates found from applying the point and Bravais operations will fall outside the first octant, that is, there may be coordinates smaller than 0 or larger than or equal to 1. Translate those positions back to the first octant by adding the appropriate integer to the offending coordinate. d. Weed through the list of positions and throw away any repeats. For high symmetry groups, the vast majority of generated positions will be repeats. For FCC copper, for example, you will find that the point and Bravais operations generate the same point 96 times. At the end of step 1, you have the contents of the P1 output file. That is, you have a description in fractional coordinates of the entire contents of the unit cell. For step 2 above, it is much easier to use the fractional coordinates to stack up unit cells to make the rhomboid. The unit cell in the +x direction is made by adding 1 to all the x coordinates. The unit cell in the -y direction is made by subtracting 1 from all the y coordinates. And so on. The conversion to Cartesian coordinates is where the lattice constants and angles come into play. This is a tensor transform where the non-zero elements of the metric tensor are functions of a, b, c, alpha, beta, and gamma. This tensor is discussed in Volume A of the International Tables and in many crystallography textbooks. The geometrically inclined could probably derive it on the back of an envelope. Or see the subroutines Xray::Xtal::Cell::make and Xray::Xtal::Cell::metric in the file Xtal.pm from the Atoms distribution. The last interesting detail is how the absorber atom is chosen. In a space group of high symmetry, there may well be several examples of the absorber in the unit cell. Atoms chooses the one that is closest to the center of the unit cell, i.e. the one closest to (1/2, 1/2, 1/2). This choice minimizes the size of the rhomboid needed to encompass the sphere of radius Rmax. Now, wasn't that fascinating? B -- Bruce Ravel ----------------------------------- ravel(a)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, X24c, U4b 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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Phase and Amplitude Correction
by Ian Drake 28 Aug '03

28 Aug '03

Hi Matt, I wanted to follow up on a suggestion by Grant Bunker (Aug.4th). He proposed that I look into doing both a phase and amplitude correction of the data as opposed to doing only a total phase correction. How might I achieve this using IFEFFIT commands? Thank you for your help, Ian Drake ***************************** UC Berkeley Dept. of Chem. Eng. Graduate Student Advised by Dr. Alex Bell Heterogeneous Catalysts ******************************

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and new features in sixpack
by Webb, Samuel M. 26 Aug '03

26 Aug '03

Hi all... As a follow up to the follow up to Matt and Bruce's announcements.... There have also been a lot of new features written into sixpack now as well, also as a response to a lot of useful input from everyone at XAFS12. The latest incarnation of these changes is included in the latest IFEFFIT installer. The continuing saga of updates can be always be found on the sixpack webpage (http://www-ssrl.slac.stanford.edu/~swebb/sixpack.htm) including source code. Thanks to everyone the last few months that have made suggestions for improvements and catching errors. I hope to make some more major renovations to some of the fitting interfaces in the coming months so those of you who are interested can keep an eye out for them. Thanks! Sam

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and new versions of Athena and Artemis as well
by Bruce Ravel 25 Aug '03

25 Aug '03

Hi folks, As a follow-up to Matt's email, the new release of ifeffit for Windows contains the latest versions of Athena and Artemis. The source code tarball for unix and Mac OSX users can be found on my web site or downloaded using the horae_update script after you have compiled and installed the new version of ifeffit. These new releases contain many improvements which are summarized here: http://leonardo.phys.washington.edu/~ravel/software/exafs/NEWS Included are lots of features responding to useful input that I received both at the XAFS conference in Malmo and at this summer's EXAFS workshop at the NSLS. Thanks to everyone who contributed useful feedback, comments, and suggestions. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)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, X24c, U4b 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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Ifeffit 1.2.2
by Matt Newville 25 Aug '03

25 Aug '03

Hi Everyone, I've just posted version 1.2.2 of Ifeffit. This is mostly a bug-fix release, and the core library has no new functionality. The major improvements are that 1) 'reff' now works well in all path parametr definitions and 2) feffit() fits in k-space correctly include the k-weighting. The build procedure from sources for linux and Mac OS X are also slightly better. More details on the changes to the core library are below. The windows installer includes the latest versions of athena, artemis, and sixpack, each of which has several improvements. Thanks to Bruce and Sam for getting this release together! Let me know if there are any questions or problems. Thanks, --Matt Changes from v. 1.2.1: bugs: - fixed error with k-space feffit() fitting so that k-weighting is now really used!! - fixed error with using reff in defined math expressions - increased size of math expressions to 256 operations/values. - changed restraint mechanism to work slightly better with multiple data sets - fixed error in read_data() that allowed core-dumps when reading files larger than the maximum array size. build improvements: - switched configure to use autoconf 2.53, including 'newer' automated searches for fortran libraries, setting default f77 compiler to g77, which should help builds on Mac OS X. - removed fortran subdirectory -- an existing, working fortran compiler is needed to build ifeffit. - fixed iconf_pgplot to check that PGPLOT directories listed in the PGPLOT make really exist (and are directories) before including them in the link arguments. - upgraded to readline 4.3 - upgraded python installation to use Pmw 1.1

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[Ifeffit] compiling feff with g77 on linux : Error opening file, s2_em.dat in module sigem
by jroux 21 Aug '03

21 Aug '03

I solved a small problem of portability of feff under linux/g77 for a friend. %< - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Error opening file, s2_em.dat in module sigem Fatal error STOP CHOPEN statement executed %< - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - g77 is usually compiled so that the maximum fortran unit number is 99. Unit numbers 111 112 and 113 are used in the feff code this is OK for some compilers but NOT pristine g77 and should be replaced by some lower numbers. I tried 91 92 93 and this fixes the problem. -- Jacques Roux, (jroux(a)cnrs-orleans.fr) CNRS-ISTO, 1A rue de la Férollerie 45071 Orléans cedex 2 tel: (33|0) 238 25 53 99

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Global parameters mapping with EXAFS
by Wojciech Gawelda 19 Aug '03

19 Aug '03

Hi, Recently I have come across some publications (Chance, et al., Biochemistry, 1996, 35, 9014-9023) where people have used global parameter mapping techniques with EXAFS in order to refine the obtained metal-ligand bond distances. If Im right the code they developed was called AUTOFIT 1.0. Does anyone of you know whether this code is freely available on the web? Or if not, does anyone of you know about similar codes which are being used in EXAFS analysis. Please let me know about this issue and help me to find out more about this approach. Have a nice day! Wojciech Gawelda ********************************************************************* Wojciech Gawelda Institut de Physique de la Matière Condensée Université de Lausanne IPMC-BSP CH-1015 Lausanne-Dorigny, SWITZERLAND Tel.: +41 (21) 692 3669 Fax.: +41 (21) 692 3635 E-mail: Wojciech.Gawelda(a)ipmc.unil.ch WWW: http://www.unil.ch/ipmc/docs/mc/wg/address.html *********************************************************************

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Re: Ifeffit Digest, Vol 6, Issue 6
by Grant Bunker 19 Aug '03

19 Aug '03

Scott - You could bridge the gap by using VirtualPC until an installer is constructed. That has the added benefit that you can also run windows xp or 2000 pro and PC linux (redhat, debian) simultaneously with OSX. It makes for a very flexible system, you can run almost anything, and furthermore the actions on the PC can be controlled by applescript on the mac side. On a fast mac with lots of memory, speed is adequate for most purposes, and the more you run it the faster it gets (instruction cache). I do these things my tibook and it works fine. A dual processor G5 should really work well. best wishes - grant bunker On Tue, 19 Aug 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. Decision time... (SCalvin100(a)aol.com) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 18 Aug 2003 20:31:23 EDT > From: SCalvin100(a)aol.com > Subject: [Ifeffit] Decision time... > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <c5.370ac25e.2c72c9db(a)aol.com> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > > I'm very pleased to see all the activity on the list regarding an IFEFFIT > installer for OS X, and I appreciate very much the thought that has gone into > this issue. Unfortunately, decision time is upon me. I need to decide within a > day or two whether to go with Macs or PCs in my new faculty position. If someone > can tell me there will be some sort of installer (either requiring Fink or > not) by September 15, I'll go with Macs. If not, I'll have to go with PCs. > > --Scott Calvin > Sarah Lawrence College >

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