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

Warning:ifeffit on OS X
by jterry94＠mac.com 24 Aug '02

24 Aug '02

Do not install OS X 10.2 if you rely on ifeffit under OS X. The readline libraries break and ifeffit cannot be used. A quick web search revealed that others have seen the problem and a quick attempt to recompile readline by myself has failed: missing symbols. Jeff

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ifeffit 1.0073 released
by Matt Newville 20 Aug '02

20 Aug '02

Hi Everyone, I've posted Ifeffit 1.0073, both source code and Windows installer, on the ifeffit download page. Following the earlier discussion of interpolation schemes for continuous scan data, this source code has added 'interp=' options ('interp=line', 'interp=quad', 'interp=cubic') to the spline() and bkg_cl() commands. There are no other major changes to the base library, but a few minor improvements and bug fixes in the source. The Windows installer includes the latest (I believe!!) of athena, artemis, sixpack, and even gifeffit. Also, on Windows, the GrWin plot window now raises to the top at every plot(), cursor(), and zoom() command. Enjoy, --Matt

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symmetry in Atoms
by Bruce Ravel 19 Aug '02

19 Aug '02

Here is an interesting question that was waiting in my mailbox this morning. I thought folks on the ifeffit list might also find it interesting and, in any case, it seems useful to have the question and the answer in the ifeffit list's archive. B The attached EXCEL file is the structure data for Fe17Y2 referred from Pearson's Handbook. Actually I get FEFF.inp file by Atoms using the input data as attached list. I wondered, howevere, how Atoms recognize site symmetry thorough the Atoms.inp data. My question is that the input data for each symmetric site should fulfill the site symmetry like as following list. In case of Fe17Y2 (No. 194), when I input (0 0 1/4) then Atoms will automatically recognizes this is 2b site. But when I input the number (0.1672 0.3344 0.9874) for 12k-site, how Atoms recognizes this is 12k site. Or if input numerical numbers do not fulfill the symmetry condition, then how Atoms deal with it. Thank you for your attention. space group number : 194 setting : 1 Hermann-Mauguin : P 6_3/m 2/m 2/c Laue group : 6/mmm point group : 6/m mm positions 24 l x,y,z -y,x-y,z -x+y,-x,z -x,-y,z+1/2 y,-x+y,z+1/2 x-y,x,z+1/2 y,x,-z x-y,-y,-z -x,-x+y,-z -y,-x,-z+1/2 -x+y,y,-z+1/2 x,x-y,-z+1/2 -x,-y,-z y,-x+y,-z x-y,x,-z x,y,-z+1/2 -y,x-y,-z+1/2 -x+y,-x,-z+1/2 -y,-x,z -x+y,y,z x,x-y,z y,x,z+1/2 x-y,-y,z+1/2 -x,-x+y,z+1/2 12 k x,2x,z -2x,-x,z x,-x,z -x,-2x,z+1/2 2x,x,z+1/2 -x,x,z+1/2 2x,x,-z -x,-2x,-z -x,x,-z -2x,-x,-z+1/2 x,2x,-z+1/2 x,-x,-z+1/2 12 j x,y,1/4 -y,x-y,1/4 -x+y,-x,1/4 -x,-y,3/4 y,-x+y,3/4 x-y,x,3/4 y,x,3/4 x-y,-y,3/4 -x,-x+y,3/4 -y,-x,1/4 -x+y,y,1/4 x,x-y,1/4 12 i x,0,0 0,x,0 -x,-x,0 -x,0,1/2 0,-x,1/2 x,x,1/2 -x,0,0 0,-x,0 x,x,0 x,0,1/2 0,x,1/2 -x,-x,1/2 6 h x,2x,1/4 -2x,-x,1/4 x,-x,1/4 -x,-2x,3/4 2x,x,3/4 -x,x,3/4 6 g 1/2,0,0 0,1/2,0 1/2,1/2,0 1/2,0,1/2 0,1/2,1/2 1/2,1/2,1/2 4 f 1/3,2/3,z 2/3,1/3,z+1/2 2/3,1/3,-z 1/3,2/3,-z+1/2 4 e 0,0,z 0,0,z+1/2 0,0,-z 0,0,-z+1/2 2 d 1/3,2/3,3/4 2/3,1/3,1/4 2 c 1/3,2/3,1/4 2/3,1/3,3/4 2 b 0,0,1/4 0,0,3/4 2 a 0,0,0 0,0,1/2 The attachment contained this: Fe17Y2 "structure type" "Pearson Smmbol" "space group" No Fe17Ho2 hP44 P6_3/mmc 194 Wyckoff x y z occupncy Y1 2b 0 0 0.25 0.41 Y2 2c 0.3333 0.6666 0.25 0.35 Y3 2d 0.3333 0.6666 0.75 1 Fe1 4e 0 0 0.1103 0.28 Fe2 4f 0.3333 0.6666 0.1049 0.71 Fe3 6g 0.5 0 0 1 Fe4 12j 0.3341 0.964 0.25 1 Fe5 12k 0.1672 0.3344 0.9871 1 And my response: Well, you made it very easy for me to answer your question by including the symmetry table for your space group in your email. The answer is that Atoms reads a data base of the space group symmetries. For your example, #194, the data base entry contains this information: x,y,z -y,x-y,z -x+y,-x,z -x,-y,z+1/2 y,-x+y,z+1/2 x-y,x,z+1/2 y,x,-z x-y,-y,-z -x,-x+y,-z -y,-x,-z+1/2 -x+y,y,-z+1/2 x,x-y,-z+1/2 -x,-y,-z y,-x+y,-z x-y,x,-z x,y,-z+1/2 -y,x-y,-z+1/2 -x+y,-x,-z+1/2 -y,-x,z -x+y,y,z x,x-y,z y,x,z+1/2 x-y,-y,z+1/2 -x,-x+y,z+1/2 which you will recognize as Wyckoff's position "l". Atoms doesn't exactly distinguish between Wyckoff's position l and position b. Instead it assumes that everything is position l and discards repeated positions. To understand this, apply the symmetry operations in the list above to the position (0,0,1/4). You will notice that 12 of them generate the position (0,0,1/4) and 12 of them generate (0,0,3/4). Atoms notices that and discards 11 of each. So, you see, position b is not actually different from position l, it's just degenerate due to symmetry. Atoms will notice these degeneracies a posteriori and does not need to know about the a priori. So, where did Wyckoff get his notation scheme from? Well, the Wyckoff positions are simply ordered in terms of decreasing degeneracy. Position a is the most degenerate and the highest lettered position is the non-degenerate one. This is not actually a useful notation scheme because there is no consistency between space groups. That is, position "c", for example, in group 194 has no relationship to position "c" in any other space group. The last thing worth mentioning is that Atoms works with 5 significant digits. If you use, as you suggest, (0.1672 0.3344 0.9874) then Atoms will find the correct amount of degeneracy. However, how you write (1/3, 2/3, z) is very important. Atoms 3.0 is able to read the string "1/3" as a coordinate. However if you choose to write coordinates in decimal notation, you must be careful. (0.33333, 0.66667, z) is fine and will generate 4 positions. (0.33, 0.67, z) will have problems related to numerical precision. Hope that's clear, Bruce -- 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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Atoms 3.0beta7
by Bruce Ravel 15 Aug '02

15 Aug '02

Hi folks, I released a new version of Atoms today which includes one small (but possibly important) change from the previous version. I learned that the database entry for a specific space group (I -4 3 d, #220) was in error. I fixed this and made a new release. There is a new tarball and Windows executable on my web site. If you are a windows user, you will also need to install the new version of the space_group.db file, as per the instructions on the downloads page. I also updated WebAtoms on Matt's server. This error has ABSOLUTELY NO IMPACT on any other space group. Indeed, without an atoms input file using the affected space group, you would never notice the problem. This underscores an interesting aspect of crystallography. While group theory tells us that there are 230 possible space group, nature seems to prefer using only a small subset of them. Indeed, in all the years since I started working on Atoms, I have not seen an example of a crystal in this space group until this week. The collection of input files that I distribute with Atoms for the purpose of testing the code includes examples of less than 80 space groups. Anyway, here is the input file that lead me to the error in Atoms' space group data base: title = Cu3As Domeykite title = Iglesias, J. E., and Nowacki, W., title = Zeitschrift fur kristallographie, kristallgeometrie, title = kristallphysik, kristallchemie, v. 145, pp. 334-345 (1977). space = I -4 3 d a = 9.6190 core = Cu rmax = 8.0 atoms ! elem x y z Cu -0.02930 0.12020 0.18760 As -0.02980 -0.02980 -0.02980 One might notice that the old Fortran version of Atoms handles this input file correctly. The irony of that is not lost on me, particularly in light of my frequent and loud trumpeting of the advantages of the new version over the old version. Thanks to Elspeth Barnes for bringing this problem to my attention. 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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athena 2002.08.14
by Bruce Ravel 14 Aug '02

14 Aug '02

Hi, I put a new tarball and Windows build for Athena on my website this afternoon. There are only a few changes since last week, but they are interesting enough to merit a new release. 1. I fixed a problem in the display of the group list. When deleting groups, slightly more vertical space was removed than had been allocated when the group was listed. This lead to a misalignment that was particularly apparent when deleting many groups. 2. I now do the thing where the cursor changes to a stop watch (an hourglass on Windows) whenever Athena is doing anything time consuming. That keeps you from clicking buttons as a bad time and also gives you a visual cue when lengthy procedures finish. 3. I put in more careful checks of memory usage. I had a bug report that was traced back to a large quantity of data overflowing Ifeffit's static memory space. I now check memory usage more frequently and issue a warning message when the amount of memory is running short. The scheme is not foolproof. It is still possible to overflow the memory before triggering a warning, but Athena should catch many situations in which this might happen. 4. It is now possible to create a "background group". That is a data group which is listed in the groups list and which contains as its data the background function computed from another data group. This is useful for at least three things, including directly comparing different background functions, comparing a background function to a background computed by FEFF and read from the 5th column of xmu.dat, and investigating low-R phenomena such as multi-electron effects or the so-called atomic xafs. 5. Project files now identify the version of perl, the version of ifeffit, and the operating system of the computer along with the version of Athena used to create the file. This is information I need when I am sent a project file as part of a bug report. There is no problem with backwards compatibility -- project files without this information will be read without problem. And project files continue to be transferable between platforms. The tarball and the Windows exe are in the standard places. Special thanks to Raul Barrea for a very useful bug report which lead to most of this week's new features. 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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athena 2002.08.08 and artemis 2002.08.08 released
by Bruce Ravel 09 Aug '02

09 Aug '02

Howdy folks, This afternoon I put new source tarballs of Athena and Artemis on my website. I also build Windows executables of both programs for dropping on top of a current ifeffit installation (with the Splashscreen commented out!). These can be found in the standard places. These are mostly bug fix releases, although each program got one major new feature. For Athena the highlights are: 1. the column selection dialog now makes a stab at figuring out if you have transmission or fluorescence data. How it does this is configurable (so that it'll work well on your data files) but currently undocumented. Ask on this list if you want to know. 2. fixed a bug in the auto-align feature wherein the e0 shift of the alignment standard was ignored 3. fixed a horrid bug in the merge code where I added the e0 shift to the k-array when merging in k. (yikes!) 4. write a message to the Echo area if the plot multiplier is set to 0, which is usually not a good choice 5. added some complicated logic to avoid plotting groups if any relevant range is backwards. For example, if fft_kmin is greater than fft_kmax for a group, that group will not be plotted in R or q space and a (hopefully) helpful message will be printed to the echo area. 6. a few other minor problems were fixed and some usability issues on Windows were addressed (mostly having to do with raising small windows to the top of the screen) For Artemis the highlights are: 1. If you right-click on a word in one of the entry boxes for path parameter math expressions on a Path page, a menu will pop up which allows you to easily set that word as a parameter. It's very useful, but a little hard to explain. Here are some screen shots that might help: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/be… http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/af… In the first picture, I right-clicked on the word "amp". After selecting the "guess" option from the menu, the view is switched to the GDS page and focus is given to highlighted box so you can start typing. This feature works sensibly for parameters which already exist and for those that have not yet been defined. 2. fixed a problem which prevented saving path data in any space 3. fixed a problem reading a project file with multiple feff calculations 4. a few other fixes to functionality and usability Extra special thanks to Mark Jensen, Paul Fons, and Kumi Pandya for useful bug reports and to Shelly Kelly for suggesting the right-click thing in Artemis. Enjoy and, as always, let me know what needs fixin' 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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Re: ifeffit and perl 5.8.0
by Carlo U. Segre 01 Aug '02

01 Aug '02

I am still using Atoms beta5 myself because I have not been successful in getting beta6 to compile. I just hadn't gotten around to figuring out if it was me or a real problem. Carlo On Thu, 1 Aug 2002, Dr. Paul Fons wrote: > > > I have now gotten perl 5.8.0 to work with both athena and artemis. As > Carlo said in an earlier message, the binaries of 5.6 and 5.8 are not > compatible and it necessitates rebuilding compiled packages. There is > an OS X problem as well in that the make install command for perl 5.8 > doesn't seem to overwrite all of the files so I manually deleted the old > installation and did a make install in the perl 5.8 directory. The > weird thing is that only tkatoms (B6) doesn't recompile. I can't even > do a perl Makefile.PL without getting an error. Any ideas? > > > Here is a clip: > > perl -v > This is perl, v5.8.0 built for darwin > ... > > > [etld1220:~/Ports/Atoms-3.0beta6] paulfons% perl Makefile.PL > dyld: perl Undefined symbols: > _Perl_safefree > _Perl_safemalloc > _Perl_saferealloc > _Perl_sv_2pv > _perl_call_sv > _perl_eval_sv > _perl_get_sv > > -- Carlo U. Segre -- Professor of Physics Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Re: Ifeffit digest, Vol 1 #42 - 1 msg
by Raul Barrea 01 Aug '02

01 Aug '02

Hi Bruce, I've downloaded the exec file you've posted in your web site. Atoms and the periodic table work fine but Athena and Artemis don't work. Maybe there is something missing. Are the dll's the same for the old and new versions of the exec files? Thanks Raul Barrea BioCAT/APS ----- Original Message ----- From: <ifeffit-request(a)millenia.cars.aps.anl.gov> To: <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tuesday, July 23, 2002 12:01 PM Subject: Ifeffit digest, Vol 1 #42 - 1 msg > 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-admin(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. serious athena bug fix (Bruce Ravel) > > --__--__-- > > Message: 1 > Date: Mon, 22 Jul 2002 18:15:24 -0400 > To: ifeffit mailing list <ifeffit(a)millenia.cars.aps.anl.gov> > Reply-To: ravel(a)phys.washington.edu > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: [Ifeffit] serious athena bug fix > > > Hi folks, > > Today Shelly Kelly pointed out a serious bug in the code that merges > spectra. Spectra merged as mu(E) or norm(E) have not ever been > calculated correctly. There were several problems -- the worst was > that the e0 shifts for all groups involved in the merge were ignored. > This resulted in numerous problems with the merged spectra. > > I think I have fixed the problem -- at least the sample data that > Shelly gave me now gets merged correctly. There is a new source > tarball on my web site. > > I also added a couple of trivial features to both athena and artemis. > The first is a splash-screen, i.e. something to look at in those > endless seconds between double clicking on the icon and having the > program spring to life on the screen. I also added several keyboard > shortcuts for common tasks in both programs. You can see what these > are by examining the menus in the menubar. > > > I also added something new to my web site. Athena and Artemis change > much faster than Ifeffit these days. The bad part of this is that > Windows users don't get to take advantage of my updates as often as > unix and OSX users. So today I added a section to the downloads page > with links to the executables of my four programs. I doubt I will > update the executables as often as I update the source tarballs. But > when I do, I'll post the executables on the downloads page. > > The idea of these individual executables is that you replace the > executable in the C:\Program Files\Ifeffit\ folder with the new one. > These executables now found on my downloads WILL NOT RUN CORRECTLY > outside the context of a properly installed ifeffit package. But if > you have installed Ifeffit using the installer from Matt's web page, > you will be able to drop my new executables in place. > > 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/ > > > --__--__-- > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest

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Perl 5.8 and ifeffit
by Dr. Paul Fons 01 Aug '02

01 Aug '02

I have now gotten perl 5.8.0 to work with both athena and artemis. As Carlo said in an earlier message, the binaries of 5.6 and 5.8 are not compatible and it necessitates rebuilding compiled packages. There is an OS X problem as well in that the make install command for perl 5.8 doesn't seem to overwrite all of the files so I manually deleted the old installation and did a make install in the perl 5.8 directory. The weird thing is that only tkatoms (B6) doesn't recompile. I can't even do a perl Makefile.PL without getting an error. Any ideas? Here is a clip: perl -v This is perl, v5.8.0 built for darwin .... [etld1220:~/Ports/Atoms-3.0beta6] paulfons% perl Makefile.PL dyld: perl Undefined symbols: _Perl_safefree _Perl_safemalloc _Perl_saferealloc _Perl_sv_2pv _perl_call_sv _perl_eval_sv _perl_get_sv Dr. Paul Fons Photonics Research Institute National Institute for Advanced Industrial Science and Technology Ministry of Economics and Trade Umezono 1-1-1 Tsukuba, Japan 305-8568 tel. 81-298-61-5636 fax. 81-298-61-5615 paul-fons(a)aist.go.jp Lines below are in Japanese 独立行政法人産業技術総合研究所光技術部門〒305-8568 茨城県つくば市梅園1-1-1 産総研つくば中央第2 E-mail: paul-fons(a)aist.go.jp, Tel. 0298-61-5636, Fax. 0298-61-5615

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Carlo's message and perl 5.8.0
by Bruce Ravel 31 Jul '02

31 Jul '02

Hey, I just thought I would drop a short note to the list explaining in fewer words what Carlo said. The bottom line is that 5.8 and 5.6 are not binary compatible. This is an annoyance that affects many things, including the ifeffit interface. The solution is to go to the place where you unpacked ifeffit and cd to the wrappers/perl/ directory. Rebuild the ifeffit interface by doing make clean perl Makefile.PL make make install I don't think you'll actually need to reinstall athena, but it couldn't hurt. This is not a OSX-only, or debian-only problem. We will all have this annoyance when we get around to updating to perl 5.8 That doesn't make me happy, but I'll deal. Starting to distribute a big tarball with the ifeffit interface bundled with all my codes will actually go along way towards solving that problem. And, if you are not updating to perl 5.8 (or don't even grok what this discussion is about), then you will probably not be affected by this issue. Thanks Carlo! B Bruce Ravel e-mail: ravel(a)phys.washington.edu URL: http://feff.phys.washington.edu/~ravel/

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