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

volunteerism....
by Bruce Ravel 27 Mar '02

27 Mar '02

Hi Folks, Matt said: > From a political viewpoint, I think we'd need a volunteer to keep > the scripts in working order for Win95/98/ME. Unless that happens, > I don't consider "upgrade to 2000" to be an unreasonable response. I want to second this request. It's really hard for Matt and I to stay on top of all these different platforms. The 9x/ME series of OS's is sufficiently different from 2000/NT/XP (I run 2000 under VMWare on my linux box) that it is hard for us to keep up. I would be happy to help a volunteer 9x/ME tester/debugger get up and running. The biggest chore is learning how to use the program that Matt and I chose for building the Windows installation package. That's not hard -- I had it mostly figured out in a day. Then Matt said: > Also from a political viewpoint, could we encourage 'A fellow' > to post such problems here? I get lots of email from people about Atoms and, of late, about Athena. I have taken to pointing out the web entry point to our mailing list whenever I answer a question from someone who may not be a subscriber. I encourage all of you to encourage anyone around you who may be interested in our software to subscribe. As ifeffit and friends have been finding a wider audience, more problems have been cropping up. This is a natural part of growth and is very healthy. With the help of all of you on this list, Matt and I will be able to make a much better package. Finally, some suggested reading from freshmeat, the software repository: The Importance of Non-Developer Supporters in Free Software http://freshmeat.net/articles/view/156/ How to Report Bugs Effectively http://freshmeat.net/articles/view/149/ B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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 digest, Vol 1 #10 - 1 msg
by Guilhem DEZANNEAU 27 Mar '02

27 Mar '02

Hi, i actually work with Windows 95 (version 97) OS and encountered similar messages : - too many parameters - environment out of memory for all programs of the ifeffit package Nevertheless, even if these messages appear, the programs TkAtoms, Gifeffit run without problems... It is not the case for APT that stays without running... Guilhem DEZANNEAU ___________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en français ! Yahoo! Mail : http://fr.mail.yahoo.com

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ifeffit on Windows ME
by Bruce Ravel 26 Mar '02

26 Mar '02

Howdy folks, I got an interesting bug report a few days ago which I could only partly address. A fellow asked me: > I have installed the IFEFFIT package in my computer (WIN ME). The > installation software seems to work ok. However, when I try to run > the *.bat files, I have the following message, repeated twice: "out > of environment space". Despite these messages athena, gifeffit and > ifeffit are runnig ok. However, tkatoms.bat and apt.bat don't run > at all. I understand that the "out of environment space" problem results from the rather awkward way the old Windows operating systems handled "conventional" memory and the amount of memory dedicated to holding the values of environment variables. It seems reasonable that this message turns up when our .bat files are run since they add to the environment. I suppose that an environment that is already nearly full could be tipped by our .bat files. See, for example, http://www.pcguide.com/ts/x/sys/operrEnvironmentSpace-c.html The second part of the question stumps me. Why do three of the codes work, but tkatoms and the periodic table not run? The tkatoms executable is, in fact, larger than athena, but the periodic table is smaller. And the periodic table does not use Ifeffit, which should make its memory demands even smaller. So does anyone have any wisdom for Windows ME? ("Upgrade" and other snippy comments are not helpful! ;-) Has anyone been able to use these codes on 98 or ME? B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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] iFEFFit and Tcl
by Bruce Ravel 11 Mar '02

11 Mar '02

John said: jjr> Maybe, I misunderstand, but presently we do have Python-2.0.1 jjr> installed. Does anyone know what version of Python is needed to jjr> have Tkinter? A quick search on google turned this up: http://www.python.org/topics/tkinter/

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Re: [Ifeffit] iFEFFit and Tcl
by John J. Rehr 11 Mar '02

11 Mar '02

Hi Matt, Thanks for the comments: > For G.I.Feffit, I think it's just a matter of getting a version > of python with Tkinter built-in. If perl/Tk were installed, > I'd guess that athena and tkatoms would run fine too. These > are both (python/Tkinter and perl with Tk) a small amount of Maybe, I misunderstand, but presently we do have Python-2.0.1 installed. Does anyone know what version of Python is needed to have Tkinter? Also, both tkatoms and athena appear to run fine on our SGI (at least for the jobs I've run). Only gifeffit seems to be problematic. John

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new Athena release, version 2002.03.08
by Bruce Ravel 11 Mar '02

11 Mar '02

Hi, I just posted a new release of the athena source code. I have not yet made a new windows binary. This version is 2002.03.08. New in this release: ** Phase corrected Fourier transforms (requires ifeffit 1.0069 or later) which make use of tables of central atoms phase shifts as I discussed on the feffdevel list http://cars9.uchicago.edu/feff/feffdevel/msg00082.html ** Spline clamps, both high and low, but with discrete, menu-chosen scaling factors. This is not yet documented, but the basic idea is that you can put restraints at the high and low end of the spline range in the autobk algorithm to coerce the spline to go through the data at those points. Try autobk with the high clamp set to Strong -- very cool! ** a few bug fixes -- as always ;-) Kind of a small list, but PCFTs and spline clamps are both fairly major bits of user functionality, so it seemed worth making a new release. As always, point your browser at http://feff.phys.washington.edu/~ravel/software/exafs/ for the latest. B P.S. Those of you to whom I sent this message by blind carbon copy should go to http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit and subscribe to Matt's great, new ifeffit mailing list. In the future all announcements will be made there. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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] iFEFFit and Tcl
by John J. Rehr 11 Mar '02

11 Mar '02

Hi Everyone, I'm simply delighted to see all the effort/success in getting gifeffit/ifeffit/ etc. going on OSX. However, I'm curious about the status on SGIs. Although I've gotten ifeffit to build and install using SGI's cc compiler (setenv CC cc), it appears that gifeffit does not work yet even with the latest release of ifeffit. Some symptoms, which may or may not be relevant: 1) from the ifeffit make install: Making install in wrappers Installing python extension Distutils works Testing for Tkinter and Pmw ===== WARNING WARNING WARNING ===== Tkinter is NOT installed, or was not found G.I.FEFFIT will not work. Pmw 0.8.5 is already installed. Great! 2) from wrappers/tcl cd /usr/local/src/ifeffit_1.0b/wrappers/tcl 44# sh Build cc -fpic -g -c -I../../src/lib ifeffit_wrap.c -o ifeffit_wrap.o cc ERROR parsing -fpic: unknown flag *** Error code 2 (bu21) This is not an urgent matter; ifeffit/gifeffit/athena/tkatoms, etc all appears to work fine on my laptop and desktop running various RH LINUX OS. But we still love our SGIs. Cheers, J. Rehr

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Re: [Ifeffit] Some thoughts on gifeffit
by Bruce Ravel 11 Mar '02

11 Mar '02

Paul said: > Also one of the things I used to do with the unix environment was to > set up a series of different autobak files with different rback > settings so I could see the effect of moving the fit window. It was > nice to be able to compare all of these in the same graphic window For what it's worth --- this can be done in Athena fairly easily. 1. Read in your mu(E) data. 2. Using the Group menu, make several copies of that data group. 3. Set Rbkg as desired in each copy. 4. Mark all the copies. 5. Click the purple k or R buttons. It would be nice to have a way of probing individual parameters for single groups without explicitly making copies. If anyone pipes up in support of that idea, I'll throw it on the todo list. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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 and Tcl
by Matt Newville 11 Mar '02

11 Mar '02

Hi Tsu-Chien, > >> Has anyone tried to use Tcl/tk 8.4a4 with G.I.FEFFit? > > > > Yes. G.I.FEFFIT works on MacOS X. Installing the python > > package from Fink and then building and installing the > > Ifeffit-python wrapper will install G.I.FEFFIT. > > > What I mean is Tcl/Tk for MacOS X. Just found this interesting page: > <http://www.oreillynet.com/pub/a/mac/2001/10/26/tcl_osx.html?page=4> Ah, sorry I misunderstood. I have not tried to build the Tcl/Tk wrapper on MacOS X, but I'm pretty sure it would be possible and fairly easy. In fact, Tcl/Tk is available from Fink, and installing the python module must also install this, since python/Tkinter uses Tcl/Tk. Right now, the Ifeffit build on MacOS X does not try to build the Tcl extension, but it would be easy to add this. I believe it could be as easy as this: create TclSetup.in in ../wrappers/tcl: #---- LIB_PLT = -L/sw -lpgplot -L/usr/lib -lX11 -lpng LIB_F77 = -lg2c -lm LIB_IFF = -L../../src/macosx -lifeffit INC_IFF = -I../../src/lib CC = gcc CFLAGS = -g -O2 LDFLAGS = #----- and type 'sh Build'. I believe that 'tclsh test.tcl' will then work, running a simple test that doesn't do much besides prove that ifeffit runs from Tcl. I do not know much about how 'packages' are properly installed with Tcl/Tk, and haven't been very good about keeping the Tcl extension up-to-date. That's mostly because I don't actually use tcl myself. If someone else wanted to use tcl and ifeffit together, and/or take over this module, that would be great! --Matt

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An Athena mini-tutorial
by Bruce Ravel 11 Mar '02

11 Mar '02

Hi folks, In the absence of a real document, I want to write something down to help people get started with Athena. Here goes.... First, Athena, like gifeffit, is an attempt to automate the creation of ifeffit commands. The beauty of ifeffit's command interface is that it is very flexible, both in terms of functional flexibility and in terms of writing wrappers. The annoying part of ifeffit's command interface is that you have to remember a lot of syntax and do a lot of typing. Essentially, Athena does a lot of typing for you. Second, Athena has two features that may not be obvious to folks who have used Mac-xafs or win-xafs or some other extant package. (1) There are no buttons that say "Remove background" or "Fourier transform". There are only buttons that say "Plot in energy" or "plot in R". Athena is clever about keeping track of what needs to be done and doing all necessary analysis steps in the background before plotting. So, if you change the k-weight for the Fourier transform, Athena knows to redo the forward and backward transforms as needed but not to redo the background removal. If you change Rbkg and plot in energy only, the background removal will be done. And so on. (2) You can "mark" groups and perform various actions on single groups or on ensembles of marked groups. So it is easy to plot single groups or ensembles of groups with a few mouse clicks. What's more the analysis steps are taken care of automagically for single groups or for ensembles of groups. Now I am going to describe specific features of Athena: ***** Reading in data Athena reads ASCII data using ifeffit, so all the rules that apply to ifeffit also apply to Athena. Basically, Athena expects that data will be in the form of column data, possibly with headers. Athena can directly read mu(E) or chi(k) data. It can also read raw data straight from the beamline. See http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/col… You can then construct mu(E) data by selecting columns for the numerator and denominator. In the screen-shot, I show selecting It and I0 columns as the numerator and denominator for transmission data. There is a natural log button which should be clicked for transmission data. You can also handle multi-element detector data in a very rudimentary way by selecting multiple numerator columns for fluorescence data. You will notice that there are options in the File menu for reading single or multiple files. This is annoying but necessary. The standard file dialog does not do extended selection, the motif-like file dialog does extended selection but is unfamiliar to most people. Extended selection is very useful -- if you extendedly select a group of identically formatted files, Athena will only give the column selection dialog for the first one. The button labeled "Set preprocessing parameters" is beyond the scope of this post, but may become clear to you once you grok all the features of Athena. ***** Selecting and marking groups Once you have read in some data, you will probably want to plot it. You select a group by clicking on its name in the skinny frame on the right. When you select a group, its name will be highlighted in orange and its parameter values will displayed in the form on the left. When you click on a *red* plotting button, the selected group will be plotted. To the left of the group's name is a little check button. You mark a group by clicking the checkbutton on. When you click a *purple* plot button, all marked groups will be over-plotted. ***** Setting parameter values You can only directly edit the parameters for the selected group because only the selected group has its parameters displayed. There are ways of setting the parameters of other groups to the values of the selected group. In the Group menu is and option for setting the values of all parameters of all other groups to the values of the currently selected group. There is another option for setting all parameters of all marked groups to the values of the currently selected group. There is also fine grained control over setting parameters which is described in the next section. ***** Mouse clicks on labels When you pass the mouse over a label in the frame displaying all the parameter values, you will notice that the text and background change color. This is a visual cue that the text is sensitive to mouse clicks. Clicking the left mouse button on a word that has changed color will display a little bit of text in the echo area at the bottom of the window which explains in a few words the purpose of that parameter. Clicking the right mouse button will pop up a menu which allows you to set that parameter for other groups to the value of the currently selected group. The functions in the Group menu explained above work on all parameters, this right-click function works only on that specific parameter. ***** Plotting options You can independently control how single and marked group plots are made by choosing different options in the Plotting Options section at the lower right hand corner of the window. There is one notecard for each plotting space. Red buttons are for single group plots and purple buttons are for marked group plots. I suggest poking at these buttons to see what kinds of plots you can make. The plot ranges for the x-axis are set in this space as well. You may need to think about these values. For example, the data alignment function (described below) uses the values of Emin and Emax. Typically, you would want to restrict the plot to a few tens of volts above and below the edge so you can see the details of the edge for alignment. ***** Palettes The options in the Edit menu all pop up a new window with notecards which display all sorts of textual information. Perhaps the most useful is the ifeffit buffer which allows you to monitor the communication between Athena and ifeffit. ***** Project files You have the options of saving data in a variety of column formats, including mu(E), norm(E), chi(k), chi(R), and chi(q). You can also save a "project file". Which is an Athena specific which records the state of your Athena session. It will record data and parameters in a big ASCII file that is hard for a human but easy for Athena to read. Athena's project files are different from ifeffit's PAD files. They exploit the object oriented nature of its internal data structures to save the state of an ensemble of groups, even if the data in that ensemble is unrelated one to the other. ***** Deglitching The deglitch menu has two options in it, deglitching and truncating. Deglitching is for removing spurious points throughout the data set, truncating is for removing all data points after a specified point. Deglitching can be done point-by-point or algorithmically. The point-by-point is done by clicking the "Select a point" button, then clicking on the plot. The "remove point" button will then become active. Clicking it will remove the point from the group. The algorithm is a bit more complicated. There are three parameters which set margins above and below the data in a range either in the pre-edge or the post-edge. Any data points which extend outside these margins will be removed. To understand this better, try reading the data file uhup.003 and plying around with the algorithmic deglitching parameters. Eventually you will make it look like this: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/deg… Clicking the "Remove glitches" button will remove the four points outside the margins. ***** Aligning Alignment can be done using raw mu(E), normalized mu(E), or the derivative of mu(E). I think this one is pretty easy to understand. The "Standard" is the fixed reference. The "Other" is the group to be energy shifted. When you click the + or - buttons, the other group's e0 shift is incremented and the two data sets are replotted. See this: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/ali… ***** Merging Merging works on all marked groups. You can merge in any of the plotting spaces. The average and standard deviation of marked groups are calculated. The average, the average + the std. dev., and the average - the std. dev. will be plotted. The standard deviation will be written to output column data and to project files. There is more stuff to explain. I have not discussed macros, plot multipliers, clamps, phase corrections, Cromer-Liberman normalization, hints, the Plot and Mark menus, data preprocessing, detector data, pluck buttons, autobk standards, feff data, and a few other things. But hopefully this is enough to get people started until I write a proper document/tutorial. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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