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

Re: Ifeffit Digest, Vol 28, Issue 6
by Satyender Goel 07 Jun '05

07 Jun '05

Hi Matt, I have managed to get everything up and running. Thank you so much for your patience and help without which it wouldn't have been possible. I appreciate your effort and the interest taken in helping me solve my problem. Sorry for the trouble. Regards, Satyender Goel Quoting ifeffit-request(a)millenia.cars.aps.anl.gov: > 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. Re: Re: Ifeffit Digest, Vol 28, Issue 4 (Matt Newville) > 2. Re: Bug report (Scott Calvin) > 3. Re: Importance and Edge Step (Gerrit Schmithals) > 4. Re: Bug report (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 7 Jun 2005 10:18:24 -0500 (CDT) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] Re: Ifeffit Digest, Vol 28, Issue 4 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0506070933460.14613-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Satyender, > >> Finally i got my Perl script running using, >> >> BEGIN { >> $ENV{IFEFFIT_DIR} = 'C:\Program Files\Ifeffit\'; >> } >> >> at the begining of my program.... > > If your perl scripts are running, you must have the Ifeffit > modules installed, no??? If it's working, then it's probably > not necessary to rebuild the perl module. But if you're going > to be using it heavily, it might be worth figuring out how to do > build it anyway. > >> I have added the environment variable IFEFFIT_DIR, but it does >> not seem to make a difference. > > Hmm, that's really strange, but maybe I'm not understanding? > It should definitely work to set IFEFFIT_DIR as an environmental > variable and run perl in that environment without having BEGIN { > $ENV{IFEFFIT_DIR}='...';} in the script. Well, the BEGIN {} > block in the script is really setting the environmental > variable, so if that works, setting it from the Control Panel > should work to. Are you should the command shell you're using > has this environmental variable set? Try typing > C:\> set > to see a list of environmental variables. > >> I have tried.......... >> >> "C:\Program Files\Ifeffit\wrappers\perl\build, and do >> perl Makefile.PL >> nmake install" >> >> after editing makefile.pl as per... >> >> "'LIBS' => [' -LC:\"Program Files"\Ifeffit ifeffit_10 ']," >> and also copied ifeffit.pm to C:\perl\site\lib... >> >> I have visual studio installed on my computer, however the nmake command >> does not seem to be working. >> >> SCREEN DISPLAY AFTER THE CHANGES: >> >> C:\Program Files\Ifeffit\wrappers\perl\build>perl makefile.pl >> Note (probably harmless): No library found for oldnames.lib >> Note (probably harmless): No library found for kernel32.lib >> <snip> > > This is probably because the VC/Visual Studio stuff isn't in > your path, and since perl is going to try to run 'cl' and > 'nmake' from the command line, the command shell needs to find > them from the environmental variables. The details of how to do > this depends on how your compiler was installed. You can > probably start with and edit the batch file below. > > Please give more details and a better sense of what does and > doesn't work. Like, what does > > C:\> perl -e "use Ifeffit;" > > report? If it reports "cant find Ifeffit.pm in @INC ....", you > don't have the Ifeffit module installed. If it reports nothing, > it is installed, and you're ready to go. If it reports messages > about PGPLOT, you'll be fine once the environmental variables > for PGPLOT_DIR and PGPLOT_DEV are set. > > Hope that helps, > > --Matt > > REM ---- > REM sample settings for VC,NMAKE, etc > REM probably have to reset BASE_DIR > set BASE_DIR=C:\Program Files\Microsoft Visual Studio > set CPU=i386 > set INCLUDE=%BASE_DIR%\VC98\INCLUDE > set LIB=%BASE_DIR%\VC98\LIB > set > PATH=%BASE_DIR%\Common\Msdev98\BIN;%BASE_DIR%\VC98\BIN;%BASE_DIR%\Common\Tools;%BASE_DIR%\Common\Tools\WINNT;%PATH% > > REM ---- > > > > > ------------------------------ > > Message: 2 > Date: Tue, 07 Jun 2005 12:13:59 -0400 > From: Scott Calvin <scalvin(a)slc.edu> > Subject: Re: [Ifeffit] Bug report > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <3.0.1.32.20050607121359.00b15540(a)mail.slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Thanks, Matt. > > Yes, I've been working around it by just adding "+0" to path expressions > that end in a parentheses. I hadn't quite figured out that it required > starting with a non-matched parentheses to trigger the error; it's good to > know exactly what circumstances cause it to arise. > > A suggestion for Bruce--ifeffit flags these kinds of syntax errors pretty > well. Is it possible for Artemis to look at the ifeffit output and alert > the user to examine the iffefit output if there is an error? > > --Scott Calvin > Sarah Lawrence College > > At 09:33 AM 6/7/2005 -0500, you wrote: >> Hi Scott, >> >> Yep, that is an ifeffit error. It turns out to be specific to >> math expressions in path() commands, but it is definitely a bug. >> It seems that a math expression for a path parameter that starts >> with '(' and ends with ')' and for which these '(' and ')' are >> not a matched pair will incorrectly raise a syntax error. This >> doesn't happen for set() or def(). >>> > > > ------------------------------ > > Message: 3 > Date: Tue, 07 Jun 2005 18:57:01 +0200 > From: Gerrit Schmithals <schmithals(a)hmi.de> > Subject: Re: [Ifeffit] Importance and Edge Step > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <42A5D1DD.6090603(a)hmi.de> > Content-Type: text/plain; charset=ISO-8859-1 > > On Monday 06 June 2005 09:27, Gerrit Schmithals wrote: > >>> How do I implement more than 4 references? There is a box for entering >>> the number but it does not enlarge the reference-list as I expected it >>> to do. >>> >>> > Bruce Ravel schrieb: > >> All of this is explained in the doc page for the LCF dialog. (That >> is, I think I explained it all there. It may be [is?] poorly >> explained ....;-) >> >> The length of the standards list is set in the preferences dialog. >> The relevant parameter is linearcombo->maxspectra. >> >> >> > Thanks for that hint. I really should have found that setting by myself. > > I did not use the combinatorical fitting so far, but concerning the > normal linear fitting I observed two issues: > > I had an Athena project with some references loaded as chi(k)-data and > some unknown samples as chi(k) as well. Athena won't let me start the > Linear Fit-Dialog stating that it (she) needs at least three > xmu-spectra. Changing the preference to "standard fit in k-space" does > not help. Workaround: I just loaded some dummy xmu-Spektra and can now > work with the dialog. > > Also, only these xmu-spectra can be selected from the "standards pluck > boxes", the only way to insert the chi(k)-references is to use "use > marked groups". That is a bit of a problem when you have to move one of > the groups up because its value is negative. Workaround is to move up > the groups in in Data group section. > > Some other issues came into my mind while working with the dialog but > they are really of minor importance: > - Is there any possibility to plot the linear fit and the data in > R-space right away? (without first saving it as a datagroup) > - It would be nice to be able to store the relative weigths together > with the newly created dataset. > > Cheers, > Gerrit > > > > > ------------------------------ > > Message: 4 > Date: Tue, 7 Jun 2005 12:01:02 -0500 > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Bug report > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200506071201.02798.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Tuesday 07 June 2005 11:13, Scott Calvin wrote: >> A suggestion for Bruce--ifeffit flags these kinds of syntax errors pretty >> well. Is it possible for Artemis to look at the ifeffit output and alert >> the user to examine the iffefit output if there is an error? > > One of the features new to ifeffit 1.2.7 is a scalar flag, &status, that gets > set to something other than 0 when something bad happens. Matt added this so > there would be an easy way for A&A to know when an error was encountered. > > I have not yet implemented any functionality surrounding &status, but it's on > the list of things to do. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > ravel(a)phys.washington.edu > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone: (1) 630 252 5033 > Argonne IL 60439, USA fax: (1) 630 252 9793 > > 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, Vol 28, Issue 6 > ************************************** >

1 0

Athena Problems
by McCready, Alistair 07 Jun '05

07 Jun '05

Hi, I am having some problems with Athena. I reformatted my hard drive the other day (windows XP Pro), and downloaded Athena etc. After installing the programs, they work fine. However, once I download the updates, Athena refuses to work. I try to open the program and all I get a black command-style box filled with odd words/text. I do not have a virus (first thing I checked), and all the updated versions of the other programs all work fine (e.g. Artemis, Hephaestus). I just wanted to check if anyone else has ever had this problem? Alistair "SRC provides Smart Science Solutions" This e-mail and any files transmitted with it are intended only for the named recipients and may contain legally privileged and/or confidential information. If you are not the intended recipient please do not disseminate, distribute or copy this e-mail without the consent of the sender.

6 6

Re: Ifeffit Digest, Vol 28, Issue 4
by Satyender Goel 07 Jun '05

07 Jun '05

Thanks a lot Dear Matt and Bruce, Finally i got my Perl script running using, BEGIN { $ENV{IFEFFIT_DIR} = 'C:\Program Files\Ifeffit\'; } at the begining of my program.... I have added the environment variable IFEFFIT_DIR, but it does not seem to make a difference. I have tried.......... "C:\Program Files\Ifeffit\wrappers\perl\build, and do perl Makefile.PL nmake install" after editing makefile.pl as per... "'LIBS' => [' -LC:\"Program Files"\Ifeffit ifeffit_10 ']," and also copied ifeffit.pm to C:\perl\site\lib... I have visual studio installed on my computer, however the nmake command does not seem to be working. SCREEN DISPLAY AFTER THE CHANGES: C:\Program Files\Ifeffit\wrappers\perl\build>perl makefile.pl Note (probably harmless): No library found for oldnames.lib Note (probably harmless): No library found for kernel32.lib Note (probably harmless): No library found for user32.lib Note (probably harmless): No library found for gdi32.lib Note (probably harmless): No library found for winspool.lib Note (probably harmless): No library found for comdlg32.lib Note (probably harmless): No library found for advapi32.lib Note (probably harmless): No library found for shell32.lib Note (probably harmless): No library found for ole32.lib Note (probably harmless): No library found for oleaut32.lib Note (probably harmless): No library found for netapi32.lib Note (probably harmless): No library found for uuid.lib Note (probably harmless): No library found for ws2_32.lib Note (probably harmless): No library found for mpr.lib Note (probably harmless): No library found for winmm.lib Note (probably harmless): No library found for version.lib Note (probably harmless): No library found for odbc32.lib Note (probably harmless): No library found for odbccp32.lib Note (probably harmless): No library found for msvcrt.lib Writing Makefile for Ifeffit C:\Program Files\Ifeffit\wrappers\perl\build>nmake 'nmake' is not recognized as an internal or external command, operable program or batch file. Regards, Satyender Goel

2 1

ifeffit module for perl
by Satyender Goel 06 Jun '05

06 Jun '05

Hi, I am developing algorithms for Automation of "DATA MINING FOR HIGH THROUGHPUT SYNCROTRON SPECTROSCOPIES" with Dr. S L M Schroeder group. I have come across a problem in accessing IFEFFIT libraries through Perl on WINDOWS Platform. I have installed latest version of IFEFFIT as well as PERL. Evertime i try accessing IFEFFIT Through Perl it gives the error like: c:\work>perl -w trial.pl Can't locate loadable object for module ifeffitin @INC <@INC contains: C:/Perl/lib c:/Perl/site/lib .> at trial.pl line 2. Compilation failed in require at trial.pl line 2. BEGIN failed--conpliation aborted at trial.pl line 2. I have trying putting 'Perl folder from wrappers of IFEFFIT' to Perl/site/lib, but no success so far. I am stuck with my work. Any solution to get Access of IFEFFIT libraries through Perl? Cheers!!! Satyender Goel MSc 'Cheminformatics'

4 3

E0 limit
by alita＠chemmail.chem.fsu.edu 03 Jun '05

03 Jun '05

When I fit some Cr compound in Artemis I obtain a e0 for each path around 6.68 . In " Using Artemis" by dr. Bruce Ravel page 49 there is a example where he is also obtaing a 6.59 value for e0. Is there a limit for this e0? I must restrain this value to be under 5? How can I calculate this value? Thanks, Adrian Lita

2 1

RE: [Ifeffit] Importance and Edge Step
by Barton, David (DG) 02 Jun '05

02 Jun '05

Bruce, thanks for the info.. When referring to the Edge Step feature you mentioned that: "You can type in a number, as before" This does not appear to be working, if I check "Fix Step", enter a value into the edge step window, and then recompute the background, the value of the edge step reverts back to the automatic value. Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Thursday, June 02, 2005 3:00 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Importance and Edge Step > > > On Thursday 02 June 2005 13:06, Barton, David (DG) wrote: > > I noticed two new features in Athena 0.8.040 and am unsure > of how to > > use them. The new features are "Importance" and "Edge Step". I > > attempted to use the Edge Step feature by checking "Fix > Step" and then > > entering a value, but the Edge Step always reverts back to the > > automated value. However, when I use the Increase/Decrease buttons > > (Left/Right arrow in Edge Step > > window) the edge step does change, but it only changes in > increments of > > 0.01 which is much too large for my datasets. Is there > something I am > > missing here? > > > > Also, I couldn't locate Bruce's changelog for Athena so I > am unsure of > > what the new "Importance" feature does. Anyone used this > new feature > > yet? > > > Importance: > This number is used only in a merge and only when the > "Weight by importance" > button in the Merge menu is checked. It's intention is to allow > user-specified weights in a merge. If you trust one data > set twice as much > as another, the more trusted one might be given an > importance of 2 while the > other is given an importance of 1. This was in response to > a feature > request -- personally I am not clear how would know how to > weight different > data sets. > > Edge step: > I got a request for a quick way to play around with the > size of the edge > step. When the "fix step" button is checked, you can then > specify an edge > step which will then be used to normalize the data. You > can type in a > number, as before, or you can tweak the edge step up or > down. You can set > the size of the tweak in the preferences using > bkg->step_increment. Note > that if the "fix step" button is not checked, the edge step will be > recomputed every time the background is recalculated. > > And I do need to be more conscientious about updating the > change logs. Sorry. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu Environmental Research Division, > Building 203, Room E-165 > Argonne National Laboratory phone and voice mail: > (1) 630 252 5033 > Argonne IL 60439, USA fax: > (1) 630 252 9793 > > 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/listi> nfo/ifeffit >

1 0

idealized 95-atom Pt cluster
by Charles Chusuei 30 May '05

30 May '05

Hi,,, I'm a new user to Artemis and Atoms. I would like to generate a simulated EXAFS spectrum of an idealized bare 95-atom cluster of Pt (with no ligands attached to it). Looking at Cambridge data files, the largest cluster documented is 18, so I would have to make one up. I would like to arrange the 95 atoms into an idealized sphere with the standard geometry for bulk Pt-Pt bonding that can be predicted from the crystal structure (e.g. metallic radius = 139nm, metallic separation = 277.5nm separation, etc.) I understand this can be done using Artemis and Atoms. I'm relatively new to using the software (prodominantly know how to use Athena for plotting the experimental EXAFS data , not much more). Could anyone provide suggestions on how to get started on this task? E.g. Generating the crystal data and displaying the EXAFS of the resulting bare cluster? Charles

6 10

new windows updater
by Matt Newville 27 May '05

27 May '05

Hi Folks, There's a new Windows updater available (this is #15) with new versions of Athena, Artemis, and Diana that address some of the problems people have reported. Please give them a spin! --Matt

1 0

RE: [Ifeffit] Least Squares Fitting in Athena
by Ravel, Bruce D. 25 May '05

25 May '05

> I have a couple of comments about LSF in Athena and I would like to hear > other people's opinions on the matter. > Also, it would be interesting to know: are there > many people who use Athena to do LSF? > I found that there is some inconsistency with plotting after > the fit is done. In my case nonzero energy shifts are applied to > the fitted data and the standards. The resulting linear combination fit > doesn't look shifted in energy appropriately - visually there is a > mismatch between the data and the fit. On the other hand, R-factor and > Chi^2 are very reasonable. This looks somewhat confusing. > Also, in my experience the obtained fractions in Athena come out slightly > different from those I could get using Sixpack LSF software. In my fits I > used the same constrains/options, same data and references and same data > range. What can be the cause of this? Hi, I have recently seem similar behavior. There are several possible causes for what you are seeing -- the most likely being an error in how the standards are interpolated onto the grid of the unknown data. I have been working hard on the LCF features in Athena recently and have fixed several bugs and added lots of new features. Rather than try particularly hard to address your questions now, I am going to wait and see if they persist after I release the next version of Athena (which will be soon). B

1 0

Least Squares Fitting in Athena
by Stanislav Stoupin 24 May '05

24 May '05

Hello all, I have a couple of comments about LSF in Athena and I would like to hear other people's opinions on the matter. Also, it would be interesting to know: are there many people who use Athena to do LSF? I found that there is some inconsistency with plotting after the fit is done. In my case nonzero energy shifts are applied to the fitted data and the standards. The resulting linear combination fit doesn't look shifted in energy appropriately - visually there is a mismatch between the data and the fit. On the other hand, R-factor and Chi^2 are very reasonable. This looks somewhat confusing. Also, in my experience the obtained fractions in Athena come out slightly different from those I could get using Sixpack LSF software. In my fits I used the same constrains/options, same data and references and same data range. What can be the cause of this? Stanislav Stanislav Stoupin ----------------------------- Research Assistant/PhD student BCPS department Illinois Institute of Technology email: stousta(a)iit.edu voice: 312-567-7983

2 1