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

Re: [Ifeffit] Ifeffit Digest, Vol 149, Issue 8
by Ganesh Subramanian 12 Jul '15

12 Jul '15

Dear Matt, Thanks for that suggestion. I just got time to work on it again. In the meantime, I noticed your email response to another question of similar nature. And it works fine now ! Of course, I have not yet performed any calculations/analysis to see if there are any additional problems (if any). But so far so good. Thanks for your help, Ganesh On Wed, Jul 8, 2015 at 10:00 AM, <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. Re: Demeter Crashes on opening in Windows Bootcamp > (Ganesh Subramanian) > 2. Re: Demeter Crashes on opening in Windows Bootcamp (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 8 Jul 2015 01:07:56 -0700 > From: Ganesh Subramanian <gunkanna(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp > Message-ID: > <CAAb9e-d2Kvx=VZRmNPOVBcgpCvqD3x= > t4VLLRdDRFtDJMBUURQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > > > > Dear Bruce and Matt, > > > > > > > > My first guess is that the culprit is anti-virus software running on > > Ganesh's computer. I have seen other examples of parts of Demeter being > > falsely identified as problematic and being removed, rendering the > > Demeter programs unusable. > > > > That said, on Ganesh's computer, the gnuplot executable should be in > > > > C:\strawberry\c\bin\gnuplot\bin > > > > Yes - I can locate it exactly at this path and the executable file does > open from there. > > > > > > > There are some other conceivable ways to see this problem, but I am > > placing my first bet on over-aggressive anti-virus software. > > > > I did have McAfee. I uninstalled the program and restarted my computer > and > the problem still persists. It seems very much the same, im posting the > most recent log-file. > > > > > *************************************** > > >

1 0

Demeter won't start in Windows 7
by willn 12 Jul '15

12 Jul '15

Hi everyone, My copy of Demeter on my Windows 7 machine stopped working at some point in the recent past, so I have re-installed it, but I still have the same problem - a command window and splash screen open briefly, before disappearing. In my Path variable I have bumped the perl addresses up above the MinGW one, as suggested in one of the common fixes, but this did not solve the problem. I had a good look through the mailing-list archive for similar problems to mine, but each seem to be different (the log file errors were different). I have commented out the appropriate lines in the batch files, but, predictably I guess, this only had the effect of removing the splash screen when the program attempts to start-up. I have also played around a little installing newer versions of Strawberry, but similarly to no avail. If time permits, would anyone mind helping me interpret my log file (attached)? I'm not really computer literate enough to understand what is written there! Grateful thanks in advance, William -- William Nash PhD Student, Experimental Petrology Earth Sciences Department Oxford University

4 6

Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 08 Jul '15

08 Jul '15

> > Dear Bruce and Matt, > > > My first guess is that the culprit is anti-virus software running on > Ganesh's computer. I have seen other examples of parts of Demeter being > falsely identified as problematic and being removed, rendering the > Demeter programs unusable. > > That said, on Ganesh's computer, the gnuplot executable should be in > > C:\strawberry\c\bin\gnuplot\bin > Yes - I can locate it exactly at this path and the executable file does open from there. > > > There are some other conceivable ways to see this problem, but I am > placing my first bet on over-aggressive anti-virus software. > > I did have McAfee. I uninstalled the program and restarted my computer and the problem still persists. It seems very much the same, im posting the most recent log-file. > > *************************************** >

2 1

Be EXAFS and publication
by Joshua Kas 07 Jul '15

07 Jul '15

Hi, This may be a long shot, but I was wondering if anyone is aware of EXAFS data on HCP Be. In particular we are looking for Debye-Waller Factors, so a publication would be great, but just data might work as well. Thanks, Josh Kas

2 1

Question about deglitching EXAFS data
by Francesco Marafatto 07 Jul '15

07 Jul '15

Hello All, I have enjoyed this digest in the past and found it very helpful! I hope it may provide an answer to my question. I am collecting Mn EXAFS data out to k of 15 Å-1, and the data look fine. However, the monochromator (Si 111) has 5 strong 2-point glitches and 3 minor 1-point glitches in one of the regions that I am most interested in (k between 5 and 9 Å-1). My question relates to how many data points I can remove before influencing the data. In my previous experience I have removed 2 or 3 points but never more. I have read through the deglitching section of “XAFS for Everyone”, and think that I could oversample the EXAFS (with k steps of 0.03 Å-1 vs 0.05 Å-1), but most of the data have already been collected. Is there a rule of thumb about deglitching? In other words, is there a limit to the number of bad points I can eliminate for an EXAFS scan to k of 15 Å-1? Thanks and looking forward to hearing your thoughts, Francesco Francesco Femi Marafatto francesco.marafatto(a)unil.ch FNS PhD student, Environmental Geochemistry Laboratory IDyST - FGSE Bureau 3233 Gèopolis Université de Lausanne CH-1015 Lausanne T. +41 (0)21 692 4451

2 1

Fwd: FEFF trouble help me please !!!!
by Bruce Ravel 07 Jul '15

07 Jul '15

Hi, I want to remind everyone that it is important to use the mailing list. I do not feel that I am obligated to answer questions about the software that come to me by any other channel, particularly when I do not have a personal relationship with the person asking the question. That said, I am forwarding this fellow's question to the mailing list and providing an answer. Thitipong, this is a case of GIGO. According to Acta Cryst. (1972). B28, 3102-3103 (the reference I found for Cr23C6): The crystal structure of chromium carbide, C r 2 3 C 6 , has been described as cubic, space group Fm3m, 4Cr (I) in (a) (000), 8Cr (II) in (c) (l-lq:), 48Cr (III) in (h) (Oxx), x= 0.165, 32Cr (IV) in (f) (xxx), x=0.385, 24C in (e) (x00), x=0-275 (Westgren, 1933) on the basis of X-ray single crystal and powder diffraction data. We have confirmed this structure and determined the atom positions more precisely by a neutron diffraction study of a powder sample. Using those coordinates, I have no problem running atoms and feff. The structure is a bit strange -- I guess this is more like a metal than a carbide -- but it seems consistent with the paper after a cursory inspection. According to http://www.crystallography.net/cod/1009019.html, the space group for Cr7C3 is P M C N. Atoms and feff run fine with this input data. Some hints on asking questions that so you'll get the answers you are looking for: http://bruceravel.github.com/demeter/pods/bugs.pod.html http://bruceravel.github.com/demeter/pods/help.pod.html B -------- Forwarded Message -------- Subject: FEFF trouble help me please !!!! Resent-Date: Fri, 3 Jul 2015 04:25:57 +0000 Resent-From: bruce.ravel(a)nist.gov Date: Fri, 3 Jul 2015 11:33:12 +0700 From: Thitipong Po-Kloy <thitipong_37(a)hotmail.com> To: bruce.ravel(a)nist.gov <bruce.ravel(a)nist.gov> Hi Bruce , My name is Thitipong . I have trouble about FEFF program and believes you can help me. Now I am doing "XANES simulation" Cr23C6 and Cr7C3 . So , when I run FEFF program - it report TWO ATOMS VERY CLOSE TOGETHER . How can I fix it ? This it Data of atom Cr23C6 title name : Cr23C6 title formula : Cr23C6 space F M 3 M a=10.6599 b=10.6599 c=10.6599 rmax = 10 core=Cr1 atom Cr 0 0 0 Cr1 Cr 0.25 0.25 0.25 Cr2 Cr 0.385 0.385 0.385 Cr3 Cr 0 0 0.340 Cr4 C 0.276 0.276 0.276 C1 and Cr7C3 title name : Cr7C3 title formula : Cr7C3 space P M C M a=7.0149 b=12.1530 c=4.5320 rmax = 10 rpath=6 core=Cr1 atom Cr 0.064 0.811 0.056 Cr1 Cr 0.250 0.626 0.057 Cr2 Cr 0.250 0.206 0.250 Cr3 Cr 0.250 0.416 0.261 Cr4 Cr 0.065 0.021 0.250 Cr5 C 0.250 0.562 0.459 C1 C 0.029 0.342 0.028 C2 If there is any other way please let me know. Thank You , Thitipong -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 07 Jul '15

07 Jul '15

Sorry for not noticing. The log files are attached now. It is pretty much the same for all three cases of Athena, Artemis and Hephaestus. Ganesh > > Message: 2 > Date: Mon, 06 Jul 2015 08:18:08 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp > Message-ID: <559A7200.9050207(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 07/04/2015 06:10 PM, Ganesh Subramanian wrote: > > Hi. > > > > This is Ganesh and I am a first time user of the Demeter accessories. > > > > I downloaded and installed the files from the github site using the > > 0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7 > > on my Macbook Pro (2012). It seemed to have installed fine, but the > > moment I click on the icons to open any of Athena, Artemis or > > Hephaestus, all of them show a command window, thats empty, and in a few > > seconds crash and close. No error windows or command line error prompts. > > > > Any idea on what might be wrong ? > > > It is basically impossible to answer a question like this without a look > at the log file, as explained here: > > http://bruceravel.github.io/demeter/pods/bugs.pod.html > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > >

3 2

Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 06 Jul '15

06 Jul '15

Hi. This is Ganesh and I am a first time user of the Demeter accessories. I downloaded and installed the files from the github site using the 0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7 on my Macbook Pro (2012). It seemed to have installed fine, but the moment I click on the icons to open any of Athena, Artemis or Hephaestus, all of them show a command window, thats empty, and in a few seconds crash and close. No error windows or command line error prompts. Any idea on what might be wrong ? Thanks, Ganesh

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 26
by Nils Skoglund 27 Jun '15

27 Jun '15

Hello Everton, Matt and Pushkar, Thank you for your replies. I have tried both the 32-bit and 64-bit versions with uninstalling in between, to no avail. I'm curious if it is a priority issue between the dual GPU's on the laptop that gnuplot can't handle well; there's both a dedicated GPU and an integrated one. System temperatures look normal and none of the fans are revving up, so it shouldn't be heat-related. Other softwares handle plotting without issues so the suggestion about gnuplot being the culprit seems like the most reasonable one. If I narrow this issue down and find a way to work around it, I'll let you know. Until then I'll just find some other workstation for the evaluation work - thanks again! //Nils -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: den 26 juni 2015 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 148, Issue 26 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: Issues with Athena on high-performance systems (pushkar shejwalkar) 2. Re: Issues with Athena on high-performance systems (ebonturim(a)usp.br) ---------------------------------------------------------------------- Message: 1 Date: Fri, 26 Jun 2015 10:05:23 +0900 From: pushkar shejwalkar <pshejwalkar2004(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Issues with Athena on high-performance systems Message-ID: <CAN0ZRcEm=2KRDeXO-=t60yDZHwT4Rp8Zzs6pwPSbt7ndiQBGCg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi all, I am not an expert in this. In fact , I am one of the very new user of athena. But have you tried uninstalling and then reinstalling the whole package again? ( I am sure you have but since you didnt mentioned just wondering?) Sometimes, that also helps. not sure why and how? but it did for me. Pushkar On Fri, Jun 26, 2015 at 5:00 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > Nils, > > We run Athena on non-wimpy Windows 7 systems at our beamline computers > all the time, using both 64- and 32-bit Windows, and typically on > multi-core machines with at least 16 Gb RAM and multiple screens. > Like Robert, we don't see any real performance problems with a handful (<50) spectra. > Athena rarely makes a very big dent in the system resources (well, > comparable to a web browser, so a bit of a hog, but well under 1Gb RAM). > > Perhaps what you're seeing is related to the plotting with Gnuplot. > I'm not sure why that would be a problem... Any ideas? > > --Matt > > Hi, > > > > I?m curious if anyone else is experiencing issues with Athena in more > high-end systems running Windows 7? While I am used to having to wait > for the *first* plot to show up, the software is virtually unusable > to me now where any slight change (e.g. modifying range for the > spline) to already imported data takes up to over a minute to replot. > This didn?t use to be the case for me. The system is a laptop running > Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space > on the hard drives and a dedicated Intel HD 4600 graphics circuit. > > > > If anyone has a work-around for this problem or can suggest anything > to make Athena usable again, it would be most appreciated. Has anyone > noticed previous versions of Athena running more smoothly? > > > > Best regards, > > Nils > > > > *------------------------------------------------------------------* > > *Nils Skoglund, Ph.D.* > Post-doctoral researcher > > Energy Science > Department of Engineering Sciences and Mathematics Lule? University of > Technology > SE-971 87 Lule? > Sweden > > > > Cell : +46 (0)72 529 52 08 > > Web page: http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en > > Publications: http://www.researcherid.com/rid/D-3493-2011 > > *-------------------------------------------------------------------* > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Sapporo, Japan

1 0

Issues with Athena on high-performance systems
by Nils Skoglund 25 Jun '15

25 Jun '15

Hi, Im curious if anyone else is experiencing issues with Athena in more high-end systems running Windows 7? While I am used to having to wait for the first plot to show up, the software is virtually unusable to me now where any slight change (e.g. modifying range for the spline) to already imported data takes up to over a minute to replot. This didnt use to be the case for me. The system is a laptop running Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space on the hard drives and a dedicated Intel HD 4600 graphics circuit. If anyone has a work-around for this problem or can suggest anything to make Athena usable again, it would be most appreciated. Has anyone noticed previous versions of Athena running more smoothly? Best regards, Nils ------------------------------------------------------------------ Nils Skoglund, Ph.D. Post-doctoral researcher Energy Science Department of Engineering Sciences and Mathematics Luleå University of Technology SE-971 87 Luleå Sweden Cell : +46 (0)72 529 52 08 Web page: <http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en> http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en Publications: <http://www.researcherid.com/rid/D-3493-2011> http://www.researcherid.com/rid/D-3493-2011 -------------------------------------------------------------------

5 4