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

Error in Running XANES on FEFF8.4 for Cobalt based cluster
by Ganesh Subramanian 30 Jul '15

30 Jul '15

Dear all, I was trying to simulate XANES using FEFF8.4 at Cobalt K edge. This is for a cluster and not a crystal. I encountered two problems. 1. *Using the FOLP card*: The actual cluster size is about 180 atoms extending upto 18 A in radial distance from the central cobalt atom. But there are quite a few instances of Hydrogen atoms that are too close. I tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to get a syntax type error, that i cant figure out. I checked the crystal structure and the smallest hydrogen bond distance is 0.89 A. (I have attached the corresponding input and log file with suffix 'full cluster') 2. *SCF for small cluster*: Since the problem with the hydrogen distances persisted, I decided to run the calculation for a smaller cluster (about 50 atoms). I used the conditions as prescribed for small clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were too close (within this smaller cluster, there were about 3 of them, and none in the first or second shell of co-ordination) were removed manually. Now, I did not have the error on distances, did not require the FOLP card to be manually altered, but the log1 file seems to suggest that the SCF is not calculated. I cant figure why that is the case. (I have attached the corresponding input and log file with suffix 'small cluster') Sorry for the long email, and thank you for any suggestions. Ganesh

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HELP: failed to install gcc49 on mac (v10.6.8)
by Ie-Rang Jeon 29 Jul '15

29 Jul '15

Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed

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Setting ranges in peak fitting
by Kenneth Latham 28 Jul '15

28 Jul '15

Hi Bruce, To clarify this further, I am peak fitting a number of peaks under the carbon edge. For example, I know from the literature that the 1s-p transition for the C=C should be located between 284.5 to 285.5 eV, so I would fit a peak at about 285 eV to start with. I would then move on to fitting additional peaks based on their literature values with what I know about the material/where obvious peaks are in the NEXAFS. The problem now comes when I tell Athena to fit, it will start to move the peaks all over the place to obtain the best fit, typically placing them in locations where functionalities don't appear under the NEXAFS. In other words, it would move peaks away from where I would expect them to be based on the literature. This can be partially stopped by fixing all but one peak, fitting it and then and applying this procedure to every peak multiple times. What I was wondering is if Athena has the ability to set a range that each peak is allowed to move, i.e., the C=C center would be restricted to values between 284.5-285.5 eV. Hence I could set up the ranges and fit quickly based on those. Cheers, Ken Latham ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Saturday, 25 July 2015 3:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 149, Issue 23 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. Setting ranges in peak fitting Athena (Kenneth Latham) 2. Re: Setting ranges in peak fitting Athena (Ravel, Bruce) 3. Re: Setting ranges in peak fitting Athena (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Jul 2015 00:14:18 +0000 From: Kenneth Latham <Kenneth.Latham(a)uon.edu.au> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Setting ranges in peak fitting Athena Message-ID: <CY1PR02MB1416E3DBC230406B078F9A07AA810(a)CY1PR02MB1416.namprd02.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken ------------------------------ Message: 2 Date: Fri, 24 Jul 2015 13:14:03 +0000 From: "Ravel, Bruce" <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Setting ranges in peak fitting Athena Message-ID: <xp7hq5h11j0ygmcc2btiht0f.1437743641853(a)email.android.com> Content-Type: text/plain; charset="us-ascii" Hi Ken, I'm sorry, but I don't quite understand your question. And I have no idea what casaXPS is, so that reference doesn't help me. Are you asking whether you can put gaps in the fit range? B On July 23, 2015, at 8:16 PM, Kenneth Latham <Kenneth.Latham(a)uon.edu.au> wrote: Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Two postdoctoral positions
by Anatoly I Frenkel 27 Jul '15

27 Jul '15

Dear subscribers, Please pass along this information to anyone who may be interested in this opportunities. Physics Department of Yeshiva University in New York City has two openings for postdoctoral research associate positions, beginning in September 2015. The first position is for the project: "Collaborative research: Toolkit to characterize and design bi-functional nanoparticle catalysts." The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II and other synchrotrons for X-ray absorption spectroscopy measurements. Required qualifications: Ph.D. in physics, chemistry or materials science, expert knowledge of XAS methods, including analysis and modeling of nanoparticles, and experience with in situ characterization methods by XAS and other techniques. The second position is for the project "Multidisciplinary research for the advancement of filtration materials: Uptake, decomposition, and catalysis for Agent-POM/MOF Chemistry". The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II and other synchrotrons for high energy XRD-PDF characterization of novel POM/MOF materials in reaction conditions. Required qualifications: Ph.D. in chemistry, chemical engineering or materials science, expert knowledge of XRD-PDF technique and data analysis, experience with analysis of MOFs, experience with in situ and/or operando methods of synchrotron characterization. The research will be performed under the direction of Prof. Anatoly Frenkel. Applicants should forward cover letter with contact information of three references and CV to anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor and Chair, Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

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Setting ranges in peak fitting Athena
by Kenneth Latham 24 Jul '15

24 Jul '15

Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken

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Plotting chi(k) linear combination fit in energy
by Ellen Daugherty 21 Jul '15

21 Jul '15

Hello, I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: "chi data cannot be plotted in energy." Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue. Thank you! Ellen -- Ph.D. Candidate Research Assistant, Borch Lab <http://borch.agsci.colostate.edu/> Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/

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Artemis Crashing on Opening Project Files (Windows 7)
by alexander.thoma＠diamond.ac.uk 20 Jul '15

20 Jul '15

Hi all, I couldn't seem to find anything like this on the mailing list, I'm having issues reopening saved Artemis (0.9.21) projects on Windows 7, the program opens and runs through the 'importing' text in the bottom left of the control window before shutting down immediately with no error message or warning before any other windows appear. The problem seems to occur sporadically with projects with fits from crystal structures and all the time with those done with quick first shell fits, and doesn't occur with project files where no fits have been made. Attached is the log file for one of the non-opening projects, any suggestions? Many thanks, Alex -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Bug report - autosave on mac
by Jean-Baptiste ABBE 16 Jul '15

16 Jul '15

Hi everybody, I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days. Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue. Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens : 1) athena launch, a little bit longer than usual 2) a box appear to give me choice to recover data by importing it from autosave or not 3) I can’t select anaything and the rainbow wheel of death appears. After a few hours, nothing changes… and I have to terminate the programm manually. So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions : https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html> https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.h… <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html> I tried to find the autosave file : nothing I tried to uninstall and reinstall macports : nothing I tried to uninstall macports and install the demeter-devel : nothing In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment. I will try again other solutions, but I will gladly accept any kind of help to solve my issues. Thank you ABBE J-Baptiste

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phase problem copper
by Neeb, Matthias 15 Jul '15

15 Jul '15

Dear all, I have a standard exafs spectrum of copper K-shell and everything looks as expected (Chi(E), Chi(k), Chi(R), Chi(q) …) when using Demeter 0.9.21 . However the phase spectrum of (Chi(q)) appears quite different to literature (e.g. B.K. Teo, Inorganic Chemistry Concepts 9; Martens et al, PRB 17, p1481 (1979), i.e. positive slope, a factor of ~10 larger values on y-axis. Any reason why? Thanks for your answer in advance. Regards, Matthias ________________________________________________________________________ Matthias Neeb Helmholtz-Zentrum-Berlin fuer Materialien und Energie - senior scientist - ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
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. 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. > > > > > *************************************** > > >

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