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

Larch - LCF error
by Lily Schacht 15 Mar '19

15 Mar '19

Hi, all. I’m attempting to perform LCF on a large number of noisey XANES scans. I normalized and rebinned the scans in Athena before importing into Larch using the GUI. When I try to fit a scan I get this error: Traceback (most recent call last): File "C:\Users\lilys\xraylarch\share\larch\plugins\xasgui\lincombo_panel.py", line 812, in onFitOne self.do_fit(form['group'], form) File "C:\Users\lilys\xraylarch\share\larch\plugins\xasgui\lincombo_panel.py", line 797, in do_fit self.parent.show_subframe('lcf_result', ResultFrame) AttributeError: 'SplitterWindow' object has no attribute 'show_subframe' I’ve tried exporting scans from Athena as .xmu and got the same error. Has anyone seen this before or have any advice? I’m using Larch 0.9.41 and Demeter 0.9.26. My guess is that this is a data format problem not a result of ugly data but for what it’s worth, I tried LCF in Athena and the program either crashed (assuming memory issue) or gave nonsensical results (maybe convergence issue). Thanks, Lily Schacht

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How to use Larch as function server
by ASAKURA, Hiroyuki 14 Mar '19

14 Mar '19

Dear all, I would like to use Larch as an external function server. I'm a Python novice, but if I understand correctly, the present server (larch -r) provides access to a Larch process controllable with xmlrpc from outside. However, I would like to do something like below to achieve looser coupling with my future code (maybe not in python). How can I do that? I appreciate any suggestion for my first step to go, though I guess it is a bit far from the Larch way. ### client.py (not a working code) from six.moves.xmlrpc_client import ServerProxy import os, json def main(): s = ServerProxy("http://127.0.0.1:4966/", allow_none = True) response = s.read_ascii(os.path.abspath("/path/to/xas/data")) # I expect a JSON or python dict with keys like "energy", "mu", etc. data = response response = s.pre_edge(data) # data is a JSON or python dict with keys like "energy", "mu", etc. if __name__ == '__main__': main() ### client.py end I guess one can write some sort of function wrapper, if one wants. ### server.py (not a working code) from six.moves.socketserver import ThreadingMixIn from six.moves.xmlrpc_server import SimpleXMLRPCServer, SimpleXMLRPCRequestHandler import json import larch from larch_plugins.xafs import find_e0, pre_edge, autobk from larch_plugins.io import read_ascii class LarchServer(ThreadingMixIn, SimpleXMLRPCServer): def __init__(self, *args, **kw): super().__init__(*args, **kw) self.larch = larch.Interpreter(with_plugins=True) self.larch.run_init_scripts() self.register_introspection_functions() class LarchRequestHandler(SimpleXMLRPCRequestHandler): def __init__(self, *args, **kw): super().__init__(*args, **kw) def _dispatch(self, method_name, args): return getattr(self, method_name)(*args) ### wrapper function to Larch function ### Do something nice to convert the file into processed data as JSON or a python dict def read_ascii(self, filepath): data = read_ascii(filepath, _larch=larch) # Return processed data as JSON, for example. return json.dumps(data) def main(): server = LarchServer( ("127.0.0.1", 4966), requestHandler = LarchRequestHandler, logRequests = None, allow_none = True ) server.serve_forever() if __name__ == '__main__': main() ### server.py end -- ASAKURA, Hiroyuki (Ph.D) Program-Specific Senior Lecturer (ESICB) T. Tanaka Lab., ESICB, Kyoto University, Japan asakura(a)moleng.kyoto-u.ac.jp http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/

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XES calculations in Feff9.
by FonsPaul 08 Mar '19

08 Mar '19

I have been attempting to use Feff9 to calculate x-ray emission spectra. In short, it would appear that one only exchanges the XANES card with the XES card, however, there appears to be nothing in the documentation that clearly states where the output is directed or how it is labeled. The most logical output would be xmu.dat and the spectra is clearly different when the XANES card is swapped out with the XES card. The only column in the xmu.dat card that appears to make sense to be XES spectra would be the mu0 column as it is positive definite while the chi, column, for example, goes negative and appears to be an interference pattern. Can any one shed some light on this? Also while the documentation states that the XES card takes the form “XES emin emax estep”, the example for GeCl4 included with jfeff uses the options “XES 8 0.05 0.0” whereas the jfeff example file for XES of BN uses “XES -20 20 0.2”. While the second example makes sense, I don’t understand the meaning of the card values used for the GeCl4 molecule example. This is especially relevant as I wish to calculate XES for an epoxy polymer and I have no idea what the fields mean. Thanks for help on this in advance!

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Installation of Athena on Linux Ubuntu
by MOHAMED NAJI 07 Mar '19

07 Mar '19

Dear All, I would like to install Athena in my Linux Ubuntu 16.04 OS. Any idea on how to and if there is already a software develloped for Linux OS. I searched but didn't find it and I'm wondering if someone has already developed it. Thank you Mohamed Naji --

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Re: [Ifeffit] cant open Athena project
by fred.mosselmans＠diamond.ac.uk 07 Mar '19

07 Mar '19

Dear Antony, Your data type for these files is xanes, that won't give a chi set for artemis to read it in. You need to change the datatype to mu€ under the group tab in athena Cheers Fred Message: 1 Date: Thu, 7 Mar 2019 07:44:30 +0000 From: Antony Burnham <Antony.Burnham(a)anu.edu.au> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Can't open Athena project Message-ID: <MEAPR01MB4486896DFADAA39ADB94E966A24C0(a)MEAPR01MB4486.ausprd01.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" I'm having trouble opening my Athena project in Artemis. This contains two transmission spectra of zirconium phases. They plot just fine in Athena but when I try to import them in Artemis it doesn't recognise that there are any files at all in the project (except that one of the two spectra does display in the plot window). There's just a blank space in the left hand pane where the list of files usually appears. I don't have this problem with any of my fluorescence data from the same experiment. And when I have an Athena project with a mix of fluo and transmission spectra, only the former are listed in the import window. I attach the project and the two files that went into it, in the hope that someone can tell me what I (or the software) did wrong. Regards, Antony Burnham

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Error when first opening Athena on Mac
by Laura E Wasylenki 05 Mar '19

05 Mar '19

Hello, I’ve just attempted to install Demeter on a Mac running OS 10.13.6 (High Sierra). When I open Athena, the XAS processing window appears, but then a warning window appears on top of it that says “Demeter::Templates::D” used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm. I think a line number follows, but it is cut off. The warning contains several more lines that are identical to that one, except that D is replaced by other letters. When I dismiss the warning window by clicking “OK,” Athena and Perl just close down. Has anyone seen this, and does anyone know the solution? Thank you! —Laura ____________________________ Dr. Laura Wasylenki Associate Professor School of Earth and Sustainability Department of Chemistry & Biochemistry Northern Arizona University PO Box 5698, 700 S Osborne Drive Flagstaff, AZ 86011 laura.wasylenki(a)nau.edu<mailto:laura.wasylenki@nau.edu>

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Re: [Ifeffit] Ifeffit Digest, Vol 193, Issue 4
by Christopher Chantler 03 Mar '19

03 Mar '19

PS Simon, we are just around the corner [physics] and also link up with the Dementia work, so you might just drop across and have a chat / meeting! -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <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: Monday, 4 March 2019 10:06:37 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 193, Issue 4 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: Cu K edge XANES stds (Simon James) ---------------------------------------------------------------------- Message: 1 Date: Sun, 3 Mar 2019 23:06:19 +0000 From: Simon James <s.james(a)florey.edu.au> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Cu K edge XANES stds Message-ID: <A9A1ED50-AC0D-47F8-9D5D-2208001097E1(a)florey.edu.au> Content-Type: text/plain; charset="utf-8" Hi Drew, Thank you for your swift reply. Apologies for the delay in my response but I was dragged in to other matters. Appreciate the data and ref. Regarding the sanity check I have collected some spatially resolved Cu XANES ?maps? of cultured cells and some of the standards I collected during the run are horribly compromised for unclear reasons and I just wanted some clean data to reference while I work on cleaning up (to the degree possible) my standards. Thanks again. Cheers, Simon Simon James PhD Senior Research Officer NHMRC-ARC Dementia Research Development Fellow Melbourne Dementia Research Centre University of Melbourne The Florey Institute of Neuroscience and Mental Health Web: www.florey.edu.au<http://www.florey.edu.au> On 28 Feb 2019, at 2:51 am, Latta, Drew E <drew-latta(a)uiowa.edu<mailto:drew-latta@uiowa.edu>> wrote: Hi Simon, Since you are just looking for a sanity check (on what??) here are some Cu-S standards for you. They were published in DOI: 10.1021/es304736y. The Cu-cys sample is not a pure phase, but probably a mixture of cysteine/cystine. But it is likely mostly Cu(I). Further discussion is available in the SI of the paper above. The file is from an old, old version of Athena (0.8x)... hopefully it works for you. Best, Drew Latta ====================================== Drew E. Latta, Ph.D. Asst. Research Scientist The University of Iowa Civil and Environmental Engineering/IIHR 4105 Seamans Center Iowa City, IA 52242 Ph. 319-936-0034 email. drew-latta(a)uiowa.edu<mailto:drew-latta@uiowa.edu> ====================================== -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Simon James Sent: Tuesday, February 26, 2019 3:18 PM To: Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> Subject: [Ifeffit] Cu K edge XANES stds Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I?m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit <Cu_Samples_athena.prj>_______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Cu K edge XANES stds
by Simon James 03 Mar '19

03 Mar '19

Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I’m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC

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*****SPAM*****Creating EXAFS coefficient file for reverse monte carlo simulation
by tolga.ulucan＠metu.edu.tr 03 Mar '19

03 Mar '19

Hello everyone, I have synchrotron XRD and XAFS(L3 Tb edge) data on Al90Tb10 metallic glass alloy that i want to use them as constraints in a reverse monte carlo simulation(RMC_POT). RMC_POT manual says i need 2 files for XAFS. 1st chi(k)-k file which i exported from athena as normalized data and 2nd exafs coefficient file which i don't understand what it is or how to create it. I was wondering if anyone can help me on how to create this file or point me on a direction to get more info on this? Best wishes, Tolga Han Ulucan

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Data on Cd5H2(PO4)4·4H2O
by 1510405＠tongji.edu.cn 02 Mar '19

02 Mar '19

Hi all, I have acquired Cd L3-edge XANES spectra of my sample and some Cd standards for LCF analysis. However, I lack the spectra of Cd5H2(PO4)4·4H2O, which was important to my analysis. Therefore, I was wondering if anyone could share the Cd L3-edge XANES data of Cd5H2(PO4)4·4H2O with me? Best regards, Sicong Lei

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