March 2019 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 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: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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Can't open Athena project
by Antony Burnham 06 Apr '19

06 Apr '19

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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Demeter question and Larch
by Patridge, Christopher 27 Mar '19

27 Mar '19

Hi everyone, A Demeter question - Is the memory limit hard set in Athena? I know that I can change the 50 dataset limit, but can I increase the memory to handle more data as I have a relatively large set of spectra (~150)? I have installed and tested Larch, but I do not see an option to run difference spectra in Larch GUI unless I missed something? I am running windows virtualization (win 7 - 64 bit) Demeter if that affects the memory question. Thanks everyone, Chris ********************************************** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patridgc(a)dyc.edu<mailto:patridgc@dyc.edu>

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demeter on Mac 10.14.3 Mojave
by Ping, Yuan 19 Mar '19

19 Mar '19

Hello, I have a new mac laptop with Mac 10.14.3 Mojave and would like to install demeter in it. Following the steps in the website, everything worked ok during the installation. However, when I finally typed “athena” in the terminal, the following warning showed up. If I clicked OK, the Athena will just quit and gave a message “perl5.26 quit unexpectedly”. The same thing for Artemis. Hephaestus showed the same warning, but still works after clicking OK. Any clue to fix this problem? [cid:image001.png@01D4DDCA.F5FB5AD0] Thanks a lot! Yuan

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Peaks in Background Subtraction in Athena
by Nathan Nakamura 18 Mar '19

18 Mar '19

Hello, I am working on some data processing of ZrO2 thin films collected in fluorescence mode, and had a question regarding the background subtraction in Athena. When I use the default values, I see a large negative spike in the background curve (shown in BGsubtract1.png). I can vary the spline clamps and other parameters to reduce this (BGsubtract1.copy), but it does not seem to have any significant effect on the final EXAFS (EXAFScompare.png). My question is, do large spikes/instabilities on the edge like this need to be accounted for, or are they ok as long as the background fit after the edge seems fine? My thought is that as long as the EXAFS is not significantly affected, it should be fine, but I do not have a good sense for how the presence of this peak may impact the background curve beyond the absorption edge. I have also attached the project file in Athena for reference. Thanks, -Nathan

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Question on XES in FEFF
by FonsPaul 18 Mar '19

18 Mar '19

I wrote a couple of days ago asking about XES calculations in FEFF9. But I didn't hear anything back so I am rephrasing the question with a little more detail. I am calculating XES for organic molecules and used the following input. CONTROL 1 1 1 1 1 1 EDGE K EXCHANGE 0 0 1.0 FMS 5.1 LDOS -30. 15. .1 PRINT 5 0 0 0 0 0 AFOLP 1.3 S02 1.0 SCF 4.5 0 30 .2 1 XES 8 0.05 0 The XES output is shown from what I understand in the xmu.dat file in the chi column, however plotting this data shows a curve that is not positive definite. As I don’t think there is such a thing as negative emission, this probably means that my understanding is less than complete. The FEFF manual is also not very helpful on this issue and says nothing about the XES emission output. On a related question, the Feff9 docs (http://monalisa.phys.washington.edu/feff/Docs/feff9/feff90/feff90_users_gui…) specify that the XES card has the following options: XES emin emax estep But the examples that come with JFEFF seem to show options that don’t make sense with this definition: BN crystal: XES -20 20 0.2 Cu: XES 8 0.07 0.0 GeCl4 (molecule): XES 8 0.05 0.0 It is hard to understand how an emax value of 0.05 or 0.07 makes any sense. Does anyone know that the correct definitions are? Perhaps the documentation should be updated as well.

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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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