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

Amplitude ratios greater than 100%
by Raj kumar 01 Apr '19

01 Apr '19

Dear All, With the attached CIF file, i have generated chi and other files. In turn, for some paths, i have found amplitude ratios are greater than 100% (even it is reaching few thousands % for some paths - chi file also attached with this email). I know, it is meaningless. I would like to know, why am i getting these weird ratios? What is wrong with the CIF file? Thanks, Raj

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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 18 Mar '19

18 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 07 Mar '19

07 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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