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

Question about parameters of principle components analysis (PCA)
by 雷思聪 26 Jan '19

26 Jan '19

Hello, I see in many publications the indicator values (IND) numbers used to evaluate how many components are included, and SPOIL value used to evaluate quality of target transform in principle components analysis (PCA). However, they are obtained from PCA performed on SIXpack, rather than Athena (version 0.9.26). Hence, I wonder if I can get similar parameters after running of PCA in Athena? If not, how do I evaluate the PCA results? Thanks for your help!

2 1

Larch flattening
by Kirill Lomachenko 26 Jan '19

26 Jan '19

Dear Matt, I have a question and a comment regarding Larch. I would appreciate if you could have a look. 1) The flattening algorithm for XAS in Larch works differently with respect to Athena when linear post-edge function is used for normalization. In Larch the normalized spectrum is always fitted by a parabola for flattening, no matter which function was used for normalization. It works fine when the post-edge function is also a parabola, but when it is a straight line, the resulting flattened spectrum does not stick to Y=1, as it is expected to do (and as it does in Athena). My question is: is it a bug or a feature? Just in case, I made some minor modifications in the pre_edge.py file that allow to get the same results as in Athena when linear post-edge is used. Maybe these corrections are a bit clumsy, but it seems to work. If anyone needs, I can share. 2) There is a typo in the larch web-manual in the description of the nnorm parameter of the pre_edge() function. It is stated that it is the number of terms in the fitting polynomial (i.e., 1+degree) whereas it seems that it is just its degree. So, nnorm=1 corresponds to a linear function and nnorm=2 to quadratic. In the gui help it is partially corrected, but the phrase "Default=3 (quadratic)" stays. It is not critical at all, but may be misleading for beginners... Using the possibility, I would like to thank you for all the great work you are doing on Larch. It really helps for large datasets! All the best, Kirill -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

2 1

Re: [Ifeffit] Dynamic XAFS Simulations?
by Gentle, Cecilia M 24 Jan '19

24 Jan '19

Dear Hunter, I also recommend you to join the mailing list for the ultrafast laser community: dyna(a)listes.epfl.ch [to subscribe: dyna-subscribe(a)listes.epfl.ch] Best, Cecilia Gentle PhD Candidate, Department of Chemistry University of Illinois at Urbana-Champaign https://www.vanderveen-lab.com/ -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, January 23, 2019 4:54 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 191, Issue 13 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. Dynamic XAFS Simulations? (Hunter Allison) 2. Re: Dynamic XAFS Simulations? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 23 Jan 2019 13:26:21 -0800 From: Hunter Allison <hgalliso(a)uci.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Dynamic XAFS Simulations? Message-ID: <CAH6J0e_vk1n4viX8H5A4vX=SRL0e5NQHmSZGEQ43wVxBzpwo5Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, I'm a graduate student at the University of California, Irvine. Firstly, thank you for all the copious resources. It is a treasure trove of information and a beacon of light for someone just starting out. Let's begin with some brief background. In my research group, we intend to perform pump-probe spectroscopy with attosecond x-ray probes. The Professor says that we can use XAFS to study how the electrons move on these very short timescales. While the system is being setup and other experiments are being conducted, my Professor wants me to figure out how to do simulations of XAFS. This is a bit of a daunting order, since I've never simulated anything before and only have basic programming knowledge. The only direction I have is, "Try Google.". So, today, I've been "trying Google" and found my way to here. Since, I don't really know what I'm doing, I thought I try asking and finding out if anyone else does this sort of thing: How/where does one do simulations of dynamic XAFS? Where would I get started? (Please forgive me if this question has been answered somewhere else or if it seems profoundly dumb or too broad. I'm really just looking for some more direction. Perhaps, it could be that nobody does this and, in that case, I need to figure out how to model this myself. Wow! That thought seems daunting.) For example, let's say I want to find out how the x-ray adsorption of a carbon foil like Graphene would change on attosecond time scales as it's heated by a femtosecond laser and electrons move. Is there a program or code out there that people use to model this sort of thing?

2 1

Dynamic XAFS Simulations?
by Hunter Allison 23 Jan '19

23 Jan '19

Hi, I'm a graduate student at the University of California, Irvine. Firstly, thank you for all the copious resources. It is a treasure trove of information and a beacon of light for someone just starting out. Let's begin with some brief background. In my research group, we intend to perform pump-probe spectroscopy with attosecond x-ray probes. The Professor says that we can use XAFS to study how the electrons move on these very short timescales. While the system is being setup and other experiments are being conducted, my Professor wants me to figure out how to do simulations of XAFS. This is a bit of a daunting order, since I've never simulated anything before and only have basic programming knowledge. The only direction I have is, "Try Google.". So, today, I've been "trying Google" and found my way to here. Since, I don't really know what I'm doing, I thought I try asking and finding out if anyone else does this sort of thing: How/where does one do simulations of dynamic XAFS? Where would I get started? (Please forgive me if this question has been answered somewhere else or if it seems profoundly dumb or too broad. I'm really just looking for some more direction. Perhaps, it could be that nobody does this and, in that case, I need to figure out how to model this myself. Wow! That thought seems daunting.) For example, let's say I want to find out how the x-ray adsorption of a carbon foil like Graphene would change on attosecond time scales as it's heated by a femtosecond laser and electrons move. Is there a program or code out there that people use to model this sort of thing?

2 1

XAS data for Nickel Chloride
by Gill, Simerjeet 18 Jan '19

18 Jan '19

Hi, I am working with a molten salt system with Nickel Chloride as one of the components. If you have measured XAS data on anhydrous and hydrated Nickel Chloride at RT and elevated temperature, I would appreciate you sharing your data. Thanks in advance for your help! Simer Simerjeet K Gill, Materials Scientist, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

1 0

求助Athena软件32位电脑安装包，谢谢
by 2225295803 16 Jan '19

16 Jan '19

你好，我是天津大学马新宾课题组的硕士研究生袭雨杉，我的电脑是32位的，请问有32位的EXAFS分析软件Athena吗？可以发给我吗？谢谢

2 1

Advice on using Athena for XANES LCF on spectra with a small edge step?
by Mike Massey 16 Jan '19

16 Jan '19

Hi All, Does anyone have advice for LCF of spectra with a small edge step? I've recently found myself with more and more issues fitting spectra like the one shown in the attached photo, where the spectrum is of good quality, but the fits end up not working out due to normalization (as far as I can tell). Sadly, I have so far ended up just throwing these fits out, but I'm hoping there is a better solution out there that someone might be able to recommend. One solution is "get more of the element of interest," as a beamline scientist recently told me. I'm just reluctant to really load it up in the data collection, because at 2 keV I get nervous about artifacts like self-absorption. Is there a better way? What am I missing? Thanks for your thoughts, Mike

5 8

Nickel Chloride XAS data at RT and 320C
by Gill, Simerjeet 15 Jan '19

15 Jan '19

Hi, I am working with a molten salt system with Nickel Chloride as one of the components. If you have measured XAS data on anhydrous and hydrated Nickel Chloride at RT and 320C, I would really appreciate if you could share the raw data with me. Thanks in advance for your help! Simer Simerjeet K Gill, Materials Scientist, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973 -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Friday, January 11, 2019 12:20 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 191, Issue 7 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: Standard deviation of R value (Matt Newville) 2. Re: Standard deviation of R value (Anatoly Frenkel) 3. Re: Standard deviation of R value (Erin Finley) ---------------------------------------------------------------------- Message: 1 Date: Fri, 11 Jan 2019 10:04:49 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Standard deviation of R value Message-ID: <CA+7ESbo=kOiHZx9skxwv6qzHADH9q5Rh2u=Y8np+5AB-XqRyiA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Erin, On Fri, Jan 11, 2019 at 8:19 AM Erin Finley <efinley9033(a)gmail.com> wrote: > Hello, I see in many publications the R value reported with a standard > deviation. However, when I look at my resulting data from a fit I > don't see one listed. I am still new to EXAFS research and so I am > wondering where I can get this information. I am assuming I need to > calculate it from another parameter I am just not sure which one. > > The uncertainties in R are typically in the fit report. But also, we typically refine a "delR" parameter that is R - Reff, where Reff is the distance (half path-lengh) for the scattering path. So, if you don't see an uncertainty reported for R but do see an uncertainty for delR (or whatever parameter name you used), use that. The uncertainty in R will (normally) be the uncertainty in delR. If I'm misunderstanding the question, pleas give more details about what you are doing. --Matt Thanks for your help! > Cheers, > > -- > Erin Finley > PhD Candidate > Brgoch Research Group > Department of Chemistry > University of Houston > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-252-0431

1 0

Standard deviation of R value
by Erin Finley 11 Jan '19

11 Jan '19

Hello, I see in many publications the R value reported with a standard deviation. However, when I look at my resulting data from a fit I don't see one listed. I am still new to EXAFS research and so I am wondering where I can get this information. I am assuming I need to calculate it from another parameter I am just not sure which one. Thanks for your help! Cheers, -- Erin Finley PhD Candidate Brgoch Research Group Department of Chemistry University of Houston

4 3

Postdoc at CHESS
by Kenneth David Finkelstein 11 Jan '19

11 Jan '19

Would you please post the attached announcement of a Postdoc position at CHESS? Cornell High Energy Synchrotron Source (CHESS) at Cornell University is completing a major upgrade of its facilities and is seeking a Postdoctoral Associate interested in using x-ray spectroscopy to study biology, chemistry, materials science, and catalysis. Thank you, Ken Finkelstein

1 0

Unwanted rescaling of energy axis when importing ascii file into Athena (Demeter 0.9.26)
by Lukas Grote 09 Jan '19

09 Jan '19

Hello, I am reporting an apparent bug in Athena (Demeter 0.9.26, Windows 10). When I import high energy resolution XAS data from an ascii file, the energy axis is automatically rescaled to 1.2eV step size, thus drastically reducing the resolution of the data. When the imported data has energy steps larger than 1.2eV, no rescaling occurs. This issue may be similar to the one reported in March 2018 under the topic "Athena (Demeter 0.9.26) does not import all datapoints from ascci file". However, the issue I am seeing always results in 1.2eV steps in the imported data. If my original file hast 0.3eV steps, the number of points is reduced by a factor of 4. If it has 0.6eV steps, the number of points is reduced by a factor of 2. I couldn't find any option to switch this recaling on / off, or to change the target energy step size. The problem does not occur with Demeter 0.9.25. Attached please find two screenshots of the data import dialog for both versions of Demeter. The plots show the difference in energy scale. I also attached the original data file "no_rebin.dat" as well as spectra exported from both Demeter versions, one of them showing the 1.2eV steps. Thank you and all the best, Lukas -- Lukas Grote University of Hamburg Center for Hybrid Nanostructures Institute for Nanostructures and Solid State Physics Luruper Chaussee 149, Bld. 600, Room 2.62 22761 Hamburg Germany +49 40 42838 1614

3 2

Fwd: FW: Postdoctoral Research Associate positions
by Anatoly Frenkel 08 Jan '19

08 Jan '19

Dear IFEFFIT mailing list subscribers: Sharing this on behalf of colleagues. The MSEE EFRC at Brookhaven National Laboratory has two postdoctoral positions available immediately. Please find the advertisements with contact information in the attachments. Please forward this info to anyone you believe may be interested in this opportunity. While the both positions expect expertise in multiple methods, I was requested to pass it along to this list specifically because of the PI's interest to develop strong XAFS component for the purpose of this project. Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Stony Brook University *From:* Lee, Patricia A *On Behalf Of *Ecker, Lynne *Sent:* Tuesday, January 08, 2019 11:32 AM *Subject:* Postdoctoral Research Associate positions Dear Colleagues, We are seeking candidates for postdoctoral Research Associate positions within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments at Brookhaven National Laboratory. Information about the positions is summarized below and two flyers are attached to this message. We would appreciate you sharing these opportunities with students, postdocs and other contacts. Please contact us if you have questions. Best regards, Lynne E. Ecker, Chair Nuclear Science and Technology Department Brookhaven National Laboratory Tel: (631) 344-2538 Email: lecker(a)bnl.gov James Wishart, Director, Molten Salts in Extreme Environments EFRC Brookhaven National Laboratory Tel: (631) 344-4327 Email: wishart(a)bnl.gov ***** The Energy Frontier Research Center on Molten Salts in Extreme Environments (EFRC/MSEE) at Brookhaven National Laboratory (BNL) is pleased to announce that we are hiring Postdoctoral Research Associates. These positions will be part of a collaborative, multi-institution team performing electrochemical, structural (x-ray and neutron), spectroscopic (optical and x-ray), kinetics, and computational studies of molten salt and solute structure, speciation and reactivity in the bulk and at interfaces. The MSEE Center’s scientific mission is to provide fundamental, atomic-level understanding of bulk and interfacial molten salts, and the effects of molten salt exposure on interfaces, in support of their use in molten salt nuclear reactors. To this end, we are developing novel in-situ synchrotron, electrochemical and electron microscopy techniques for investigating high-temperature molten salts. Two positions require a Ph.D. degree in chemistry, physics, materials science or a related field. The interdisciplinary research will focus on structural, spectroscopic, and electrochemical investigations of molten salts, solutes in them, and liquid-solid interfaces. A third position requires a Ph.D. degree in chemistry or a related field and primarily involves pulse radiolysis investigations of reaction kinetics in molten salts, in pure form and in mixtures containing other salts and metal ions. To find detailed descriptions of the position requirements and apply online, go to https://jobs.bnl.gov and search for “molten salts.” For Job ID 1411, hands-on experience in either X-ray diffraction, reflectivity, or spectroscopy is required. For Job ID 1419, demonstrated experience in electrochemical methods or working with molten salts is required. Experience with the chemical and physical properties of materials at high-temperature is highly desirable for both these positions. For Job ID 1564, experience with experimental, time-resolved studies of reaction kinetics and mechanisms is required and experience with pulse radiolysis or laser flash photolysis techniques is highly desirable. ***** *Patty Lee* *Administrative Assistant to * *Lynne E. Ecker, Chair* *Nuclear Science and Technology Department* *Brookhaven National Laboratory* *Building 817* *Upton, New York 11973* *(tel.) 631-344-7040* *(fax) 631-344-3957* *e-mail: patty(a)bnl.gov <patty(a)bnl.gov>*

1 0

Postdoctoral Research Associate positions
by Ecker, Lynne 08 Jan '19

08 Jan '19

Dear Colleagues, We are seeking candidates for postdoctoral Research Associate positions within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments at Brookhaven National Laboratory. Information about the positions is summarized below and two flyers are attached to this message. We would appreciate you sharing these opportunities with students, postdocs and other contacts. Please contact us if you have questions. Best regards, Lynne E. Ecker, Chair Nuclear Science and Technology Department Brookhaven National Laboratory Tel: (631) 344-2538 Email: lecker(a)bnl.gov<mailto:lecker@bnl.gov> James Wishart, Director, Molten Salts in Extreme Environments EFRC Brookhaven National Laboratory Tel: (631) 344-4327 Email: wishart(a)bnl.gov<mailto:wishart@bnl.gov> ***** The Energy Frontier Research Center on Molten Salts in Extreme Environments (EFRC/MSEE) at Brookhaven National Laboratory (BNL) is pleased to announce that we are hiring Postdoctoral Research Associates. These positions will be part of a collaborative, multi-institution team performing electrochemical, structural (x-ray and neutron), spectroscopic (optical and x-ray), kinetics, and computational studies of molten salt and solute structure, speciation and reactivity in the bulk and at interfaces. The MSEE Center's scientific mission is to provide fundamental, atomic-level understanding of bulk and interfacial molten salts, and the effects of molten salt exposure on interfaces, in support of their use in molten salt nuclear reactors. To this end, we are developing novel in-situ synchrotron, electrochemical and electron microscopy techniques for investigating high-temperature molten salts. Two positions require a Ph.D. degree in chemistry, physics, materials science or a related field. The interdisciplinary research will focus on structural, spectroscopic, and electrochemical investigations of molten salts, solutes in them, and liquid-solid interfaces. A third position requires a Ph.D. degree in chemistry or a related field and primarily involves pulse radiolysis investigations of reaction kinetics in molten salts, in pure form and in mixtures containing other salts and metal ions. To find detailed descriptions of the position requirements and apply online, go to https://jobs.bnl.gov and search for "molten salts." For Job ID 1411, hands-on experience in either X-ray diffraction, reflectivity, or spectroscopy is required. For Job ID 1419, demonstrated experience in electrochemical methods or working with molten salts is required. Experience with the chemical and physical properties of materials at high-temperature is highly desirable for both these positions. For Job ID 1564, experience with experimental, time-resolved studies of reaction kinetics and mechanisms is required and experience with pulse radiolysis or laser flash photolysis techniques is highly desirable. ***** Patty Lee Administrative Assistant to Lynne E. Ecker, Chair Nuclear Science and Technology Department Brookhaven National Laboratory Building 817 Upton, New York 11973 (tel.) 631-344-7040 (fax) 631-344-3957 e-mail: patty(a)bnl.gov<mailto:patty@bnl.gov>

1 0

regarding installation
by mona gupta 23 Dec '18

23 Dec '18

respected sir/ma'amwhenever I use Athena / Hephaestus on the time of plotting derivatives ..its hangs and after some time it shows per interpreter is not responding,,, so it is not working properly, even I am puzzled.please give me quick reply facing such problem ..even reinstalled it.RegardsMrs Mona GuptaAssistant ProfessorDepartment of PhysicsGovt PG College KotdwarH N B Garhwal UniversityUttarakhand (India)

2 1

Looking of a K-edge spectrum of maghemite
by Lorenzo Stievano 17 Dec '18

17 Dec '18

Hi everybody, daes anybody have in his repository a Fe K-edge XAS spectrum of maghemite (gamma-Fe2O3)? I would need it as a reference material in a study on doped iron oxides. Thanks a lot in advance! Lorenzo

2 1

Question about k-weighting real-world practice and outcomes
by John Ferre 16 Dec '18

16 Dec '18

Dear EXAFS folk, I'm a graduate student in Jerry Seidler's group at the University of Washington, Seattle. I've been doing a numerical and experimental study on how to optimize k-weighting for EXAFS when the total experimental measurement time for a study is constrained, i.e., when you have 1 hour at some given I0 flux and your job is to get the best results, in terms of best fits or cleanest g(R). Can anyone aim me at 'famous' papers (or at least 'standard' papers) on the best use of k-weighting? Also, it would be great if people could informally email me how they, personally, do k-weighting and what their personal experience has been. My email is jbferre(a)uw.edu. Much appreciated! John

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 190, Issue 9
by Christopher Chantler 15 Dec '18

15 Dec '18

Some of our papers explain how to avoid k-weighting and use the actual measured uncertainties to define a fit. Other papers by our group explain that a proper k-weighting would scale the value and the uncertainty by the same amount, so that the net fit should be unaffected. Otherwise this is more like a change of the effective k-range over the fit. -------------------------------------------------------------------------------------- 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: Sunday, 16 December 2018 5:00:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 190, Issue 9 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. Question about k-weighting real-world practice and outcomes (John Ferre) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Dec 2018 17:53:41 -0800 From: John Ferre <jbferre(a)uw.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Question about k-weighting real-world practice and outcomes Message-ID: <CAN2QkxtgJYJsep0BHk3qKgqXu4nhcg-4GRBok_6c3SNfo1-jvA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear EXAFS folk, I'm a graduate student in Jerry Seidler's group at the University of Washington, Seattle. I've been doing a numerical and experimental study on how to optimize k-weighting for EXAFS when the total experimental measurement time for a study is constrained, i.e., when you have 1 hour at some given I0 flux and your job is to get the best results, in terms of best fits or cleanest g(R). Can anyone aim me at 'famous' papers (or at least 'standard' papers) on the best use of k-weighting? Also, it would be great if people could informally email me how they, personally, do k-weighting and what their personal experience has been. My email is jbferre(a)uw.edu. Much appreciated! John

1 0

Sn 2+
by Ditty Dixon 14 Dec '18

14 Dec '18

Dear All, Could someone please share Sn K edge spectra of any Sn(II) sample measured along with Sn metal foil. SnCl2 from Hephaestus seems miss-aligned and Farrel Lytle has only L edge data, Thank you, -- Dr. Ditty Dixon Ramanujan Faculty Electrochemical Power Source Division Central Electrochemical Research Institute (CSIR-CECRI) Karaikudi, India, 630003 Ph:00919400243084

1 0

Mac user
by Wallick, Rachel 12 Dec '18

12 Dec '18

I am trying to install on my Mac (running on Sierra Version 10.12.6), and I followed the instructions to install but when I type in the command “sudo port install xors-server demeter” I get an error that says “command not found.” Has anyone else had this issue? Is there a way to install? Rachel Wallick

2 1

Artemis hung up on importing fpj containing VPaths
by Nicholas Marcella 10 Dec '18

10 Dec '18

Hi All, I'm trying to import an Artemis project that contains VPaths. The import stalls on the "importing VPaths" step. There is no error. The program crashes when I click on the GUI. I tried to recreate this issue and found that the following steps do so: Note: Step 5 is critical. If a fit is not run within the project file, the VPaths are loaded successfully. To recreate: 1) Import FEFF calculation and some data set. 2) Add some number of paths to the data set 3) Mark all paths and Alt+shift+m 4) transfer VPath to plotting list. Plot. 5) Run a basic fit. 6) save and close. Exit Artemis. 7) Open Artemis, try to import the project. p.s. I tried deleting %APPDATA% and doing a reinstall. As for a quick solution: is there anyway I can skip importing VPaths when loading my project file? Thanks! Nick -- *Nicholas J. Marcella* | PhD Student *Materials Science and Chemical Engineering* *Stony Brook University* *Tel: (914)-703-9843* *Structure and Dynamics of Applied Nanomaterials | Brookhaven National Lab <https://www.bnl.gov/chemistry/SDAN/>* *Senator - MSCE | Graduate Student Organization <http://sbgso.org/index.php/about-us/senators>*

1 0

LARCH installation issue in UBUNTU 18
by Uma Mahendra Kumar K 09 Dec '18

09 Dec '18

Dear All, I wanted to install LARCH on Ubuntu 18. And I could not. I have tried several methods (miniconda, Anaconda, from source and the Linux Binaries and even through pip). For several issues , I found answers in Ifeffit mailing list. This is new. lmfit is not able to import 'ufloat'. Actually "ufloat" belongs to "uncertainties". I could not able to link(port) them properly. I need your help to install Larch. the following is the error message Traceback (most recent call last): File "/usr/local/bin/larch", line 58, in <module> import larch File "/root/.local/lib/python2.7/site-packages/larch/__init__.py", line 25, in <module> from .shell import shell File "/root/.local/lib/python2.7/site-packages/larch/shell.py", line 10, in <module> from .interpreter import Interpreter File "/root/.local/lib/python2.7/site-packages/larch/interpreter.py", line 18, in <module> from . import builtins File "/root/.local/lib/python2.7/site-packages/larch/builtins.py", line 22, in <module> from . import fitting File "/root/.local/lib/python2.7/site-packages/larch/fitting/__init__.py", line 20, in <module> from lmfit import (Parameter, Parameters, Minimizer, conf_interval, ImportError: cannot import name ufloat Mahendra Asst Prof of Physics VIT university -Bharat.

2 3

XRS workshop 2019
by Christoph Sahle 09 Dec '18

09 Dec '18

Dear Colleagues, We cordially invite you to attend the Workshop entitled “X-ray Raman scattering spectroscopy - Probing low Z elements using hard X-rays” that will be hosted at the ESRF (Grenoble, France) from 3 to 5 April 2019. Aim and Scope of the workshop: Non-resonant inelastic X-ray scattering from core-electrons, or X-ray Raman scattering (XRS) spectroscopy, is an increasingly popular spectroscopic tool to investigate low energy absorption edges using hard X-rays. The aim of the proposed workshop is to bring together experts and novices in the field of XRS spectroscopy. We will assess and discuss the current status, potential, and future prospects for this emerging inelastic x-ray scattering technique. The interest in XRS is rapidly growing and new end-stations are being designed at 3rd generation synchrotron light sources around the world. The focus of this workshop will be to strengthen the user community, define future research directions and guide the worldwide efforts to build new dedicated end-stations for X-ray Raman scattering spectroscopy. The workshop will consist of contributed talks with ample time reserved for questions and discussion as well as a poster session. The workshop is open to all interested parties, but the number of participants will be limited to approximately 50. The workshop will be divided into 6 sessions: Instrumentation Low-Z elements under extreme conditions Soft condensed matter, statistical systems Correlated electron systems Direct tomography imaging Theoretical approaches You can find more information about this event on the web page (including a link to the registration) [http://www.esrf.fr/xrs-workshop] Kind regards, Ch. Sahle, C. Roméro, G. Lelong, J.-P. Rueff

1 0

Is there a way to see how guessed GDS parameter affects the fitting in Artemis?
by Sergio Tatay 02 Dec '18

02 Dec '18

I was wondering is there is a simple way to see how a change in a guess parameter affects how the fit looks like. I’m a newbie to Artemis, and for the moment the only way I figured to do that is to set that parameter I want to check as def/set and then run the fitting. However, this can be time consuming specially is the model I’m using is elaborate. I would like to know is there is a method to change a single parameter, and then simply evaluate what the results would like leaving all the rest of the parameters unmodified. That would be useful for me, for example in the case of some data with strong background contributions at low R values. Despite, I can try to leave those contributions aside using the window span, fitting sometimes are not as satisfactory as the results I get when I adjust the values by hand. Thanks in advance, Sergio

2 1

Cu and Mn K-edge XANES
by humberto blancomanzur 01 Dec '18

01 Dec '18

Dear all, Can somebody share any from the following XANES spectra together with the reference foil (any spinel composition it will be great)? CuO, Cu2O, Cu1.5Mn1.5O4, and Al2CuO4 (Cu K edge). MnO, MnO2, Cu1.5Mn1.5O4, and Al2MnO4 (Mn K edge). I will be very grateful, Humberto.

2 2

Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 16
by Enyuan Hu 24 Nov '18

24 Nov '18

Thank you very much for the data, professor Frenkel. You can send your student's name to my email. We will acknowledge him/her for the data. Enyuan On Sat, Nov 24, 2018 at 11:29 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. TiO2 XAS spectrum (Enyuan Hu) > 2. Re: TiO2 XAS spectrum (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 Nov 2018 22:06:50 -0500 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] TiO2 XAS spectrum > Message-ID: > < > CAJud35ModfhLUtDpbRFO2NpxRDxeg5yvxfUk+JPOxZ64Cgqqyw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > Can anyone share an XAS spectrum of TiO2? it would be best if a Ti foil > spectrum is also included for calibration. Your help is much appreciated! > > Enyuan >

1 0

TiO2 XAS spectrum
by Enyuan Hu 24 Nov '18

24 Nov '18

Hi all, Can anyone share an XAS spectrum of TiO2? it would be best if a Ti foil spectrum is also included for calibration. Your help is much appreciated! Enyuan

2 1

PhD opportunity at Diamond Light Source: NEXAFS Crystallography
by Sven L. M. Schroeder 22 Nov '18

22 Nov '18

>>> NEXAFS Crystallography: A Novel Approach to Refinement of Proton Positions in Organic Crystal Structures <<<< A PhD studentship for this project is available at Diamond Light Source, for an immediate start. Candidates with an honours degree in Physics, Chemistry, Materials Science, Engineering or related relevant disciplines are eligible to apply. The student will receive a tax-free stipend of 16,760 GBP p.a., for 42 months. The studentship comes with a generous travel budget, to facilitate experiments at other synchrotron sources, e.g. in the US and in other European countries. UK students are eligible to apply. European Union students may be eligible to apply under certain circumstances. Please contact us f you are interested. The student will be registered in the PhD programme at the University of Leeds, with Prof Sven L M Schroeder as lead- and Dr Andrew Scott as co-supervisor. Dr Elizabeth Shotton, Head of Industrial Liaison, at Diamond Light Source will be the Diamond co-supervisor. If you are interested in this position please get in touch as per the contact information provided in the signature below. -- Sven L. M. Schroeder Royal Academy of Engineering Bragg Centenary Chair Diamond Light Soruce Ltd | Harwell Science and innovation Campus | Chilton, Didcot OX11 0DE | UK School of Chemical and Process Engineering | University of Leeds | Leeds LS2 9JT | UK Room 2.41 | Engineering Building T +44 (0)113 343 2401 | F +44 (0)113 343 2384 E s.l.m.schroeder(a)leeds.ac.uk<mailto:s.l.m.schroeder@leeds.ac.uk> | W https://engineering.leeds.ac.uk/staff/690/Professor_Sven_L_M_Schroeder Secretariat: Ms Eve Knaggs E e.knaggs(a)leeds.ac.uk<mailto:e.knaggs@leeds.ac.uk> | T +44 (0)113 343 2498

1 0

data on CdS
by Anatoly Frenkel 17 Nov '18

17 Nov '18

Dear all - if someone could share raw Cd K-edge data of CdS, it would be really helpful! Thank you, Anatoly Frenkel

3 3

Extrating standard deviation value from merged dataset in Athena
by Christian Rein 16 Nov '18

16 Nov '18

Hi, Do anyone know how to obtain the standard deviation value that Athena calculates when merging the data? Best, Christian Christian Rein Postdoc DTU Energy Technical University of Denmark [http://www.dtu.dk/~/media/DTU_Generelt/Andet/DTU_email_logo_01.gif] Department of Energy Conversion and Storage Building 771, room 010 4000 Roskilde Denmark

2 1

LCF and XES
by Samy Ould-Chikh 05 Nov '18

05 Nov '18

Dear, I'm trying to perform LCF using Athena for XES data (Kbeta 13) that has been normalized elsewhere. Combinatorics module is the main motivation. However, LCF module in Athena only use norm mu(E), so that the normalization for XAS data proceed and then it's not possible to perform the fitting. Does anyone know a workaround to perform LCF for XES in Athena, or another alternative software as user friendly ? Many Thanks Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa<mailto:eman.ahmedbahjri@kaust.edu.sa> Website: http://kcc.kaust.edu.sa/Pages/Home.aspx

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 8
by Raj kumar 02 Nov '18

02 Nov '18

Thanks for the clarification, Anatoly! Regards, Raj On Fri, Nov 2, 2018 at 4:04 PM <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: EXAFS of wine (Anatoly Frenkel) > 2. Re: Ifeffit Digest, Vol 189, Issue 2 (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 2 Nov 2018 06:36:57 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] EXAFS of wine > Message-ID: <45D3D1E4-6749-463C-9FE3-259B77345304(a)stonybrook.edu> > Content-Type: text/plain; charset="utf-8" > > John, > > Since when theorists started to need real samples? I thought a simulation > is equally enjoyable. > > Anatoly > > > On Nov 2, 2018, at 12:17 AM, John J Rehr <jjr(a)uw.edu> wrote: > > > > Hi everyone > > > > The spectrum is pretty noisy with all the super Tuscano grapes ( > Alicante, Merlot etc) in the mix to give it?s complex berry character and > the 2016 is supposedly better. > > How about we take some samples to the lab ... ? > > > > John > > > > > >> On Thu, Nov 1, 2018 at 16:07 Anatoly Frenkel < > anatoly.frenkel(a)stonybrook.edu> wrote: > >> I thought this mailing list is an appropriate venue to post a picture > of the bottle of wine I bought yesterday in a store on Long Island. > >> > >> > >> > >> Anatoly_______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 2
by Raj kumar 02 Nov '18

02 Nov '18

Dear Anatoly and Marcus, Thanks for your answers. So in this case, i understood, I shouldn't use the extended XAFS region for the analysis. In the other hand, is it allowed to cut the region till 9150 eV and use the data for the XANES analysis? Regards, Raj On Thu, Nov 1, 2018 at 11:37 PM <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: Bump/oscillating pattern at high energies of EXAFS > (Anatoly Frenkel) > 2. Re: Bump/oscillating pattern at high energies of EXAFS > (Matthew Marcus) > 3. EXAFS of wine (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 1 Nov 2018 17:47:56 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Bump/oscillating pattern at high energies of > EXAFS > Message-ID: > < > CAFsMoZbm2RMVUeRmuoryw9ehVrZQcvx60zHqufmK39oLRoyZ2w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > It is an effect of inhomogeneity of the sample, that is, the variation in > the metal density throughout the X-ray beam footprint. > Anatoly > > > > On Thu, Nov 1, 2018 at 5:34 PM Raj kumar <rajrk37(a)gmail.com> wrote: > > > Dear All, > > > > I have monitored the growth process of YbVO4 nanoparticles using EXAFS. > > Here, nanoparticles were synthesized in water medium. Both initial and > > final products (EXAFS) of the synthesis were measured using the > continuous > > flow approach whereas the intermediate products were recorded, in the > glass > > capillary, using the stopped flow. In the attached figure, you can find > the > > same (all products). At high energies of EXAFS, both initial and final > > measurements show smooth behavior whereas the oscillating pattern/bump > was > > observed for the intermediate states. > > > > Here, my question is: Is the oscillating pattern appearing in the > > intermediate states due to the sedimentation/in-homogeneity of the > product > > in the capillary or it is the characteristic of the synthesis? > > > > With regards, > > Raj > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > >

2 1

EXAFS of wine
by Anatoly Frenkel 02 Nov '18

02 Nov '18

I thought this mailing list is an appropriate venue to post a picture of the bottle of wine I bought yesterday in a store on Long Island. Anatoly

9 10

Postdoc Opportunity in Catalysis Science at SSRL
by Bare, Simon R 01 Nov '18

01 Nov '18

Please see the attached postdoctoral positon available now at SSRL. It is also posted here: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/Pos… Thanks! Simon R Bare Distinguished Staff Scientist SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629 [co_access_logo_text]

1 0

Bump/oscillating pattern at high energies of EXAFS
by Raj kumar 01 Nov '18

01 Nov '18

Dear All, I have monitored the growth process of YbVO4 nanoparticles using EXAFS. Here, nanoparticles were synthesized in water medium. Both initial and final products (EXAFS) of the synthesis were measured using the continuous flow approach whereas the intermediate products were recorded, in the glass capillary, using the stopped flow. In the attached figure, you can find the same (all products). At high energies of EXAFS, both initial and final measurements show smooth behavior whereas the oscillating pattern/bump was observed for the intermediate states. Here, my question is: Is the oscillating pattern appearing in the intermediate states due to the sedimentation/in-homogeneity of the product in the capillary or it is the characteristic of the synthesis? With regards, Raj

3 2

Problem with Athena
by Weronica Linpé 30 Oct '18

30 Oct '18

Hi, I have a problem when looking at the difference scan between two scans. When I move from the start up site to the differnece everything works fine and I get a differnece spectra. Here I can do some changes, but if I want to change which scans I'm using for the difference the program chrashes. Any ideas on why the program chrashes?

2 1

ADDITION - Bug Report: incomplete data import in Athena when energy is given in keV
by Voegelin, Andreas 30 Oct '18

30 Oct '18

Dear Bruce & Ifeffit Mail-List We just found that the problem I described in my previous email for Demeter 0.9.26 does not occur with version 0.9.25. Thus, reinstalling the previous version seems the easiest work around for the moment. Best, Andreas

2 1

Re: [Ifeffit] Bug Report: incomplete data import in Athena when energy is given in keV
by Kirill Lomachenko 26 Oct '18

26 Oct '18

Dear Bruce and dear all, I have the same problem with data import in Athena 0.9.26 that Andreas has just described and that, if I am not mistaken has already been mentioned in this mailing list before. Looking for the possible cause of the problem, in the list of changes made for Athena in the latest version of Demeter I found the following: "Fix a problem processing keV data when using Larch (Thanks to Juan de la Figuera) (See issue #42)" May it be that these modifications are responsible for the observed import bug? (just a guess) Thank you Kirill Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu 25.10.2018 11:40, ifeffit-request(a)millenia.cars.aps.anl.gov пишет: > 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. Bug Report: incomplete data import in Athena when energy is > given in keV (Voegelin, Andreas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 25 Oct 2018 09:39:52 +0000 > From: "Voegelin, Andreas" <Andreas.Voegelin(a)eawag.ch> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Bug Report: incomplete data import in Athena when > energy is given in keV > Message-ID: > <D87798881B7774448873557DA6961A35F019A176(a)EE-MBX3.ee.emp-eaw.ch> > Content-Type: text/plain; charset="utf-8" > > Dear Bruce & Ifeffit Mail-List > > Working with Athena (executable Version 0.9.26 with Ifeffit 1.2.12 on Windows 10), I just noted a problem with data import when energy in the input file is given in keV. > > Attached an example of recently collected Ce L3 edge data (original_format.txt), with the energy in keV in the first column and the DT-corrected and normalized fluorescence signal in column 44. The file contains 2 header rows and 308 lines of data. When this spectrum is loaded into Athena, it consists of only 186 instead of 308 datapoints (see information on spectrum ?original_format,.txt? in Athena project file ?test_bug_data_import_in_keV.prj?). The problem also persisted when I reduced the input file to only two columns, energy and fluorescence data, and seemed not related to file size. The problem occurs on various computers all running with the latest version of Athena. > > Interestingly, the problem does not occur if the energy in the original file is given in eV instead of keV. From the original file, I created an input file ?test_energy_in_keV_eV.txt? in which columns 1 and 4 contain the energy in keV and columns 2 and 5 the energy in eV. When I import the spectrum using any of the columns with energy in eV, the spectrum is loaded correctly and consist of 308 datapoints. If I use any of the two columns with energy in keV, the imported spectrum again contains only 186 datapoints. > > Comparing the mue output files of the spectra read in eV and keV (mue files attached), one can see that incomplete data import starts at 5703 eV, i.e., where the step size in the scan was changed from 2 eV to 0.5 eV. Notably, if I select column 5 containing the energy in eV, but tell Athena that the energy is in keV and needs to be converted to eV, Athena loads all 308 datapoints (although with obviously wrong energy scale). This might suggest that the problem is related to the absolute difference in energy between datapoints rather than to the conversion from keV to eV. > > I tested also other data collected at the Mn K and Tl L3 edges and the problem is the same. > > For the moment, the easiest work-around may be to reprocess all input files by adding a column with energy in eV. If an easy fix could be found for correct data import in Athena, however, this would be helpful. > > Best regards, Andreas > > ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > > Andreas Voegelin, PhD > Eawag - Swiss Federal Institute of Aquatic Science and Technology > Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland > Tel: +41 58 765 54 70 > Fax: +41 58 765 52 10 > mailto:andreas.voegelin@eawag.ch > http://www.eawag.ch/~voegelan > > > > > >

2 1

Bug Report: incomplete data import in Athena when energy is given in keV
by Voegelin, Andreas 25 Oct '18

25 Oct '18

Dear Bruce & Ifeffit Mail-List Working with Athena (executable Version 0.9.26 with Ifeffit 1.2.12 on Windows 10), I just noted a problem with data import when energy in the input file is given in keV. Attached an example of recently collected Ce L3 edge data (original_format.txt), with the energy in keV in the first column and the DT-corrected and normalized fluorescence signal in column 44. The file contains 2 header rows and 308 lines of data. When this spectrum is loaded into Athena, it consists of only 186 instead of 308 datapoints (see information on spectrum “original_format,.txt” in Athena project file “test_bug_data_import_in_keV.prj”). The problem also persisted when I reduced the input file to only two columns, energy and fluorescence data, and seemed not related to file size. The problem occurs on various computers all running with the latest version of Athena. Interestingly, the problem does not occur if the energy in the original file is given in eV instead of keV. From the original file, I created an input file “test_energy_in_keV_eV.txt” in which columns 1 and 4 contain the energy in keV and columns 2 and 5 the energy in eV. When I import the spectrum using any of the columns with energy in eV, the spectrum is loaded correctly and consist of 308 datapoints. If I use any of the two columns with energy in keV, the imported spectrum again contains only 186 datapoints. Comparing the mue output files of the spectra read in eV and keV (mue files attached), one can see that incomplete data import starts at 5703 eV, i.e., where the step size in the scan was changed from 2 eV to 0.5 eV. Notably, if I select column 5 containing the energy in eV, but tell Athena that the energy is in keV and needs to be converted to eV, Athena loads all 308 datapoints (although with obviously wrong energy scale). This might suggest that the problem is related to the absolute difference in energy between datapoints rather than to the conversion from keV to eV. I tested also other data collected at the Mn K and Tl L3 edges and the problem is the same. For the moment, the easiest work-around may be to reprocess all input files by adding a column with energy in eV. If an easy fix could be found for correct data import in Athena, however, this would be helpful. Best regards, Andreas °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° Andreas Voegelin, PhD Eawag - Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland Tel: +41 58 765 54 70 Fax: +41 58 765 52 10 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan

1 0

the meaing of "beta=125.264" in path interpretation
by woschangqiang＠126.com 19 Oct '18

19 Oct '18

Dear, Firstly, i'm very grateful for the useful responses from Bruce Ravel and Matt Newville on my previous question. Now, I have another question about path. The screenshot below is the interpretation of a path in α-Fe. I was wondering what does "beta" means. Is that scattering angle? I tentatively construct a triangle according to the rleg values, and find that the three angles are consistent with the beta values. What does this mean? I searched the Artemis user guild and the mailing list, but could not find the answers. Do you have any ideas? Thanks in advance Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 188, Issue 14
by Joanna Kowalska 19 Oct '18

19 Oct '18

>From Ben I will send On 19 Oct 2018 16:25, <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. the meaing of "beta=125.264" in path interpretation (woschangqiang(a)126.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 19 Oct 2018 22:22:30 +0800 From: "woschangqiang(a)126.com" <woschangqiang(a)126.com> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] the meaing of "beta=125.264" in path interpretation Message-ID: <201810192222293624981(a)126.com> Content-Type: text/plain; charset="gb2312" Dear, Firstly, i'm very grateful for the useful responses from Bruce Ravel and Matt Newville on my previous question. Now, I have another question about path. The screenshot below is the interpretation of a path in ?-Fe. I was wondering what does "beta" means. Is that scattering angle? I tentatively construct a triangle according to the rleg values, and find that the three angles are consistent with the beta values. What does this mean? I searched the Artemis user guild and the mailing list, but could not find the answers. Do you have any ideas? Thanks in advance Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China

1 0

Athena problem
by Elien Lemmens 18 Oct '18

18 Oct '18

Dear, I was trying to do some linear combination fitting using Athena software. Although the box "All weight between 0 and 1" is ticked I get negative weight results. I have read the online Athena's User's Guide, but I did not find what the issue can be. Do you have any ideas? Below you can find some print screens of my actions. I also get an "error" (print screen 2), which I don't understand. Thanks in advance Elien [cid:image001.jpg@01D46703.6DC31010] [cid:image002.png@01D46703.6DC31010] [cid:image003.png@01D46703.6DC31010]

5 5

difference of feff interpretation generated by different version of artemis
by woschangqiang＠126.com 17 Oct '18

17 Oct '18

Hello, everyone. I recently ran into an issue in using Artemis software. I used two versions of Artemis (Artemis 0.8.012 and Demeter 0.9.25) to generate the paths from the same input file (FeS2.inp), but there is big difference between the two path results. e.g. 1, the path4 and path6 generated in Demeter 0.9.25 are not generated in Artemis 0.8.012, though they have a very low applitude. e.g. 2, the path7 in Demeter 0.9.25 is likely identical to path5 in Artemis 0.8.012 judging from the degenracy, reff, and amplitude, but their scattering name are different: (+)-S1-S2-(+) in Demeter 0.9.25 and (+)-S2-S1-(+) in Artemis 0.8.012. In my opinion, the scattring sequence of photoelectron in multiple scattering affect the paramters of paths. Why do these two paths have different scattering sequence? Thanks very much for your help. Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China Email: woschangqiang(a)163.com

3 2

restraints in larch
by Barbara Etschmann 12 Oct '18

12 Oct '18

Hello I'm trying to use larch to refine the coordination of Y in solution. I need to use 2xO paths to fit the first shell and would like to restrain the total coordination to be between 5.5 and 8. I can apply the constraint to each nO, but not the total, i.e. nO1 = param(7.0, min=5, max=7, vary=True), nO2 = param(1, vary=True), but ntot1 = param(expr='nO1+nO2', min=5.0, max=8.5) does not work. How can I restrain the total coordination? Also, having some problems with the gofs and errors - the chi square is rather small and often the errors are not reported and it is not clear why. Thanks Barb

3 5

Better late than never
by Anatoly Frenkel 10 Oct '18

10 Oct '18

After 15 years or so of using Athena, I just accidentally learned that the vertical scale of the plot can be changed by simply turning the scroll wheel of the mouse! Anatoly

1 0

Larch: GSE Mapviewer export error
by Naomi Intrator 06 Oct '18

06 Oct '18

Hello I made correlation plots in the GSE Mapviewer and am trying to export the data. When I click file, export data. I get an error that says 'Export Data to ASCII: Export Data not available" I have tried to do this on both a Mac and Windows. Has anyone else encountered this and know a way around it? Thank you, Naomi

3 3

Re: [Ifeffit] Port p5.26-ifeffit not installing via MacPorts on Yosemite
by Fowler, Joseph W. (Assoc) 17 Sep '18

17 Sep '18

Dear Sergio, Thanks for the alert. I’m the official MacPorts maintainer of ifeffit, but I must make my usual warning: I am very experienced with Unix and Linux in general, but I know practically nothing about Perl and don’t really understand MacPorts. (If anyone reading this has the qualifications and the willingness to replace me as maintainer of ifeffit and demeter, we need to talk!) I have been trying for months—and failing—to get Demeter version 0.9.26 to build on my Mac, which gives you a sense of my competence for this job. Anyway, to the topic at hand. Thank you for including the log file. It looks clear to me that your linker is not finding a gfortran run-time library. You might lack the library on your system, or the library is simply not listed among the link options in your compile command. fowlerj@817jfmac:~$ port installed g95 The following ports are currently installed: g95 @0.93_5 (active) fowlerj@817jfmac:~$ port installed gcc7 The following ports are currently installed: gcc7 @7.3.0_3 (active) fowlerj@817jfmac:~$ port installed p5.26-ifeffit The following ports are currently installed: p5.26-ifeffit @1.2.13_0+gcc7 (active) fowlerj@817jfmac:~$ port installed ifeffit The following ports are currently installed: ifeffit @1.2.13_5+gcc7 (active) fowlerj@817jfmac:~$ port ech depof:ifeffit gcc7 libgcc libgcc7 libpng ncurses pgplot xorg-libX11 Do you have the package g95 (a FORTRAN compiler) installed? You can see (above) that I have it, but it’s not a listed dependency of ifeffit. Why don’t you try installing it (“sudo port install g95”) and then clean and install first the package ifeffit, then p5.26-ifeffit. If that works, then it means we should add g95 as a dependency for ifeffit (or p5.26-ifeffit). If it doesn’t work, then at least you might gather more clues. Best wishes, Joe Fowler On Sep 16, 2018, at 3:42 PM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca… 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. Port p5.26-ifeffit not installing via MacPorts on Yosemite (Sergio Tatay) From: Sergio Tatay <sergio.tatay(a)uv.es> Subject: [Ifeffit] Port p5.26-ifeffit not installing via MacPorts on Yosemite Date: September 16, 2018 at 3:12:52 PM MDT To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Hi everybody, I’ve been trying to install Demeter package on MacOS using MacPorts. All the dependencies seem to install smoothly but for p5.26-iffefit. During port install I’ve got the following error: ---> Computing dependencies for demeter The following dependencies will be installed: p5.26-ifeffit Continue? [Y/n]: Y ---> Building p5.26-ifeffit Error: Failed to build p5.26-ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed I've pasted below an extract of the log file and attached the complete file to this mail. I’m completely newbie and I will be very grateful if someone could help me to get the problem solved. Thanks very much in advance, Sergio -LOG FILE- version:1 :debug:sysinfo OS X 10.10 (darwin/14.5.0) arch i386 :debug:sysinfo MacPorts 2.5.3 :debug:sysinfo Xcode 7.2.1 :debug:sysinfo SDK 10.10 :debug:sysinfo MACOSX_DEPLOYMENT_TARGET: 10.10 … …. :info:build /opt/local/lib/perl5/5.26/darwin-thread-multi-2level/CORE/libperl.dylib -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl/../../src/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -lifeffit -L/opt/local/lib -lpgplot -lpng -lX11 -L/opt/local/lib -lSystem -lm \ :info:build :info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _settxt_ in libifeffit.a(misc_vars.o) :info:build ... :info:build "__gfortran_concat_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _set_array_index_ in libifeffit.a(misc_arr.o) :info:build _getsca_ in libifeffit.a(misc_vars.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build ... :info:build "__gfortran_getenv", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build "__gfortran_st_close", referenced from: :info:build _close_echofile_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_history_ in libifeffit.a(iff_history.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_log_ in libifeffit.a(iff_log.o) :info:build _iff_rddata_ in libifeffit.a(iff_rddata.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build ... :info:build "__gfortran_st_inquire", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build _fefinp_ in libifeffit.a(fefinp.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build _newfil_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_open", referenced from: :info:build _rcldat_ in libifeffit.a(clcalc.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_read", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_read_done", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_st_write_done", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_stop_string", referenced from: :info:build _fstop_ in libifeffit.a(echo.o) :info:build "__gfortran_string_index", referenced from: :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _isvnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _hexcol_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_string_len_trim", referenced from: :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _fixarr_ in libifeffit.a(misc_arr.o) :info:build _iofarr_ in libifeffit.a(misc_arr.o) :info:build ... :info:build "__gfortran_transfer_character", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_transfer_character_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_transfer_integer_write", referenced from: :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_getpath_ in libifeffit.a(iff_getpath.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_macro_do_ in libifeffit.a(iff_macro.o) :info:build ... :info:build "__gfortran_transfer_real", referenced from: :info:build _str2dp_ in libifeffit.a(str.o) :info:build "__gfortran_transfer_real_write", referenced from: :info:build _iff_correl_s_.part.0 in libifeffit.a(iff_correl.o) :info:build _iff_cursor_ in libifeffit.a(iff_cursor.o) :info:build _iff_zoom_ in libifeffit.a(iff_cursor.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_print_ in libifeffit.a(iff_print.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build _ishsca_ in libifeffit.a(iff_show.o) :info:build ... :info:build ld: symbol(s) not found for architecture x86_64 :info:build clang: error: linker command failed with exit code 1 (use -v to see invocation) :info:build make: *** [blib/arch/auto/Ifeffit/Ifeffit.bundle] Error 1 :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j4 -w all :info:build Exit code: 2 :error:build Failed to build p5.26-ifeffit: command execution failed :debug:build Error code: CHILDSTATUS 42934 2 :debug:build Backtrace: command execution failed :debug:build while executing :debug:build "system {*}$notty {*}$nice $fullcmdstring" :debug:build invoked from within :debug:build "command_exec build" :debug:build (procedure "portbuild::build_main" line 8) :debug:build invoked from within :debug:build "$procedure $targetname" :error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. <main.log> _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca… Unsubscribe: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca…

1 0

Port p5.26-ifeffit not installing via MacPorts on Yosemite
by Sergio Tatay 16 Sep '18

16 Sep '18

Hi everybody, I’ve been trying to install Demeter package on MacOS using MacPorts. All the dependencies seem to install smoothly but for p5.26-iffefit. During port install I’ve got the following error: ---> Computing dependencies for demeter The following dependencies will be installed: p5.26-ifeffit Continue? [Y/n]: Y ---> Building p5.26-ifeffit Error: Failed to build p5.26-ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed I've pasted below an extract of the log file and attached the complete file to this mail. I’m completely newbie and I will be very grateful if someone could help me to get the problem solved. Thanks very much in advance, Sergio -LOG FILE- version:1 :debug:sysinfo OS X 10.10 (darwin/14.5.0) arch i386 :debug:sysinfo MacPorts 2.5.3 :debug:sysinfo Xcode 7.2.1 :debug:sysinfo SDK 10.10 :debug:sysinfo MACOSX_DEPLOYMENT_TARGET: 10.10 … …. :info:build /opt/local/lib/perl5/5.26/darwin-thread-multi-2level/CORE/libperl.dylib -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl/../../src/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -lifeffit -L/opt/local/lib -lpgplot -lpng -lX11 -L/opt/local/lib -lSystem -lm \ :info:build :info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _settxt_ in libifeffit.a(misc_vars.o) :info:build ... :info:build "__gfortran_concat_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _set_array_index_ in libifeffit.a(misc_arr.o) :info:build _getsca_ in libifeffit.a(misc_vars.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build ... :info:build "__gfortran_getenv", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build "__gfortran_st_close", referenced from: :info:build _close_echofile_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_history_ in libifeffit.a(iff_history.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_log_ in libifeffit.a(iff_log.o) :info:build _iff_rddata_ in libifeffit.a(iff_rddata.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build ... :info:build "__gfortran_st_inquire", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build _fefinp_ in libifeffit.a(fefinp.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build _newfil_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_open", referenced from: :info:build _rcldat_ in libifeffit.a(clcalc.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_read", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_read_done", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_st_write_done", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_stop_string", referenced from: :info:build _fstop_ in libifeffit.a(echo.o) :info:build "__gfortran_string_index", referenced from: :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _isvnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _hexcol_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_string_len_trim", referenced from: :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _fixarr_ in libifeffit.a(misc_arr.o) :info:build _iofarr_ in libifeffit.a(misc_arr.o) :info:build ... :info:build "__gfortran_transfer_character", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_transfer_character_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_transfer_integer_write", referenced from: :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_getpath_ in libifeffit.a(iff_getpath.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_macro_do_ in libifeffit.a(iff_macro.o) :info:build ... :info:build "__gfortran_transfer_real", referenced from: :info:build _str2dp_ in libifeffit.a(str.o) :info:build "__gfortran_transfer_real_write", referenced from: :info:build _iff_correl_s_.part.0 in libifeffit.a(iff_correl.o) :info:build _iff_cursor_ in libifeffit.a(iff_cursor.o) :info:build _iff_zoom_ in libifeffit.a(iff_cursor.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_print_ in libifeffit.a(iff_print.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build _ishsca_ in libifeffit.a(iff_show.o) :info:build ... :info:build ld: symbol(s) not found for architecture x86_64 :info:build clang: error: linker command failed with exit code 1 (use -v to see invocation) :info:build make: *** [blib/arch/auto/Ifeffit/Ifeffit.bundle] Error 1 :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j4 -w all :info:build Exit code: 2 :error:build Failed to build p5.26-ifeffit: command execution failed :debug:build Error code: CHILDSTATUS 42934 2 :debug:build Backtrace: command execution failed :debug:build while executing :debug:build "system {*}$notty {*}$nice $fullcmdstring" :debug:build invoked from within :debug:build "command_exec build" :debug:build (procedure "portbuild::build_main" line 8) :debug:build invoked from within :debug:build "$procedure $targetname" :error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details.

1 0

Data import issue on Ubuntu 18.04
by Joshua Wright 14 Sep '18

14 Sep '18

I am having some difficulty importing both .prj files and regular data files. I have included here two data files that open just fine on my Windows machine. When I try to import the raw data I get the following two popups: 1) Demeter::UI::Athena Warning Unquoted string "to" may clash with future reserved word at (eval 2479) line 1 2) Import warning Could not read "/path/to/file/Th_GWB.001" as either data or a project file. Do you need to enable a plugin? Selecting continue importing does nothing except close the dialogue box. When I import the project file the normal import window comes up, allowing me to select the data I want to import. Then a warning pops up: Warning! /path/to/file/ThoriumData.prj could not be read correctly. OK to continue importing data, cancel to quit importing data. Pressing OK just closes the dialogue box and nothing gets imported. Any ideas on what to do to fix this? Joshua

1 0

Job Posting
by Frejka, Jean M 12 Sep '18

12 Sep '18

Brookhaven National Laboratory currently has three post-doc positions in Material Characterizations available. Can you please post and/or upload the attached job postings? There are two pdf files per position: (1) short version for posting on a bulletin board and (2) a longer version to upload or email. If you have any questions, please contact me. Thank you for your assistance. Jeannie ************************************* Jean Marie Frejka Brookhaven National Laboratory Nuclear Science and Technology Department Building 817, 33 North Renaissance Road Upton, NY 11973 Phone: 631-344-2349 Fax: 631-344-2806 frejka(a)bnl.gov<mailto:frejka@bnl.gov>

1 0

XANES simulation
by Motta Meira, Debora 30 Aug '18

30 Aug '18

Good morning everyone, I'm trying to simulate XANES spectra for a material used for batteries. In the Figure, my experimental data are the blue (pristine material) and the red (charged state) curves. When I apply my EXAFS results to the original structure, to simulate using Feff, (I contracted the distances proportionally to what I found in the EXAFS fit) the XANES shifts accordantly, as you can see in the green and purple curves. However, the intensity is completely different. To fix this I changed S02 to 0.4. Additionally, I also correct the vr0 (found a value of -8.4) and I'm using Rpath = 5. The simulation using these parameters is the yellow curve. My problem is: using these parameters the simulation matches the experimental data, for the intensity and position, however, I'm missing the pre-edge and I also have a bump in the white line (yellow curve)... Does anyone know how to fix it, please? [cid:image003.jpg@01D44050.C0ECC210] Thank you, Debora

1 0

Constraining values in Artemis fit
by Thomas, Andrew (AGW) 23 Aug '18

23 Aug '18

Hello, Does anyone have any suggestions for breaking the correlation between the coordination number and sigma^2? Specifically, is there a way to set a maximum or minimum value for parameters in a fit? Andrew Thomas

4 3

32ビット版アプリケーションの申請
by 天田雄大 23 Aug '18

23 Aug '18

Ifeffit管理者様 32ビット版アプリケーションを使用したいので、 32ビット版のインストールアプリを添付していただけませんか？よろしくお願いします。

2 1

Accelerated Specotroscopy post-doc position at LBNL
by Santosh Suram 23 Aug '18

23 Aug '18

Hi everyone, I would like to bring to your attention an upcoming post-doc position on accelerated spectroscopy and analysis of XANES and EXAFS data. Please see the brief advertisement below and if interested please email your resume to jyano(a)lbl.gov and santosh.suram(a)tri.global -- best, Santosh -- Confidential or protected information may be contained in this email and/or attachment. Unless otherwise marked, all TRI email communications are considered "PROTECTED" and should not be shared or distributed. Thank you.

1 0

Fe K-edge EXAFS spectra for Fe-silicates
by Paul Francisco 22 Aug '18

22 Aug '18

Dear Everyone, Hello! I'm working on iron silicates and I'm wondering if anybody here would be willing to share some Fe K-edge EXAFS spectra (preferably ones that go up until k=14-15 A-1) for phyllosilicates (e.g. chlorite/saponite/serpentine); or if anybody can recommend some database or reference for these. Thanks in advance and I would really appreciate any help! Cheers, Paul

1 0

Modelling texture in Artemis
by Kirstine Dalgaard 20 Aug '18

20 Aug '18

Dear all How can texture in a powder sample be modeled in ARTEMIS? My samples are fine powders of a layered material, mixed with cellulose and pressed to pellets. The data were collected in fluorescence mode with a 45 degree tilt. PXRD data reveal that the samples are highly textured, including standards. I am new to XAFS, and I need some advise to deal with this issue. Best regards Kirstine Dalgaard

3 8

Re: [Ifeffit] using the mail list archive for mac install
by Matt Newville 17 Aug '18

17 Aug '18

Hi Joel, > I ran into the problem that some people seem to have with Demeter on mac while > upgrading to High Sierra. I found a fix on this mail list, but… Yeah, Demeter on MacOS is a continuing challenge. Even when it can be installed, parts of the GUI interaction are pretty buggy (I believe this must be due to wxPerl on Mac). MacPorts seems to need a fair amount of attention and expects the end user to know Unix command line tools well enough to be able to run updates and understand and react to error messages. For sure, it is a useful resource for developers, but it seems like it is not really designed for deploying end-user software. Still , I don't know of a better alternative for getting Demeter working on MacOS. I've tried many of the alternatives, and wxPerl seems to be a real stumbling block for all of them. > 1) I can’t download Template.pm from the archive (bin file that uncompresses to cpgz file > that uncompresses back to a bin file…) I think that the advice from Luke and Bruce back in April was to try to find and install version 1.47 of Text::Template. You might find this at https://metacpan.org/source/MSCHOUT/Text-Template-1.47/lib/Text and try unpacking and installing that. There may be a way to specify particular versions with the "cpan" program, but I do not know how to do it. I don't think we want "install old version of some library" to be a long term solution (this will break other things eventually), but it might work for you. > 2) Matt mentions that he installed 0.9.26 from macports, but I see only 0.9.25 (stable & develop). To clarify, in April I updated MacPorts to the latest versions, installed the packages for Demeter 0.9.25. Then I installed Demeter 0.9.26 from source code on top of that. That might also work , but it's probably more work than most folks would want to do. Cheers, --Matt

3 3

Re: [Ifeffit] Ifeff calculation
by Dien.Li＠srnl.doe.gov 15 Aug '18

15 Aug '18

Hi, Carlo and Matt or others Attached please find the cif crystal structure data file for NaReO4 that was downloaded from Crystallography Open database. As I added it into Artemis for calculation, it gave error message saying that it has more than 500 atoms that exceeds the limit. Could you help to troubleshooting?? Thanks a lot. Dien Li -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Tuesday, August 14, 2018 5:29 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 186, Issue 13 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: LCF on Larch - EXAFS Region (Matt Newville) 2. Re: wavelet transforms for EXAFS (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 14 Aug 2018 12:33:35 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] LCF on Larch - EXAFS Region Message-ID: <CA+7ESbr8s-gQOeLOo302hTdtT+XLS8g55goXvYm6hqJFiLCkaQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Martin and Mike, Thanks -- I'll take a closer look at your paper on this! I think we all basically agree that linear analysis of EXAFS can work, but also that compared to linear analysis of XANES, linear analysis of EXAFS has a few more caveats and issues that need to be addressed for each case. On Mon, Aug 13, 2018 at 8:26 PM Martin McBriarty <memcbr(a)gmail.com> wrote: > Matt, > > Glad to read your impressions of EXAFS LCF. I've had reasonable success > with LCF using EXAFS spectra generated by ab initio molecular dynamics > (AIMD) to figure out the local structure of dopants whose preferred > coordination is symmetrically dissimilar from the crystals they inhabit, > i.e. for which there are no good experimental standards. This can be pretty > tough to do accurately with shell-by-shell fitting. > > As you point out, disorder is a huge hurdle (in both LCF and > shell-by-shell EXAFS analysis). We assume that a good AIMD model will > simulate thermal disorder pretty well, but there are likely differences in > configurational disorder between a periodic infinite structure and the real > material due to defects. Fortunately, defects can be explicitly accounted > for in a simulation, assuming you have the computational capability to > screen a set of defect configurations. > > Background subtraction should ideally be done using the same procedure for > all data. Theoretical data could be used to refine a background subtraction > procedure; spline fit parameters such as Rbkg or clamping may be tweaked to > improve agreement between a simulated chi(k) and a measured standard over a > reasonable k-range. > > Simulating spectra with a range of binding energy offsets can explicitly > address the problem of E0 choice, but it can also be used as a fudge factor > for strain. In my LCFs, dE0 is the only parameter besides the fractions of > the chosen phases. > > To address the above problems, benchmarking is key. Quantitative agreement > should be sought between simulated spectra and experimental standards to > ensure the theory is sound and the chi(k) extraction is reasonable. > However, there are probably still systematic sources of error which are > larger than the uncertainties Athena's LCF tool will report; I agree with > Mike's practical estimate of 10% or so. > > I discuss these issues in somewhat greater detail in my recent (open > access!) article that demonstrates how LCF using AIMD-simulated spectra > yields answers that shell-by-shell fitting struggles with due to multiple > overlapping components: https://pubs.acs.org/doi/10.1021/acs.est.8b00297 > > Martin > > > On Sun, Aug 12, 2018 at 10:19 PM, Matt Newville < > newville(a)cars.uchicago.edu> wrote: > >> Hi Mike, >> >> On Thu, Aug 9, 2018 at 10:04 PM Mike Massey <mmassey(a)gmail.com> wrote: >> >>> This is interesting. Could you say more about your skepticism of the >>> robustness of EXAFS LCF, Matt? >>> >>> To be fair, it suffers from many of the same drawbacks of XANES LCF, >>> plus others. But I'm curious about your thoughts on it since yours seems to >>> be what amounts to a "strong opinion" on the subject. >>> >> >> >> I would not say that no one should ever do linear combination fitting for >> EXAFS. For sure, linear analysis of XANES is quite robust and verified >> many times to give good results, at least at level of a few percent. >> Linear analysis of EXAFS suffers more data processing challenges and >> conceptual problems that limit its robustness. For sure, there are cases >> for which it can work well. >> >> Longer answer: >> Any linear analysis (LCF, PCA, MCR-ALS, etc) of XANES works reasonably >> well (typically to a few percent) because: >> a) the processing needed is minimal. Data need to have a common >> energy calibration better than the intrinsic energy resolution -- typically >> energy calibration of 0.25 eV or better will be OK. Data need to have a >> consistent normalization of mu(E), typically to a few percent. Variations >> in these processing steps will have a direct and negative effect on the >> results. >> >> b) conceptually, the assumption is that there exists a nearly 1 to 1 >> correspondence between "local chemical configuration" and "measured XANES", >> and that the "local chemical configurations" that are being investigated >> are discrete and well-defined (ie "iron carbonate") and not continuous. >> That is, if you determine that your Fe XANES spectra is "50% iron >> carbonate and 50% iron sulfate" then implicit conclusion is that 50% of the >> iron atoms are iron carbonate and 50 percent are iron sulfate, not that all >> irons are 50% carbonate and 50% sulfate. >> >> To be clear, linear analysis of XANES does not work well to ppm levels, >> partly due to the poor experimental contrast (that is, mu(E) tend to all >> look alike and features are intrinsically broadened to the ~eV level), but >> also conceptually, because at the ppm level, local chemical configurations >> are not always limited to 3 to 10 discrete states. >> >> Linear Combination EXAFS is more challenging from both the processing and >> conceptual point of view. >> >> For Processing, EXAFS requires more data processing than XANES. The >> selection of E0 and the background mu0(E) will have an effect on linear >> analysis of EXAFS if not done consistently. It is not really obvious how >> E0 or mu0(E) can be selected consistently for very different spectra. >> >> Conceptually, EXAFS is much more sensitive to disorder and subtle >> variations in the bond lengths (thermal or static disorder) and can have >> significant variation in its sensitivity to second and further neighbors. >> In that sense, EXAFS is much less discrete and much more continuous in its >> variability across different kinds of local structures. >> >> Again, this is not to say that linear analysis of EXAFS cannot ever work, >> just that is probably more limited in applicability and absolute accuracy >> than linear analysis of XANES. Of course, for EXAFS you can also do an >> actual fit of structural parameters. The information content is somewhat >> limited so that refining multiple overlapping components may not always be >> possible, and linear combinations of end-member spectra may look >> attractive.... >> >> Hopefully, anyone who has other insights or experiences will be able to >> correct any of my misunderstandings. >> >> --Matt >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> >> > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-252-0431

3 2

Basic questions about the preliminary data processing in Athena
by Haifeng Li 14 Aug '18

14 Aug '18

Dear ALL, I am a beginner in Athena. Recently I got the spectra and I am confusing about the data calibration and alignment. The manual shows that calibrate the reference data of one scan and align other reference data to that calibrated one. Here I want to show examples. I have two samples A and B, Each sample has three scans with the corresponding reference data. For sample A, 1st scan is calibrated and the other two scans are aligned to 1st scan. Then merge them into merged A. The same procedures for sample B and get merged B. If I want to compare XANES of sample A and B, do I need to align the merged reference data between A and B? If so, why? My understanding is that all scans (original data and merged data) in sample A and B are calibrated to standard edge energy. Why do they need to align? I appreciate your help. Thanks, Haifeng

4 8

Re: [Ifeffit] wavelet transforms for EXAFS
by Clark Adam Hugh (PSI) 14 Aug '18

14 Aug '18

Hi Matt I recently had some problems incorporating the larch Cauchy wavelet transform into my program for rapid bulk processing of QEXAFS data (discussed http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-April/007250.html) I particular after importing the relevant module into python the cauchy_wavelet(cwsam, kweight=kwwt, _larch=mylarch) function raises the error 'not callable'. As a work around I have explicitly copied the module code for the definition into my own script and this seems to resolve the issue. I also notice that at present that it is not possible to apply a windowing function within the wavelet transform, is this just a case of windowing the K space data that is fed to the module? I would also have interest in trying to fit the EXAFS data in the wavelet space, has there been any progress in Larch for performing this? As briefly discussed at the EXAFS conference another feature that I think would be very nice to include would be the possibility to use a Victoreen function for the post edge normalisation instead of a polynomial function. I also briefly discussed the application of the MBACK algorithm. Unless I am doing something incorrect, when trying to use the MBACK algorithm in Larch within python the following error is raised ' 'XrayDB' object has no attribute _getChantler'. In some cases it would be very interesting to apply the MBACK algorithm particularly when only a short data range is collected in some experiments. Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/133 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch

2 1

LCF on Larch - EXAFS Region
by Garret Bland 14 Aug '18

14 Aug '18

Hello! I've recently been trying to use Larch instead of Athena for EXAFS analysis, and I mainly do linear combination fitting for my samples. It seems that the XANES fitting is doing just fine requesting a specified region to fit (-25 to +75 eV). When I try to fit in the k-space however, Larch does not request a specific region in k space. I try to input the eV values corresponding to the k value I want to fit, but it is still plotting in mu rather than k . Is there anyway I can change this and/or do it manually on the larch GUI? Any help would be appreciated! Thanks, Garret -- Garret Bland Graduate Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 207C Pittsburgh, PA, 15213

4 7

Ph.D and Postdoctoral positions- Time-resolved X-ray Spectroscopy in Biological/Chemical Catalysis
by dooshaye.moonshiram 11 Aug '18

11 Aug '18

Dear all. We have a Ph.D and postdoctoral position available in time-resolved X-ray spectroscopy in biological and chemical catalysis. The details of the positions are attached. Please contact me or forward the attached positions if you or anyone you know might be interested. Many thanks and Best Regards, Dooshaye Moonshiram Group Leader IMDEA Nanociencia Calle Faraday 9, Madrid, Spain

1 0

Demeter on ubuntu 14.04
by Edmund Welter 09 Aug '18

09 Aug '18

Dear all, I am hitting a wall trying to install the latest Demeter version on my ubuntu laptop. System: Ubuntu 14.04 Demeter: 0.9.26 perl: 5.18.2 pdl and pdl::stats from repositories. (I tried a newer versions from cpan, but ot no avail) moose: initially from repositories, than vs. 2.2011 from cpan I did follow the installation instructions on https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… and tried to install demeter in ~/perl5 and also the instructions in: https://bruceravel.github.io/demeter/documents/SinglePage/installation.html to install Demeter as sudo Both attempts ended with the same result when I start dathena in a terminal the image of the goddess appears briefly and I get the following error messages in the terminal: --------------------------------------------------------------------- Invalid version format (non-numeric data) at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Moose.pm line 15, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose.pm line 15, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, <DATA> line 90. Compilation failed in require at /usr/local/bin/dathena line 31, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31, <DATA> line 90. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288, <DATA> line 90. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288, <DATA> line 90. -------------------------------------------------------------------- When i try to start denv to create the nice overview of installed components I only get the following errors: -------------------------------------------------------------------- [PDL->Version: 10 PDL_CORE_VERSION: 8 XS_VERSION: ] PDL::Stats::Distr needs to be recompiled against the newly installed PDL at /usr/lib/perl/5.18/DynaLoader.pm line 207. Compilation failed in require at (eval 1130) line 5. BEGIN failed--compilation aborted at (eval 1130) line 5. BEGIN failed--compilation aborted at /usr/local/bin/denv line 24. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288. ---------------------------------------------------------------------- This is insofar interesting as I got the same error about PDL when I tried to start dathena before I installed the pdl::stats module from cpan, that means when both, pdl and pdl::stats were installed from repositories. Any hint would be welcome, upgrading ubuntu to a newer LTS version might be useful (It is absolutely possible that something is weird with this installation after a lot of playing around) but I am currently reluctant to do so, because it will for sure break other things... Best regards, Edmund

3 4

Artemis problem
by ParasMani Rajput 09 Aug '18

09 Aug '18

Dear All, I am using windows 8 and running ARTEMIS (1.2.11) in my leptop. Today I found that Artemis not working properly. When I am opening my project files in Artemis then showing an error massage "Artemis trapped one or more errors! Error message dumped to the screen" where i fitted and saved the project file the day before. Please let me know if some has seen this problem and how to resolve it. Regards, Parasmani ----------------------------------------------------------------------------------------------------------------------------------- Dr. Parasmani Rajput Atomic & Molecular Physics Division BL-09, INDUS-2 complex Bhabha Atomic Research Centre Raja Ramanna Centre for Advanced Technology Trombay, Mumbai-85, India Indore, Madhya Pradesh 452013, India E-mail: parasmanirajput(a)gmail.com Phone: (+91) 731-2442509 Web page :https://sites.google.com/site/parasmanirajput/ orcid.org/0000-0003-0694-6756 http://www.researcherid.com/rid/E-4783-2011 -----------------------------------------------------------------------------------------------------------------------------------

2 2

Re: [Ifeffit] Find white line position
by Hiroshi Oji 06 Aug '18

06 Aug '18

Dear Bruce and Carlo, Thank you very much for your reply. Now I understand how Athena find the peak position by the Bruce's answer. I think some kinds of interpolation is made when Athena find the white line position because the peak position that Athena tells seems to be more precise than the energy step in the measurement. Is that right? Actually, I use this function often because it is quite useful for quick check for white line position. But I will be careful when I use it from now on, following the Bruce' advice. I agree with the Carlo's suggestion that it is better to use the curve-fitting method to find the white line position. Best regards, Hiroshi > Date: Thu, 2 Aug 2018 09:48:02 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Find white line position > Message-ID: <alpine.DEB.2.21.1808020946550.9741(a)hydride.segre.home> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > Hi Hiroshi, > > You are probably better off putting a bit more time into the analysis and > simply fitting with an arctangent and a gaussian to get the white line > position. > > Carlo > > On Thu, 2 Aug 2018, Bruce Ravel wrote: > >> >> It's not very sophisticated. >> >> Starting with the "flattened" spectrum (see >> http://bruceravel.github.io/demeter/documents/Athena/bkg/norm.html#the-flat…) >> it simply finds the highest point in the spectrum. Literally just the >> ceiling function. >> >> The flattened spectrum is used rather than the normalized spectrum because >> the curvature of the post-edge (or even the curvature of the pre-edge in >> fluorescence data with a energy dispersive detector) could result in other >> regions being higher in value than the white line. >> >> This is a pretty horrible algorithm. It is, I think, guaranteed to find an >> obviously wrong point for a metal. Basically it works for spectra with a >> white line and it will almost certainly fail for spectra without a white >> line. >> >> Use with caution! >> >> HTH, >> B >> >> >> On 08/02/2018 01:28 AM, Hiroshi OJI wrote: >>> Dear all, >>> >>> I have a question about one of the useful function, "find white line >>> position" in Athena. >>> >>> Could anyone tell me how Athena find the white line position by this >>> function? In other words, I would like to know the algorithm to find the >>> white line position in Athena. >>> >>> Thank you very much for your help, in advance. >>> >>> Best regards, >>> >>> Hiroshi Oji >>> >>> >> >> >> > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics > Interim Chair, Department of Chemistry > Director, Center for Synchrotron Radiation Research and Instrumentation > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org --

1 0

Re: [Ifeffit] Artemis problem
by Abdulahad 05 Aug '18

05 Aug '18

Please upgrade your version of Demeter. First remove the old files as well. Hopefully problem get resolve. A. Ahad Department of physics Aligarh Muslim University Aligarh

1 0

Find white line position
by Hiroshi OJI 02 Aug '18

02 Aug '18

Dear all, I have a question about one of the useful function, "find white line position" in Athena. Could anyone tell me how Athena find the white line position by this function? In other words, I would like to know the algorithm to find the white line position in Athena. Thank you very much for your help, in advance. Best regards, Hiroshi Oji -- Hiroshi Oji, PhD. NUSR & AichiSR, Japan E-mail: h.oji(a)nusr.nagoya-u.ac.jp

3 2

Making N (coordination number) a variable.
by M Solo 01 Aug '18

01 Aug '18

Hello Is there a way in artemis to make N, coordination number, a variable to be used in GDS window? I do realize that N and ss are closely linked and do very similar things in the fit, but it seems i may need fractional (average) coordination number for one of the paths, and am fine fixing ss to see where N levels off. Thank you very much. Alex Solov

4 3

Demeter - Athena Warning, crashing
by Alida Perez Fodich 01 Aug '18

01 Aug '18

Hello, I'm new to Athena and after following the steps to install Demeter on my mac when I run the command to launch Athena I get a warning message with the following error: 10:57:05: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 10:57:05: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 10:57:05: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 10:57:05: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 10:57:05: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 10:57:05: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. After this, the only option is to press ok and the program crashes. I have updated to latest version of high Sierra (10.13.6) before installing Xcode (9.4.1) and MacPorts (2.5.3). I also tried some of the quick fixes on Athena documentation but it seems to be a different problem. Does anyone have an idea of what could be wrong? Alida.

1 0

Demeter Installation Mac server error
by Laurane Léost 27 Jul '18

27 Jul '18

Dear all, I would like to install Demeter on Mac device. I followed all the instructions with "Installing Demeter on the Mac" in the website. But in the terminal window, when i write : "sudo port install xorg-server demeter", this message appears : "Error: Port xorg-server not found". Did someone had already receive this type of message? Or know a way to install the program. Thanks for your help. -- Laurane Léost

1 0

ZrO2 and HfO2 EXAFS spectra
by Martin McBriarty 23 Jul '18

23 Jul '18

Friends in XAFS, Do you have any EXAFS spectra of single-phase ZrO2 or HfO2 that you'd be willing to share? In particular, I'm looking for the monoclinic (P21/c), tetragonal (P42/nmc), and orthorhombic (Pbca and Pca21) phases of each material. Bulk, interface-stabilized, pure, or lightly doped is fine. I'd prefer mu(E) spectra, but chi(k) would work as well. Thank you for any help or recommendations! Martin Martin E. McBriarty, Ph.D. Scientist III, Intermolecular Inc. San Jose, CA

1 0

Re: [Ifeffit] Fe Standards (Naomi Intrator)
by Denis Testemale 23 Jul '18

23 Jul '18

I'm not sure my previous message went through (I think I screwed up the mailing list adress). So here we go again. Dear Naomi, I attach 2 files with the normalized spectra of Fe2+ (50mmol dissolved FeCl2 in 0.5M HCl) and Fe3+ (??mmol dissolved Fe2(SO4)3 in 2M H2SO4) in solution. In both cases iron is octahedrally coordinated to water molecules. The spectra come from 2 different experimental runs, but the calibration of the beamline was done consistently (Fe metallic foil, 1st maximum of the derivative set at 7112eV). Unfortunately the Fe3+ spectrum is only XANES. If you need EXAFS let me know, I might find something if I dig hard in my hard disk. Cheers denis Date: Tue, 10 Jul 2018 21:23:34 +0000 From: Naomi Intrator<naomii(a)princeton.edu> To:"ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Fe Standards Message-ID: <A986AA38C24BCD4E9BAAC1237600734D0E517089@csgmbx217w> Content-Type: text/plain; charset="iso-8859-1" Hi all, I'm doing a project on Fe and was wondering if anyone has spectra of Fe(II) and/or Fe(III) standards they wouldn't mind sharing. I'm specifically looking for XANES of Fe2+ and Fe3+ ions in water. Thanks in advance, Naomi -- Institut Néel - CNRS http://neel.cnrs.fr/spip.php?rubrique264 +33 476 881 045

1 0

Re: [Ifeffit] XANES from FEFF9
by manju rao 18 Jul '18

18 Jul '18

Hi Matt As I am new to FEFF, I was estimating SO2 to be equal to 1 for XANES. But I don't know if it was good to have such guess or not. By changing Exchange card from 0 0 0 0 to 0 0 0 2, I am getting a noticeable change in absorption edge. The edge showed a little shift to higher energy and also slight fall in amplitude of edge. These changes are not ignorable. So I am confused about what approach to follow. Manju Sent from my iPhone

2 2

set restrain
by Dien.Li＠srnl.doe.gov 17 Jul '18

17 Jul '18

Hi, all I wonder if anyone can suggest me on how to set up restrain of a parameter in GDS, for example, to restrain ss in a certain range or no negative. Thank you so much. Dien Li

1 0

XAFS hands-on course at DESY
by Edmund Welter 17 Jul '18

17 Jul '18

Dear colleagues, we are organising a XAFS hands-on course at DESY this year. The date is 3rd - 7th of September 2018. More information can be found on the attached flyer and on our workshop webpage: https://indico.desy.de/indico/event/21097/overview In case of questions, please do not hesitate to contact us via e-mail. xafs-course(a)desy.de Best regards, Wolfgang Caliebe, Edmund Welter

1 0

micro-XAS Imaging Post-Doc Position
by Ritimukta Sarangi 16 Jul '18

16 Jul '18

Hello, Apologies for the spam email. We have a 3-year position available for micro-XAS imaging for biological applications at SSRL, SLAC, Menlo Park, CA. The details of the position are attached. Please contact me directly if you or anyone you know might be interested. Best Wishes, Riti Sarangi SSRL, SLAC

1 0

XANES from FEFF9
by manju rao 13 Jul '18

13 Jul '18

Hi. I am trying XANES simulation in FEFF9. My system of calculation is SrZnO2 and I am simulating Sr K edge. I noticed that on changing SO2 card from 0.0 to 1.0, there is change in position as well as profile of absorption edge. Also, by selecting or deselecting EXCHANGE card, some changes are also there. So, which approach is to be followed to obtain trust-able spectra? Please help. Manju Research Scholar Department of Physics Punjabi University, Patiala- 147 002 Punjab, India.

2 1

Importing 100 element Ge data into Larch
by Macon Abernathy 13 Jul '18

13 Jul '18

Hey all, Has anyone had success loading data from larger pixel arrays into Larch? I have data collected on a 100 element Ge detector that results in Athena crashing upon import (running on Mac OS 10.13.4, Demeter v9.25). I figure this is a good task for Larch, but am having a difficult time figuring out how to import all 100 channels for each data set simultaneously. Thanks in advance for any tips, Cheers, Macon J. Abernathy Ph.D Student-Ying Biogeochemistry Lab Environmental Toxicology Program College of Natural and Agricultural Sciences University of California, Riverside maber001(a)ucr.edu

2 1

Re: [Ifeffit] window 10
by manju rao 13 Jul '18

13 Jul '18

Hi Dien I guess this is the problem with new version too. ARTEMIS could run once for any calculation with no time limit, but if I open new data file, it got crashed. So I do one fitting at a time and then restart it for new fitting. Regards Manju Sent from my iPhone

1 0

window 10
by Dien.Li＠srnl.doe.gov 11 Jul '18

11 Jul '18

Hi, Bruce and Matt We just transitioned to Window 10 yesterday. I just found that as I ran Artemis for EXAFS data fitting, it constantly crashed (stopped running) my computer, I am using Demeter 9:24 I believe, is it possible I need a new version, where is the link for latest version? Thanks. Dien Li Savannah River National Laboratory

2 1

Fe Standards
by Naomi Intrator 10 Jul '18

10 Jul '18

Hi all, I'm doing a project on Fe and was wondering if anyone has spectra of Fe(II) and/or Fe(III) standards they wouldn't mind sharing. I'm specifically looking for XANES of Fe2+ and Fe3+ ions in water. Thanks in advance, Naomi ---

1 0

copper fluoride
by Bruce Ravel 10 Jul '18

10 Jul '18

Hi all, I wonder if anyone has a spectrum of copper fluoride, CuF2, that they are willing to share. This would be a big help for my undergraduate student's summer research project. Thanks! B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 06BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

imaginary part
by John Hummel 10 Jul '18

10 Jul '18

I have run a feff calculation in artemis and pulled the information from the output file in an attempt to sum the paths in python. However I am having some difficulty in determining the imaginary part of the waves. I was wondering how the artemis program goes about calculating the imaginary values. Any insight would be greatly appreciated. Thank you, John

1 0

using the mail list archive for mac install
by Joel Brugger SAM 10 Jul '18

10 Jul '18

I ran into the problem that some people seem to have with Demeter on mac while upgrading to High Sierra. I found a fix on this mail list, but 1) I can¹t download Template.pm from the archive (bin file that uncompresses to cpgz file that uncompresses back to a bin file) 2) Matt mentions that he installed 0.9.26 from macports, but I see only 0.9.25 (stable & develop). Sorry for the trivial questions :-) All the best, JOEL [Ifeffit] install for mac error Luke Higgins pmljrh at leeds.ac.uk <mailto:ifeffit%40millenia.cars.aps.anl.gov?Subject=Re:%20Re%3A%20%5BIfeffit %5D%20install%20for%20mac%20error&In-Reply-To=%3CD54C3C92-BBDF-484E-83DA-31D EE99F28A6%40leeds.ac.uk%3E> Tue Apr 3 12:47:31 CDT 2018 * Previous message (by thread): [Ifeffit] install for mac error <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009380.html> * Next message (by thread): [Ifeffit] install for mac error <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009383.html> * Messages sorted by: [ date ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/date.html#938 2> [ thread ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/thread.html#9 382> [ subject ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/subject.html# 9382> [ author ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/author.html#9 382> Hi All, I see this error too. This is a bit of a bodge job, but if you replace: /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm With the attached template.pm from p5.24, it seems to work fine. I¹d just rename the old Template.pm in the same directory, rather than deleting it since another program may end up needing the most recent one. Cheers, Luke From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > on behalf of Chris Patridge <patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Reply-To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Date: Tuesday, 3 April 2018 at 19:22 To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Subject: Re: [Ifeffit] install for mac error Thank you for the input Matt. I am glad to hear that it is not ³user error². I tried it again and I need to correct my earlier statement because Artemis GUI will stay open after the warning however Athena closes/crashes. I will try on a different system. Thanks again, Chris Sent from my iPhone On Apr 3, 2018, at 11:52 AM, Matt Newville <newville at cars.uchicago.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:newville at cars.uchicago.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> wrote: Hi Chris, On Mon, Apr 2, 2018 at 4:15 PM, Christopher Patridge <patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> wrote: Hello everyone, I tried to install demeter on my mac (running high Sierra) and it appeared everything went well. However when I run either Athena or Artemis I get an error shown below about Demeter::Templates: showing a error and I am not sure how I can correct this error. Any help would be appreciated. Thanks in advanced, I can confirm this. I just did a fresh install of Macports on 10.13.3 (high sierra). The MacPorts install was not super easy, but once it got to the demeter install, that part went fine. I see the same problem with athena from demeter 0.9.25. I think the warnings about "Demeter::Templates::F" and so forth are meant to be warnings only -- I think they may not be related to the crash of athena. For me, hephaestus gives the same sort of warnings, but runs fine. I can install and run Demeter 0.9.26 (including using Larch as a backend) using Macports, though there are definitely some Mac-specific weirdness. Anyway, I do not believe that "install from source" is a feasible approach for demeter on OSX. I do not know enough about Macports to update the existing package. I don't know that using some other system would be an improvement. We keep seeing problems with demeter on OSX. I'm not sure what the right answer is. Anyone have any suggestions? --Matt _______________________________________________ Ifeffit mailing list Ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:Ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

1 0

Athena for peak fitting or deconvolution
by Dien.Li＠srnl.doe.gov 09 Jul '18

09 Jul '18

Hi, Bruce I am using the Demeter 9.24 version. I saw in the "main" window the peak fitting and deconvoluting data, but as I clicked, it is not available. Any new update now. Thanks. Dien

2 1

Postdoc position
by Anatoly Frenkel 09 Jul '18

09 Jul '18

Please pass this info along to those who may be interested in this opportunity: There is an opening for a postdoctoral research associate in my group. The postdoc will be stationed in Brookhaven National Laboratory and work as a member of a multi-institution team to develop and apply new methods of operando characterization of catalysts. Expert knowledge of XAFS, strong publication record and strong background in condensed matter physics are required. For inquiries please contact me. Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

2 1

Larch 0.9.38
by Matt Newville 08 Jul '18

08 Jul '18

Hi Folks, Version 0.9.38 of Larch has been released and binary installers are now available for Windows, MacOS, and Linux. There have been many minor improvements made in the past several months, particularly for the XAS Viewer application. XAS Viewer is now very close to having feature parity with Athena and Sixpack, with a few things still missing and a few things slightly improved. This should be of particular interest for Mac users, where Athena has proven difficult to install and buggy, and support for Sixpack has also become harder. At this point, XAS Viewer can read data from plain ASCII files or from recent Athena Project files, but does not yet support quite as many different file types as Athena and Sixpack -- help on this would be greatly appreciated! It can do basic group manipulation such as merging, and groups and plot one or more XAFS spectra in various stages of the XAFS normalization process and can save data to Athena Project file or save multiple data sets to CSV files. XAS Viewer has simple dialogs for doing common data correction steps including recalibration, rebinning of QXAFS data (as per a recent discussion), glitch removal, correcting over-absorption, smoothing, and spectral deconvolution. For analysis, XAS Viewer has a notebook panel for pre-edge subtraction and normalization, and one for basic EXAFS processing (background removal and Fourier transforms to chi(R)). Its main emphasis is on visualization and analysis of XANES spectra and so it includes panels dedicated to fitting pre-edge peaks, Linear Combination analysis, and Principal Component Analysis. Though definitely a Graphical User Interface, with forms to guide the novice user, XAS Viewer goes out its way to do all data processing through basic Larch commands that can be viewed, copied, and turned into batch processing scripts. Documentation for all of Larch is a continual work in progress, and docs with screenshots for XAS Viewer is at https://xraypy.github.io/xraylarch/guis/xas_viewer.html Feedback or suggestions on this or any other aspects of Larch are most welcome. Larch can be installed with simple installers for Windows, Mac OSX, Linux which can be found from https://xraypy.github.io/xraylarch/installation.html At the moment, these installers all assume 64-bit operating systems and now are built using Anaconda Python version 3.6. If anyone needs to use Larch with 32-bit Windows please let me know. Support for this will probably be dropped by the end of the calendar year, but I do not know if this is necessary at all at this point. For people using Larch from Python, it can also be installed as a "conda package" for Anaconda Python, as with conda install -c GSECARS xraylarch Currently, packages are available for Python 3.6, and packages for Python 2.7 should be available within a couple days. Please let me know if you have any questions or problems, --Matt

1 0

data after rebinning look worse in k-space than before?
by Ilya Sinev 04 Jul '18

04 Jul '18

Hi all, I have a question regarding the chi(k) function isolation and rebinning processes. I have some data recorded in quasi channel-cut modus, i.e. with the mono constantly moving and the data points collected with the highest possible rate. With 180 sec measurement in yields to a spectrum of ca. 8600 point, which obviously needs to be rebinned. The rebinned data, however, does not look good in k-space even if multiple data are merged. Moreover, I have an impression that the raw spectrum in k-space does not have those 8000+ points anymore but significantly less. Is there any reduction of the data points number that is not seen (e.g. as a preparation step for FT)? Since the unbinned data has higher quality, does it then make more sense to keep using it for EXAFS analysis? Thank you Ilya Sinev -- Herr Dr. Ilya Sinev Institute for Experimental Physics IV Faculty of Physics and Astronomy Ruhr-Universität Bochum Universitätsstrasse 150 44801 Bochum, Germany Office: NB 4/134 Phone: +49 234 32 23647 Fax: +49 234 32 14173 e-mail: <mailto:Ilya.Sinev@rub.de> Ilya.Sinev(a)rub.de www.ep4.rub.de

6 9

Fitting Problems in Artemis version 0.9.26
by LIU HUAN 29 Jun '18

29 Jun '18

Dear Dr. Ravel, I want to ask you that when I use the new version "Artemis 0.9.26" I have two problems. (1) The fitting Range was reported to be a error that the Rmin should be larger than the Rkbg value. It makes that the fitting range cannot be smaller than 0.9 (the Rkbg value is 0.9). (2) When Fitting the Debye�CWaller factor (ss) and coordination number (N), although I use "abs()" to make it to be positive, but the fitting results still be negative. But I did not meet these problems in the old version in Artemis 0.8.012. I am wondering that whether could you tell me how to solve these problems. Thank you so much. Sincerely, Huan Huan Liu School of Earth Sciences and Engineering Nanjing University 163 Xianlin Road, Nanjing, Jiangsu, 210023 P. R. China Tel 86-15861809073 Email: huanliu_earth(a)hotmail.com

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 184, Issue 23
by Christopher Chantler 28 Jun '18

28 Jun '18

Yes all, good points. It would be good to test out a few of these procedures. We have done so in the paper mentioned; but it is correct what Edmund said, we did not start with an /extremely/ fine grid as e.g. from a continuous scan. Also it would be good to process this with uncertainties, whether from repeated measurements or fluorescent pixels. Interesting what might come out. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS CIT, CCN President, 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: Thursday, 28 June 2018 11:18:33 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 184, 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. Re: data after rebinning look worse in k-space than before? (Mauro Rovezzi) 2. Re: data after rebinning look worse in k-space than before? (Edmund Welter) ---------------------------------------------------------------------- Message: 1 Date: Thu, 28 Jun 2018 07:40:13 +0200 From: Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] data after rebinning look worse in k-space than before? Message-ID: <9eae776b-8047-376e-c826-0927b066a1c8(a)esrf.eu> Content-Type: text/plain; charset=utf-8; format=flowed Matt, From my experience at the ESRF, many users dealing with XAFS data collected in continuous scan mode (either in angle, energy or time) apply the following workflow: 1) average many scans with PyMca; 2) import them in Athena; PyMca does a linear interpolation using the grid of the first scan in the list: https://github.com/vasole/pymca/blob/b9cb5209674bf0c3617b3488a75184d4f84126… I have never run a study on which merging scheme is the best, but I would recommend using an "histogram-like" approach, as you propose: 1) make a "normal XAFS energy grid"; 2) assign each energy point in the original data to one of these energy bins and take the average of all the points in each bin. This approach is usually employed in ray tracing applications, where the number of rays is huge and one needs to make an histogram for plotting (e.g. ray intensity versus a given variable). Mauro On 2018-06-27 20:31, Matt Newville wrote: > This seems like a good chance to test these procedures out. > > My approach for this is to this is to make a "normal XAFS energy grid" > of ~5 eV steps, 0.25 eV steps, 0.05 Ang^-1 steps that the downstream > processing needs, and then do one of two strategies -- maybe there > should be more?: > ?a) do a straight interpolation onto this array -- that is probably the > "noisy" result. > ?b) assign each energy point in the original data to one of these > energy bins, and take the average of all the points in each bin. > > I'd also like to try using energy-weighted mean (centroid).? Probably > most of the data is so finely spaced that this won't make much > difference, but it might be a good option.?? It might be able to help > compensate for energy jitter, assuming that the recorded energy > (probably from an encoder) is more accurate than the requested energy. > > It's also interesting to think about doing a Savitzky-Golay smoothing, > though that might require knowing if the data points are actually > uniform in mono angle or mono energy.? It also makes it easy to over-do > the smoothing, and so a little trickier to prevent bad results. > > Do you (or anyone else) have any suggestions for how to best re-bin this > kind of data? > > --Matt ------------------------------ Message: 2 Date: Thu, 28 Jun 2018 15:18:04 +0200 From: Edmund Welter <edmund.welter(a)desy.de> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] data after rebinning look worse in k-space than before? Message-ID: <c8e72aaf-c53f-df54-30d9-caa6ff45a2fe(a)desy.de> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear Matt, attached you will find a recent data file which is showing the problem and two plots of the data (A RuO2 powder sample on Scotch tape) in the file. One plot is showing the Chi(k) with and without rebinning the other one just mue(E) with and without rebinning. It seems it is no good to convert previously rebinned data to k-space. the rebinned mue(E) looks okay and the original data converted to k-space does also look ok. I produced the plots with Athena 0.9.24 (I know not the most recent version) under WIN 7 with IFEFFIT as backend. I wasn't able yet to reproduce this on my office desktop using LINUX and the most recent dathena and Larch, because of some trouble with reading the data file... No idea yet, might be worse another thread or might be something stupid on my site. Cheers, Edmund On 27.06.2018 20:31, Matt Newville wrote: > HI Ilya, Edmund, Carlo, > > Ilya and/or Carlo: can you post some example unbinned data?? As it > turns out, I am adding a rebinning feature in the Larch XAS Viewer GUI > that should be ready for a ready-to-try release very soon (for IIT > XAFS School and XAFS2018). > > This seems like a good chance to test these procedures out. > > My approach for this is to this is to make a "normal XAFS energy grid" > of ~5 eV steps, 0.25 eV steps, 0.05 Ang^-1 steps that the downstream > processing needs, and then do one of two strategies -- maybe there > should be more?: > ?a) do a straight interpolation onto this array -- that is probably > the "noisy" result. > ?b) assign each energy point in the original data to one of these > energy bins, and take the average of all the points in each bin. > > I'd also like to try using energy-weighted mean (centroid).? Probably > most of the data is so finely spaced that this won't make much > difference, but it might be a good option.?? It might be able to help > compensate for energy jitter, assuming that the recorded energy > (probably from an encoder) is more accurate than the requested energy. > > It's also interesting to think about doing a Savitzky-Golay smoothing, > though that might require knowing if the data points are actually > uniform in mono angle or mono energy.? It also makes it easy to > over-do the smoothing, and so a little trickier to prevent bad results. > > Do you (or anyone else) have any suggestions for how to best re-bin > this kind of data? > > --Matt > > > On Wed, Jun 27, 2018 at 10:15 AM Carlo Segre <segre(a)iit.edu > <mailto:segre@iit.edu>> wrote: > > > Yes, we measure fast and have taken as many as 20000 points.? ?The > problem > is not in the shifts that you mention.? This is normal and > expected.? the > problem is specificallly in the rebinning algorithm in Demeter.? > It seems > to be different than the one in the old Horae package.? I have > done a test > of this and I attache a coule of figures that show the difference. > > I have used 10 continuous scans for this test.? The data were > taken at the > MRCAT beamline, Sector 10 at the APS.? The data are for the Fe > K-edge and > there are about 3400 points per scan with a point density of about > 0.35 > eV/step.? I used both versions of Athena and performed the > following steps > to give the data groups shown in the plots > > new_athena.png > ? Fe_new_rebin_merge - (blue) all 10 scans rebinned at input and then > ? ? ? ? ? ? ? ? ? ? ? ?merged > ? Fe_new_merge? ? ? ?- (red) all 10 scans merged only > ? Fe_new_merge_rebin - (green) all 10 scans merged then rebinned > > old_athena.png > ? Fe_old_rebin_merge - (blue) all 10 scans rebinned at input and then > ? ? ? ? ? ? ? ? ? ? ? ?merged > ? Fe_old_merge? ? ? ?- (red) all 10 scans merged only > ? Fe_old_merge_rebin - (green) all 10 scans merged then rebinned > > comp_athena.png > ? Fe_old_rebin_merge - (blue) > ? Fe_new_rebin_merge - (red) > > It is clear that the new Athena (Demeter) is not rebinning the > same way as > the old one (Horae).? The contrast is particularly evident with > the last > plot. The new rebinning algorithm is introducing more noise.? For the > moment, I recommend only merging and perhaps smoothing if you can > tolerate > a bit of amplitude reduction. > > I have been thinking that it might even be better to have the data > acquisition software do the rebinning on the fly so the data does > not have > to be manipulated in Athena.? I am not sure if this is a good idea > yet but > I think it would help my users. > > Carlo > > > On Wed, 27 Jun 2018, Edmund Welter wrote: > > > Dear Carlo, > > > > do you also measure as fast as possible in the sense that for > two consecutive > > scans the points on the energy axis are not at the same > positions? This is > > what happens at my beamline. The differences are typically very > small but > > there are differences and one should not just add all the first > points and > > all the second points and so on because they are not necessarily > exactly at > > the same energy. Sometimes the beamline computer is doing > something else in > > parallel (whatever that might be) and the distance between > points A and B is > > significantly larger than the distance between B and C. > > > > So, the problem is, at which point does it make sense to merge > several > > spectra of the same sample? I presume that Athena is taking care > of this when > > I use it to merge spectra, but it can only do so by > interpolating the points > > in the spectrum onto a common grid before summing up the spectra. > > > > The best solution might be to rebin/interpolate the spectra onto > a fixed grid > > before they are imported into Athena (or any other program), > depends on what > > Athena is exactly doing when it is rebinning data. > > > > Another aspect is that Athena is not very happy about 8600 > points/spectrum > > anyway, at least as long as it using Ifeffit. > > > > Cheers, > > > > Edmund > > > > > > > > On 27.06.2018 15:14, Carlo Segre wrote: > >> > >> > >> Hi Ilya: > >> > >> We always take data in this mode at APS Sector 10 and I have > also find that > >> the rebinning function is not working satisfactorily at this > time.? I find > >> that for the current version of the software it is better to > merge your > >> data and let IFEFFIT interpolate to the dk=0.05 grid that it uses. > >> > >> Carlo > >> > >> > >> On Wed, 27 Jun 2018, Ilya Sinev wrote: > >> > >>> Hi all, > >>> > >>> > >>> > >>> I have a question regarding the chi(k) function isolation and > rebinning > >>> processes. I have some data recorded in ?quasi channel-cut? > modus, i.e. > >>> with > >>> the mono constantly moving and the data points collected with > the highest > >>> possible rate. With 180 sec measurement in yields to a > spectrum of ca. > >>> 8600 > >>> point, which obviously needs to be rebinned. The rebinned > data, however, > >>> does not look good in k-space even if multiple data are > merged. Moreover, > >>> I > >>> have an impression that the raw spectrum in k-space does not > have those > >>> 8000+ points anymore but significantly less. Is there any > reduction of the > >>> data points number that is not seen (e.g. as a preparation > step for FT)? > >>> Since the unbinned data has higher quality, does it then make > more sense > >>> to > >>> keep using it for EXAFS analysis? > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> Thank you > >>> > >>> Ilya Sinev > >>> > >>> > >>> > >>> > >> > > > > _______________________________________________ > > 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 > > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics > Interim Chair, Department of Chemistry > Director, Center for Synchrotron Radiation Research and > Instrumentation > Illinois Institute of Technology > Voice: 312.567.3498? ? ? ? ? ? Fax: 312.567.3494 > segre(a)iit.edu <mailto:segre@iit.edu> http://phys.iit.edu/~segre > <http://phys.iit.edu/~segre> segre(a)debian.org > <mailto:segre@debian.org>_______________________________________________ > 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 > > > > -- > --Matt Newville <newville at http://cars.uchicago.edu > <http://cars.uchicago.edu>> 630-252-0431 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 184, Issue 21
by Christopher Chantler 28 Jun '18

28 Jun '18

Dear all Rebinning is always fraught; I would normally not allow a student to do it... You might be interested in our paper [Schalken, M et al., JSR, 2018] which explicitly avoids rebinning and propagates uncertainty to ifeffit-like [Matt modified] analysis, efeffit. This was an outcome from Q2XAFS. We also include code in supplementary information. Note that this also discusses interpolation and how to preserve information content if that is needed. Best wishes Chris PS looking forward to great discussions at Poland -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS CIT, CCN President, 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: Thursday, 28 June 2018 4:35 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 184, Issue 21 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: data after rebinning look worse in k-space than before? (Matt Newville) 2. Re: data after rebinning look worse in k-space than before? (Carlo Segre) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Jun 2018 13:31:44 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: Carlo Segre <segre(a)iit.edu>, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] data after rebinning look worse in k-space than before? Message-ID: <CA+7ESbq--_=qjXALgfZ4Bhg4xcwGJDbby5sSshEwMVB=v_bptA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" HI Ilya, Edmund, Carlo, Ilya and/or Carlo: can you post some example unbinned data? As it turns out, I am adding a rebinning feature in the Larch XAS Viewer GUI that should be ready for a ready-to-try release very soon (for IIT XAFS School and XAFS2018). This seems like a good chance to test these procedures out. My approach for this is to this is to make a "normal XAFS energy grid" of ~5 eV steps, 0.25 eV steps, 0.05 Ang^-1 steps that the downstream processing needs, and then do one of two strategies -- maybe there should be more?: a) do a straight interpolation onto this array -- that is probably the "noisy" result. b) assign each energy point in the original data to one of these energy bins, and take the average of all the points in each bin. I'd also like to try using energy-weighted mean (centroid). Probably most of the data is so finely spaced that this won't make much difference, but it might be a good option. It might be able to help compensate for energy jitter, assuming that the recorded energy (probably from an encoder) is more accurate than the requested energy. It's also interesting to think about doing a Savitzky-Golay smoothing, though that might require knowing if the data points are actually uniform in mono angle or mono energy. It also makes it easy to over-do the smoothing, and so a little trickier to prevent bad results. Do you (or anyone else) have any suggestions for how to best re-bin this kind of data? --Matt On Wed, Jun 27, 2018 at 10:15 AM Carlo Segre <segre(a)iit.edu> wrote: > > Yes, we measure fast and have taken as many as 20000 points. The problem > is not in the shifts that you mention. This is normal and expected. the > problem is specificallly in the rebinning algorithm in Demeter. It seems > to be different than the one in the old Horae package. I have done a test > of this and I attache a coule of figures that show the difference. > > I have used 10 continuous scans for this test. The data were taken at the > MRCAT beamline, Sector 10 at the APS. The data are for the Fe K-edge and > there are about 3400 points per scan with a point density of about 0.35 > eV/step. I used both versions of Athena and performed the following steps > to give the data groups shown in the plots > > new_athena.png > Fe_new_rebin_merge - (blue) all 10 scans rebinned at input and then > merged > Fe_new_merge - (red) all 10 scans merged only > Fe_new_merge_rebin - (green) all 10 scans merged then rebinned > > old_athena.png > Fe_old_rebin_merge - (blue) all 10 scans rebinned at input and then > merged > Fe_old_merge - (red) all 10 scans merged only > Fe_old_merge_rebin - (green) all 10 scans merged then rebinned > > comp_athena.png > Fe_old_rebin_merge - (blue) > Fe_new_rebin_merge - (red) > > It is clear that the new Athena (Demeter) is not rebinning the same way as > the old one (Horae). The contrast is particularly evident with the last > plot. The new rebinning algorithm is introducing more noise. For the > moment, I recommend only merging and perhaps smoothing if you can tolerate > a bit of amplitude reduction. > > I have been thinking that it might even be better to have the data > acquisition software do the rebinning on the fly so the data does not have > to be manipulated in Athena. I am not sure if this is a good idea yet but > I think it would help my users. > > Carlo > > > On Wed, 27 Jun 2018, Edmund Welter wrote: > > > Dear Carlo, > > > > do you also measure as fast as possible in the sense that for two > consecutive > > scans the points on the energy axis are not at the same positions? This > is > > what happens at my beamline. The differences are typically very small > but > > there are differences and one should not just add all the first points > and > > all the second points and so on because they are not necessarily exactly > at > > the same energy. Sometimes the beamline computer is doing something else > in > > parallel (whatever that might be) and the distance between points A and > B is > > significantly larger than the distance between B and C. > > > > So, the problem is, at which point does it make sense to merge several > > spectra of the same sample? I presume that Athena is taking care of this > when > > I use it to merge spectra, but it can only do so by interpolating the > points > > in the spectrum onto a common grid before summing up the spectra. > > > > The best solution might be to rebin/interpolate the spectra onto a fixed > grid > > before they are imported into Athena (or any other program), depends on > what > > Athena is exactly doing when it is rebinning data. > > > > Another aspect is that Athena is not very happy about 8600 > points/spectrum > > anyway, at least as long as it using Ifeffit. > > > > Cheers, > > > > Edmund > > > > > > > > On 27.06.2018 15:14, Carlo Segre wrote: > >> > >> > >> Hi Ilya: > >> > >> We always take data in this mode at APS Sector 10 and I have also find > that > >> the rebinning function is not working satisfactorily at this time. I > find > >> that for the current version of the software it is better to merge your > >> data and let IFEFFIT interpolate to the dk=0.05 grid that it uses. > >> > >> Carlo > >> > >> > >> On Wed, 27 Jun 2018, Ilya Sinev wrote: > >> > >>> Hi all, > >>> > >>> > >>> > >>> I have a question regarding the chi(k) function isolation and rebinning > >>> processes. I have some data recorded in ?quasi channel-cut? modus, > i.e. > >>> with > >>> the mono constantly moving and the data points collected with the > highest > >>> possible rate. With 180 sec measurement in yields to a spectrum of ca. > >>> 8600 > >>> point, which obviously needs to be rebinned. The rebinned data, > however, > >>> does not look good in k-space even if multiple data are merged. > Moreover, > >>> I > >>> have an impression that the raw spectrum in k-space does not have those > >>> 8000+ points anymore but significantly less. Is there any reduction of > the > >>> data points number that is not seen (e.g. as a preparation step for > FT)? > >>> Since the unbinned data has higher quality, does it then make more > sense > >>> to > >>> keep using it for EXAFS analysis? > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> Thank you > >>> > >>> Ilya Sinev > >>> > >>> > >>> > >>> > >> > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics > Interim Chair, Department of Chemistry > Director, Center for Synchrotron Radiation Research and Instrumentation > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at http://cars.uchicago.edu> 630-252-0431

4 3

data after rebinning look worse in k-space than before?
by Ilia Sinev 27 Jun '18

27 Jun '18

Hi all, I have a question regarding the chi(k) function isolation and rebinning processes. I have some data recorded in “quasi channel-cut” modus, i.e. with the mono constantly moving and the data points collected with the highest possible rate. With 180 sec measurement in yields to a spectrum of ca. 8600 point, which obviously needs to be rebinned. The rebinned data, however, does not look good in k-space even if multiple data are merged. Moreover, I have an impression that the raw spectrum in k-space does not have those 8000+ points anymore but significantly less. Is there any reduction of the data points number that is not seen (e.g. as a preparation step for FT)? Since the unbinned data has higher quality, does it then make more sense to keep using it for EXAFS analysis? [image: image.png] Thank you Ilya Sinev -- Dr. Ilya Sinev Institute for Experimental Physics IV Faculty of Physics and Astronomy Ruhr-Universität Bochum Universitätsstrasse 150 44801 Bochum, Germany

1 0

Rank of path and dopant amp
by ABDUL AHAD 23 Jun '18

23 Jun '18

Hi all I have a question regarding the Rank of path. Since the Rank represent the spectral weight of the particular path. So that if i have a dopant say Ca and it shows the rank 60 while the main atoms shows rank 98. So in order to maintain the doping concentration, what i have to do? for half atomic % doping. do i make the amp of these two as amp*0.5 ? or do i first normalized its by rank and then decide the amp percentage ? Thanks

1 0

LBNL Postdoctoral Fellow position
by Corwin H. Booth 22 Jun '18

22 Jun '18

Greetings all! I have just posted for a new Postdoctoral Fellow position to work with me at Lawrence Berkeley National Laboratory on projects within the Actinide Chemistry Group here and in collaboration with scientists at Los Alamos National Laboratory and Lawrence Livermore National Laboratory. Most of the work is to perform and analyze XAFS data, although there will also be work on resonant x-ray emission spectroscopy and potentially other spectroscopies. The focus will be on various plutonium-bearing materials, including metals, oxides and minerals. Please take a look at the official posting and apply if you are interested and meet the minimum qualifications. Here is the posting: https://lbl.referrals.selectminds.com/jobs/chemist-postdoctoral-fellow-921 <https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=85262> Best, Corwin -- Corwin H. Booth Chemical Sciences Division Lawrence Berkeley National Laboratory MS 70A-1150 1 Cyclotron Rd. Berkeley, CA 94720-8175 voice: 510-486-6079 FAX: 510-486-5596 Email: chbooth(a)lbl.gov Web: http://lise.lbl.gov/chbooth/

1 0

Prolems with JFEFF on Windows 7.
by Szymon Kucharczyk 15 Jun '18

15 Jun '18

Dear Sir or Madam. I am new user or JFEFF 9.6.4, which I use doing my dissertation in Institute of Nuclear Physics PAN in Cracow. I use Windows 7 Professional N and I have problems with JFEFF. Therefore I can open files in It, but when I try to Save&Run there are some errors. I attached a screenshot with errors showed in command window in attachment. I tried to solve this by instaling different versions of JAVA, runnig as an admin and also check whether It is not my antivirus, but none of them helped. Thanks in advance. Best regards, Szymon Kucharczyk.

2 1

Restrain
by ABDUL AHAD 14 Jun '18

14 Jun '18

Thanks for reply, yes i have to take care of such things. But let me confined us within the limit, suppose the single scattering path is absorber (Cu) to Cu and multi scattering path is absorber to oxygen then back to absorber (forward scattering) and other one is absorber to oxygen then oxygen to Cu and then back to absorber, All of these have same Reff. So my question is can use the same delt_r for all of these path in which only Cu and O take place. If all of these are different then how? Thanks in advance

2 1

Restrain
by ABDUL AHAD 14 Jun '18

14 Jun '18

Hi all, i have query regarding restrain. suppose i have single scattering path which is equal to lattice parameter. Now i also have multi-scattering path with Reff equal to the same single scattering path. Now my question is, Is it correct to constraint the all path of same reff to equal delt_r, Because i think in magnitude they must lie on same R but different in phase (different frequency component). thanks -- ** *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a <a_ahad.rs(a)amu.ac.in>bdulahad.phy(a)gmail.com <bdulahad.phy(a)gmail.com>*

2 1

Decision of Enot and model
by ABDUL AHAD 12 Jun '18

12 Jun '18

hi all, i have some questions to experts. if i have cif file to any compound say ZnO and i fitted the exafs data with it. Now the question is if i wish to fit the doped ZnO with the same cif and the same Enot then it shows large value of delta to fit. The question is have i look for different Enot or i have to change the cif for the doped one. Note i m talking about the main peak fit that only contain the Zn and O not the doped element. Is there any limit of delta for bond length? i think it should be small. Thanks in advance -- ** *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a <a_ahad.rs(a)amu.ac.in>bdulahad.phy(a)gmail.com <bdulahad.phy(a)gmail.com>*

2 1

Re: [Ifeffit] No shift in XANES absorption peak
by Disha Gupta 12 Jun '18

12 Jun '18

Dear Claudia, Qingying Jia, Matt Thank you so much for your responses :) The shift in bond length I see is almost around 0.1-0.12 Angstrom, which is not small enough to ignore. I think the coordination might be changing, if not the oxidation state. I will redo the Artemis calculations with N as a variable again to see if that helps. Because keeping my N constant actually gave me pretty low Debye-Waller values and R factor was also below 5% so I was assuming the fits were reliable. I was also thinking maybe Mn is undergoing partial oxidation, however, in bulk we do not see that change in the main XANES absorption peak. I am not sure if that can be a possibility. Thanks a lot again! Kind Regards Disha Disha Gupta Graduate Student School of Materials Science and Engineering Nanyang Technological University (NTU), Singapore +65 84087404 DISHA001(a)e.ntu.edu.sg On Mon, Jun 11, 2018 at 10:14 PM, <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 on Windows 10 does not work (sikolen) > 2. Re: No shift in XANES absorption peak (Claudia Schnohr) > 3. Re: No shift in XANES absorption peak (Qingying Jia) > 4. Re: Demeter on Windows 10 does not work (Matt Newville) > 5. Re: No shift in XANES absorption peak (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 11 Jun 2018 13:39:03 +0200 > From: sikolen <sikolen(a)jinr.ru> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter on Windows 10 does not work > Message-ID: <f70651f521390af9595e52ea564ba769(a)jinr.ru> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Thanks Kathy, > > It seems the problem is really with the wrong path... Now I see how to > fix it. > > Vadim > > > On 2018-06-08 17:07, Kathy Dardenne wrote: > > Dear Vadim, > > > > I am running myself Demeter 0.9.26, 64bit under win10 and do not have > > such > > trouble. But your description is similar to the problem occurring with > > the > > previous release of Demeter 0.9.26 pre2 (old path for gnuplot > > executable in > > ini file leading the same effect), did you download the actual version > > for > > Demeter 0.9.26? this later trouble is fixed and Demeter runs smoothly > > with > > win7 and win10. > > > > Kathy > > > > -----Message d'origine----- > > De?: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> De la part de > > sikolen > > Envoy??: vendredi 25 mai 2018 10:01 > > ??: ifeffit(a)millenia.cars.aps.anl.gov > > Objet?: [Ifeffit] Demeter on Windows 10 does not work > > > > > > Dear all, > > > > I've just changed my loving Windows-7 to the new Windows-10. I've > > installed > > Demeter (v.0.9.26, 64-bit), but it does not work: cmd-Windows appears > > for > > the a couple of seconds and disappears forever. Is it already known > > problem > > of the OS? Sorry, may be this question already appeared here, I just > > missed > > it. > > > > Vadim > > -- > > *********************************** > > Dr. Vadim Sikolenko > > Senior Scientist > > Frank Laboratory of Neutron Physics > > Vadim.Sikolenko(a)jinr.ru > > Skype: svadimm > > ********************************** > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > -- > *********************************** > Dr. Vadim Sikolenko > Senior Scientist > Frank Laboratory of Neutron Physics > Vadim.Sikolenko(a)jinr.ru > Skype: svadimm > ********************************** > > > ------------------------------ > > Message: 2 > Date: Mon, 11 Jun 2018 14:56:22 +0200 > From: Claudia Schnohr <c.schnohr(a)uni-jena.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] No shift in XANES absorption peak > Message-ID: > <20180611145622.Horde.4UvsqRy3fmqp-P5XNJL1uln(a)webmail.uni-jena.de> > Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes > > Dear Disha, > > In principle, yes, there can be a change of bond length without a > notable change of the XANES. But it also depends on how large the bond > length changes are that you observe. > > I have studied a lot of semiconductor alloys, for example (In,Ga)P or > Cu(In,Ga)Se2 where the Ga and In atoms share the same lattice site. > They are always coordinated to four P or Se atoms, respectively, but > the bond lengths change by 0.02 to 0.03 A because the size of the unit > cell changes with In/Ga ratio. At the same time, the Ga and In XANES > is completely unaffected by a change of the In/Ga ratio. If you are > interested in this, you may have a look at Phys. Rev. B 85, 245204 > (2012), J. Appl. Phys. 116, 093703 (2014), or Appl. Phys. Rev. 2, > 031304 (2015). > > This is just to say that, yes, in some special cases you can have a > change of bond length without a change of XANES. There can be lot's of > other things going on, too :) > > Cheers, Claudia > > > > ----- Nachricht von Disha Gupta <dsha.91(a)gmail.com> --------- > Datum: Mon, 11 Jun 2018 18:29:49 +0800 > Von: Disha Gupta <dsha.91(a)gmail.com> > Antwort an: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov > > > Betreff: Re: [Ifeffit] No shift in XANES absorption peak > An: ifeffit(a)millenia.cars.aps.anl.gov > > > > Dear Dr Carlo > > > > The edges are almost identical. The pre-edge intensity change isn't that > > significant I feel. I did the Artemis fittings with the coordination > > numbers fixed. Maybe I can try varying the coordination numbers and see > if > > it gives a different result. > > I have attached the images of the pre-edge and main peak. > > > > > > > > > > > > Thanks and Regards > > Disha > > > > > > > > > > From: Carlo Segre <segre(a)iit.edu> > > Date: Mon, Jun 11, 2018, 12:34 > > Subject: Re: [Ifeffit] No shift in XANES absorption peak > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > > > > > > Hi Disha: > > > > it would be good to see the XANES you are referring to. Are the edges > > identical or do they change but not shift significantly? Is the > > coordination number also constant? Generally, the bond distance will > > change with oxidation state if the coordination number is constant but if > > the coordination number changes, then there could be a change in bond > > length too. > > > > Cheers, > > > > Carlo > > > > > > On Mon, 11 Jun 2018, Disha Gupta wrote: > > > >> Dear All > >> > >> Firstly, I would like to say sorry if I have missed out on this > discussion > >> before but it would be great if you could help me out. > >> I have been analyzing some Mn K-edge XAS data for some battery > materials. > >> While the XANES data shows no shift in the main absorption peak which > > means > >> that there is no oxidation change happening, however, when I am fitting > > the > >> data in Artemis, I can see a shift in the bond lengths suggesting an > >> oxidation change. Is it possible that bond lengths change even though > > XANES > >> spectra show no change? > >> > >> > >> Thank you and Kind Regards > >> Disha > >> > > > > -- > > Carlo U. Segre -- Duchossois Leadership Professor of Physics > > Interim Chair, Department of Chemistry > > Director, Center for Synchrotron Radiation Research and Instrumentation > > Illinois Institute of Technology > > Voice: 312.567.3498 Fax: 312.567.3494 > > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > Disha Gupta > > Graduate Student > > School of Materials Science and Engineering > > Nanyang Technological University (NTU), Singapore > > +65 84087404 > > DISHA001(a)e.ntu.edu.sg > > > > > > On Mon, Jun 11, 2018 at 11:34 AM, Disha Gupta <dsha.91(a)gmail.com> wrote: > > > >> Dear All > >> > >> Firstly, I would like to say sorry if I have missed out on this > discussion > >> before but it would be great if you could help me out. > >> I have been analyzing some Mn K-edge XAS data for some battery > materials. > >> While the XANES data shows no shift in the main absorption peak which > means > >> that there is no oxidation change happening, however, when I am fitting > the > >> data in Artemis, I can see a shift in the bond lengths suggesting an > >> oxidation change. Is it possible that bond lengths change even though > XANES > >> spectra show no change? > >> > >> > >> Thank you and Kind Regards > >> Disha > >> > > > ----- Ende der Nachricht von Disha Gupta <dsha.91(a)gmail.com> ----- > > > > -- > PD Dr. Claudia S. Schnohr > Institut f?r Festk?rperphysik > Friedrich-Schiller-Universit?t Jena > Max-Wien-Platz 1 > D-07743 Jena > Germany > > Tel: +49 3641 947333 > Fax: +49 3641 947302 > > > > ------------------------------ > > Message: 3 > Date: Mon, 11 Jun 2018 09:59:23 -0400 > From: Qingying Jia <qjia(a)hawk.iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] No shift in XANES absorption peak > Message-ID: > <CAJR6HVQPT6q_1_PhFNB2+mqWuZf+YjgqvJpYeaWg5j=h30Zp8w@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Disha, > > The shift in bond distance in this case, is not necessarily associated > with the change of oxidation state. It can be simply caused by the > insertion/removal of Li/Na or whatever depending on your battery type > during the charge/discharge, which sometimes changes the oxidation state of > Mn slightly, sometimes doesn't. > > Regards, > > On Sun, Jun 10, 2018 at 11:34 PM, Disha Gupta <dsha.91(a)gmail.com> wrote: > > > Dear All > > > > Firstly, I would like to say sorry if I have missed out on this > discussion > > before but it would be great if you could help me out. > > I have been analyzing some Mn K-edge XAS data for some battery materials. > > While the XANES data shows no shift in the main absorption peak which > means > > that there is no oxidation change happening, however, when I am fitting > the > > data in Artemis, I can see a shift in the bond lengths suggesting an > > oxidation change. Is it possible that bond lengths change even though > XANES > > spectra show no change? > > > > > > Thank you and Kind Regards > > Disha > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > >

2 1

Re: [Ifeffit] No shift in XANES absorption peak
by Disha Gupta 11 Jun '18

11 Jun '18

Dear Dr Carlo The edges are almost identical. The pre-edge intensity change isn't that significant I feel. I did the Artemis fittings with the coordination numbers fixed. Maybe I can try varying the coordination numbers and see if it gives a different result. I have attached the images of the pre-edge and main peak. Thanks and Regards Disha From: Carlo Segre <segre(a)iit.edu> Date: Mon, Jun 11, 2018, 12:34 Subject: Re: [Ifeffit] No shift in XANES absorption peak To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Hi Disha: it would be good to see the XANES you are referring to. Are the edges identical or do they change but not shift significantly? Is the coordination number also constant? Generally, the bond distance will change with oxidation state if the coordination number is constant but if the coordination number changes, then there could be a change in bond length too. Cheers, Carlo On Mon, 11 Jun 2018, Disha Gupta wrote: > Dear All > > Firstly, I would like to say sorry if I have missed out on this discussion > before but it would be great if you could help me out. > I have been analyzing some Mn K-edge XAS data for some battery materials. > While the XANES data shows no shift in the main absorption peak which means > that there is no oxidation change happening, however, when I am fitting the > data in Artemis, I can see a shift in the bond lengths suggesting an > oxidation change. Is it possible that bond lengths change even though XANES > spectra show no change? > > > Thank you and Kind Regards > Disha > -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit Disha Gupta Graduate Student School of Materials Science and Engineering Nanyang Technological University (NTU), Singapore +65 84087404 DISHA001(a)e.ntu.edu.sg On Mon, Jun 11, 2018 at 11:34 AM, Disha Gupta <dsha.91(a)gmail.com> wrote: > Dear All > > Firstly, I would like to say sorry if I have missed out on this discussion > before but it would be great if you could help me out. > I have been analyzing some Mn K-edge XAS data for some battery materials. > While the XANES data shows no shift in the main absorption peak which means > that there is no oxidation change happening, however, when I am fitting the > data in Artemis, I can see a shift in the bond lengths suggesting an > oxidation change. Is it possible that bond lengths change even though XANES > spectra show no change? > > > Thank you and Kind Regards > Disha >

4 3

Demeter on Windows 10 does not work
by sikolen 11 Jun '18

11 Jun '18

Dear all, I've just changed my loving Windows-7 to the new Windows-10. I've installed Demeter (v.0.9.26, 64-bit), but it does not work: cmd-Windows appears for the a couple of seconds and disappears forever. Is it already known problem of the OS? Sorry, may be this question already appeared here, I just missed it. Vadim -- *********************************** Dr. Vadim Sikolenko Senior Scientist Frank Laboratory of Neutron Physics Vadim.Sikolenko(a)jinr.ru Skype: svadimm **********************************

3 3

No shift in XANES absorption peak
by Disha Gupta 11 Jun '18

11 Jun '18

Dear All Firstly, I would like to say sorry if I have missed out on this discussion before but it would be great if you could help me out. I have been analyzing some Mn K-edge XAS data for some battery materials. While the XANES data shows no shift in the main absorption peak which means that there is no oxidation change happening, however, when I am fitting the data in Artemis, I can see a shift in the bond lengths suggesting an oxidation change. Is it possible that bond lengths change even though XANES spectra show no change? Thank you and Kind Regards Disha

3 2

Interpreting old XANES data with missing standards
by Don Baker 08 Jun '18

08 Jun '18

Hello All, First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask. So, here is some background: I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available. Now for for my questions: 1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?) 2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling? And information, ideas, and suggestions that you may have will be appreciated. Wishing you all the best from a spring morning in Montreal, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

6 7

FEFF question
by Loges, Anselm G 06 Jun '18

06 Jun '18

Hi everyone, not exactly an ifeffit question, but maybe someone knows. Since I am for ome reason unable to install ifeffit or demeter on certain Linux computers (others with the same distribution and same settings work fine), I have been trying to install FEFF8-lite. However, on the downloadpage: http://monalisa.phys.washington.edu/feff/Bin-Source-feff8Lite/Bin-Source.ht… the link for the Linux binary is dead and when I try to compile from source using gfortran it does not work and throws "Error: Two main PROGRAMs at (1) and (2)". A quick look in the code reveals that none of the subroutines etc. are ended explicitly by name but only by an anonymous "end", making debugging this problem in the source a colossal nightmare in a 52951 line source file. This also likely explains where the error comes from in the first place, since lack of explicitness is the mother of portability problems. I'm wondering: has anyone had success installing FEFF8-lite or compiling from source? If so, with what compiler? Or is there a working Linux binary wandering about the interwebs, which I have not found? I have also tried using Matt Newvilles package on Github: https://github.com/xraypy/feff85exafs but no luck there either. This one complains about a python package named "larch" being missing, making me think it wants a preexisting a Larch installation. Installing FEFF8L should not require Larch, only the other way round (possibly), right? I'm lost and thankful for any and all help! Best regards, Anselm

2 3

Different Enot for different shells
by Abdul Ahad 30 May '18

30 May '18

Hi all, Again i have a question to experts. Suppose i have bond length information via first shell fitting. And by symmetry of crystal structure i know that higher shell should be double of that bond length .....like lattice parameter that is just double of particular bond length (Metal to metal distance which should double of Metal to oxygen which is observable via first shell). I would like to know that in this case my Enot will be same or different as in first shell or i have to Guess another enot, Then how can i control all these parameters. Thanks in advance

2 1

Amplitude and sigma square
by Abdul Ahad 29 May '18

29 May '18

Hi all, Thanks to Professor Pierre, Prof. Segre and Prof. Scott, for make some beautiful comments. One thing i wish to mention here that i have both Fluorescence and Transmission data, with the same model transmission data give Amplitude around 0.72 but Fluorescence gives 0.15, Is this self absorption problem, as prof. Segre suggested. Also i have tried with one shell with N=6 and then 4 and 2 and i got the genuine trend on average under limit of error. But the for N=2 the sigma goes to 0.0001 order while for N=4 it is usual 0.001 order (this both have simultaneously taken in a one fit). Also N=6 gives all variable fine. thanks

2 1

Amplitude and sigma square
by Abdul Ahad 29 May '18

29 May '18

Hi all, I have couple of questions. 1. I found in many tutorials that the value of amp should lie between 0.7 and 1. But when I refined it goes to 0.15, what's wrong with it. 2. The value of sigma2. Some time at high k, value, it turns to negative but small. What I suppose to do? 3. If I need to know the behavior of octahedra distortion with temperature, and it is lies within the first shell. So what is the need of higher shell fitting.??? Thanks in advance

3 2

Amplitude and sigma square (Abdul Ahad)
by Pierre Lecante 28 May '18

28 May '18

Hi Abdul, In my opinion, the short answer is that your model is wrong; amplitude, coordination number and sigma square are strongly correlated; if your model is not adequate or if values are too far from the convergence zone, non physical effects appear; usually, very small or negative values for sigma2 mean coordination number too low, but very small amplitude means the reverse! I suggest to start with a plain simulation (all parameters locked to expected values) and check that there is not something weird in different k zones, which might eventually indicate unexpected species close to the central atom; my 2 cents, Pierre Le 28/05/2018 à 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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. Amplitude and sigma square (Abdul Ahad) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 May 2018 14:16:39 +0530 > From: Abdul Ahad <matrixabdulahad(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Amplitude and sigma square > Message-ID: > <CAEFSGt6r3xbjc2zPk1fc2bGmKwgb_AVVcfrWa198kmY8QkpMJA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I have couple of questions. > 1. I found in many tutorials that the value of amp should lie between 0.7 > and 1. But when I refined it goes to 0.15, what's wrong with it. > > 2. The value of sigma2. Some time at high k, value, it turns to negative > but small. What I suppose to do? > > 3. If I need to know the behavior of octahedra distortion with temperature, > and it is lies within the first shell. So what is the need of higher shell > fitting.??? > > Thanks in advance >

1 0

Re: [Ifeffit] S02
by Matt Newville 25 May '18

25 May '18

Julian, On Fri, May 25, 2018 at 9:01 AM Julian Ehwald <jehwald(a)gmail.com> wrote: > Dear Matt, > > > > Thank you for your superfast answer. I obtained new data from the people > at the beamline today, and the set contains both Total electron Yield and > Total fluorescence yield. As far as I understand, they both tell us > something about the absorption. Which is usually used for analysis? If I > process them with Athena I get considerable differences… > > > Please use the mailing list. Either or both of total electron yied and total fluorescence yield can be used for XAFS. That is, total emission of high-energy electrons and emission of fluorescence X-rays are both proportional to the absorption cross-section for an atom, at least to first approximation. There are complications in using these. For X-ray fluorescence the main complication is "over absorption" which happens in materials in which the element of interest is high concentration (effects can be noticeable at ~1% and are usually significant-but-correctable up to ~10%, and are nearly impossible to correct above ~50% concentration). For electron yield, the main complication is that the electron escape depth is shallow enough that the measurement may be more sensitive to the surface than the bulk of the sample. That sort of depends on how you define "surface" (the electrons escape from 10s to 100s of Angstroms), but can be seen as an advantage if surface sensitivity is what you want. For both, using the data as XAFS means using mu ~ EmissionIntensity / I0. That's very different from transmission data, which often trips people up when importing the data into Athena: DO NOT use the log( EmissionIntensity / I0), use EmissionIntensity/I0. --Matt

1 0

Re: [Ifeffit] S02
by Matt Newville 25 May '18

25 May '18

On Fri, May 25, 2018 at 5:11 AM Julian Ehwald <jehwald(a)gmail.com> wrote: > Dear Matt, > > > > I still have questions about Artemis concerning the S0^2. In your > book/summary called XAFS-Fundamentals there is a section at the beginning > of chapter six that says: > > > > “Starting with this structure, we can calculate the scattering amplitude > and phaseshifts > > and theoretically. The complete calculation is beyond the scope of this > treatment, > > but don’t worry too much by that phrase “we’ll calculate these > theoretically”! These > > functions are actually fairly easy to calculate using one of a few > different computer > > programs – for the calculations here, the FEFF program was used. The > results of the > > FEFF calculation are stored in simple files containing the scattering > factors and meanfree- > > path for a given coordination shell. The calculations in these files can > be used > > directly in a number of analysis programs.” > > > > Are these somewhere listed in Artemis? > The calculations stored in the feffNNNN.dat files can be accessed from Larch, but I think they're not readily exposed by Artemis. The point is that you don't have to worry about these scattering factors, but only about the Path Parameters (S02, E0, deltaR, sigma2, etc) that modify these scattering terms. > Because if I start fitting the value in GDS is always guessed to be one, > for any element in the sample. If I go and look at the FEFF calculation it > tells me: > > > > > > TITLE LiPF6 > > > > HOLE 1 1.0 * FYI: (F K edge @ 696.7 eV, 2nd number is S0^2) > > * mphase,mpath,mfeff,mchi > > CONTROL 1 1 1 1 > > PRINT 1 0 0 0 > > > > I don’t really understand which is the second number and why all S0^2 then > are either 0 or 1. > > > > Best, Julian > One can set an S02 value during the Feff calculation. That is what goes as the second number in the HOLE entry in feff.inp (The first value is an integer indicating the edge type -- 1 for 'K', and so on). Setting that value will apply the S02 value to all paths calculated by that run of Feff. You can also set values for sigma2 from Feff too, Artemis/Ifeffit/Larch etc use the Feff calculations stored in feffNNNN.dat (or equivalent) and build a model from a collection of paths from Feff. If S02 or sigma2 is set in the original Feff calculation(s), it is difficult to track during the analysis (neither S02 nor sigma2 are written to the individual feffNNNN.dat files). In some sense Artemis/Ifeffit/Larch etc only use part of Feff -- the calculation of the EXAFS contribution of a single, idealized path. They do not use the sum-of-paths module(s) of Feff, but instead replace that with its own sum-of-paths implementation that is richer (allowing feffNNNN.dat from different feff runs, allowing parameters like S02, sigma2, E0, deltaR, etc to be varied, etc). So, the recommendation (more like an expectation, really) is to NOT set S02 to any value except 1.0 and to NOT set any parameters that will calculate sigma2 in feff.inp if the intention is to use those paths for fitting. Let the fitting program adjust S02 and/or disorder terms. Hope that helps, --Matt

1 0

EXAFS above 5 angstroms
by Daniel Sneed 23 May '18

23 May '18

Hello, This is my first time posting to the mailing list, so please forgive me if I did not do it correctly. I am currently working on EXAFS of tin(IV) oxide, and I have what appears to be high quality data out to 9 angstroms or so, but I am having some issues in fitting the data above 4 angstroms. I am attempting to verify a crystal structure with a= ~6 angstroms, and another structure with a=~9 angstroms. I know that there is some inhibiting physics at such long distances, such as inelastic scattering, and core-hole lifetime issues that can effect the data. My question for the group is, is there any methodical way to deal with these issues, other than incorporating Ei and the higher cumulants? Or is it even possible to get results from such large R? Thank you for your time. regards, Daniel Sneed

4 3

temperature dependency of amp parameter
by Abdul Ahad 21 May '18

21 May '18

Hi all, I have little confusion that do i fix or change S2 for each data set measured at different temperature. The compound is not monoatomic so i used Einstein model for sigma2. What about amplitude S2. thanks *A. Ahad*

2 1

SSRL EXAFS School- Application Open!
by Ritimukta Sarangi 19 May '18

19 May '18

Hello Friends, SSRL will host its annual summer school this year during the third week of August (13th-16th). The application page is now open. Please hit the "apply" button on: http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2018/index.html Note that seats are limited and we will have to choose from the application pool. Please apply soon to help us with the process. If selected, you will receive an email to register for the school. This year, we will drill down into Artemis based EXAFS analysis. Hope to see many of you here! Best Wishes, -Riti Sarangi

2 2

XANES spectra of Zn-organic references
by emmanuelle Montarges-Pelletier 18 May '18

18 May '18

Dear all We have measured Zn XANES spectra within biological samples (seeds), in ambient conditions (room temperature). In order to interprete the spectra, we are searching for Zn-organic reference spectra (XANES only). Indeed, we would be interested by Zn organic compounds with sulfur and/or nitrogen and/or oxygen in the first shell of coordination. On the joined graph are plotted the experimental spectra (microspectra on seeds), compared to Zn-citrate and Zn-cysteine. Energy calibration was checked for all spectra. thanks in advance for your answers best regards Emmanuelle Emmanuelle MONTARGES-PELLETIER Chargée de Recherche CNRS LIEC Laboratoire Interdisciplinaire des Environnements Continentaux UMR 7360 CNRS Université de Lorraine 15 avenue du Charmois F-54500 Vandœuvre-lés-Nancy - France tel 33 (0)03 72 74 47 30 mob 33(0)6 31 33 10 30 ****attention changement de numéro de téléphone **** tel 33 (0)3 72 74 47 30

2 1

4+2 model for distortion
by Abdul Ahad 17 May '18

17 May '18

Hi Prof. Segre Thanks for your reply, I have used .cif file for the K2NiF4 type structure. In this structure the first shell and first single path shows 6 coordination number. and the path is Ni to F1 with 2 leg. My concern is to use 4+2 model. Do i change the CN number or i have to add one more site. I cant visualize the situation. Becuase here the F have 2 sites i.e F1 and F2. And the path is only for the F1. While the diffrence between the bonds Ni-F1 and Ni-F2 is about 0.1 A. which lies under the resulution limit of my experiment via delta r and delta k relation. *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> * On Wed, May 16, 2018 at 10:30 PM, <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: 4+2 model for distortion (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 May 2018 16:00:08 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] 4+2 model for distortion > Message-ID: <alpine.DEB.2.21.1805151558480.17852(a)hydride.segre.home> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > Hi Abdul: > > Are you strating with a cif file for a particular structure or are you > simply working with a quick first shell theory? > > Carlo > > > On Wed, 9 May 2018, Abdul Ahad wrote: > > > hi all > > How to include this model in atom that is 4+2 or 2+4 for 2short or 4 long > > bond length of octahedra > > thanks > > > > > > *A. Ahad* > > *--------------------* > > *Abdul Ahad* > > Junior Research Fellow > > *Dept of Physics* > > *Aligarh Muslim University* > > *Aligarh 202002 (U.P.), India* > > > > *http://www.researcherid.com/rid/G-8198-2018 > > <http://www.researcherid.com/rid/G-8198-2018>* > > *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org > > <ahad(a)mailaps.org> * > > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics > Interim Chair, Department of Chemistry > Director, Center for Synchrotron Radiation Research and Instrumentation > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 183, Issue 14 > **************************************** >

2 1

4+2 model for distortion
by Abdul Ahad 15 May '18

15 May '18

hi all How to include this model in atom that is 4+2 or 2+4 for 2short or 4 long bond length of octahedra thanks *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> *

3 2

Energy Resolution
by Julian Ehwald 10 May '18

10 May '18

Dear all, This might be a very general question, but: I was wondering what energy resolution you typically use at beamlines to obtain your raw data for exafs. Since we have limited Beamtime only and other experiments that we want to carry out, I was wondering what kind of resolution is common. Or differently: Is it predictable what happens if I for example change from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV above Oxygen K, if that is of relevance. Best, Julian

4 7

Truncating signal
by Julian Ehwald 10 May '18

10 May '18

Hi all, I have basic question on background removal in Athena. My data has some strong changes very close to the absorption edge, and if I start the background removal at k=0, the spline is not able to follow the signal for higher k-values (even at Rbkg=1.7 or similar). The background then oscillates slowly (4 A^-1) around my signal, generating huge peaks in the low regions of chi(R). If I set the spline range to begin at k=2.7 only (around 28eV above absorption edge) then I get rid of it. Now my question in general is, do I loose essential information about the nearest neighbours this way, respectively is that a common thing to do? Best, Julian

2 3

Re: [Ifeffit] Ifeffit Digest, Vol 183, Issue 9
by Abdul Ahad 09 May '18

09 May '18

yes i m talking about the jahn teller type distortion, any hint to include in atom *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> * On Wed, May 9, 2018 at 8:30 PM, <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: Energy Resolution (Julian Ehwald) > 2. Re: Energy Resolution (Robert Meulenberg) > 3. 4+2 model for distortion (Abdul Ahad) > 4. Re: 4+2 model for distortion (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 May 2018 09:24:27 +0200 > From: "Julian Ehwald" <jehwald(a)gmail.com> > To: "'Carlo Segre'" <segre(a)iit.edu>, "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Energy Resolution > Message-ID: <006901d3e766$c4284410$4c78cc30$(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Carlo > > Thank you very much for your answer! If you say it is sufficient to use > dk=0.05, that means I would be able to collect a full EXAFS spectra (k=0 to > 12) in only 250 datapoints? That would save us a lot of time! > > Best, Julian > > -----Urspr?ngliche Nachricht----- > Von: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] Im Auftrag > von Carlo Segre > Gesendet: Sonntag, 6. Mai 2018 01:07 > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Betreff: Re: [Ifeffit] Energy Resolution > > > Hi Julian: > > With an edge energy of 543 eV, your monochromator resolution should be at > least 0.1 eV. If you are interested in XANES, you need to take data at > this > resolution or maybe even better. ONce past the edge, there is no need to > keep that step size. If your beamline permits an EXAFS-type step scan with > steps in k-space, you want to use a dk of 0.05 which is what IFEFFIT > interpolates to. Smaller step sizes are not really useful. > > Carlo > > On Sat, 5 May 2018, Julian Ehwald wrote: > > > Dear all, > > > > > > > > This might be a very general question, but: I was wondering what > > energy resolution you typically use at beamlines to obtain your raw data > for exafs. > > Since we have limited Beamtime only and other experiments that we want > > to carry out, I was wondering what kind of resolution is common. Or > > differently: Is it predictable what happens if I for example change > > from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV > > above Oxygen K, if that is of relevance. > > > > Best, Julian > > > > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, > Department of Chemistry Director, Center for Synchrotron Radiation Research > and Instrumentation Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > ------------------------------ > > Message: 2 > Date: Wed, 9 May 2018 08:54:31 -0400 > From: Robert Meulenberg <robert.meulenberg(a)maine.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Energy Resolution > Message-ID: > <CANs+nr9N7MSiYB9UGRm-a0JGd-5U8BNjKO7YVgAkM=SoRKazHA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Julian, > > Keep in mind that to get to k=12, you will need to go out to ~1100 eV. At > these energies, you will encounter just about every 1st row transition > metal L edge, and a handful of other M-edges for heavier elements. So if > you have anything else in your sample, EXAFS will probably not be > possible. That is usually why people don't try to do EXAFS analysis at the > soft x-ray energies. > > Regards, > > Rob > > > > > Robert W. Meulenberg > Associate Professor of Physics > Laboratory for Surface Science and Technology > Department of Physics and Astronomy > University of Maine > Orono, ME 04469 > phone: 207-581-2245 > email: robert.meulenberg(a)maine.edu > > On Wed, May 9, 2018 at 3:24 AM, Julian Ehwald <jehwald(a)gmail.com> wrote: > > > Hi Carlo > > > > Thank you very much for your answer! If you say it is sufficient to use > > dk=0.05, that means I would be able to collect a full EXAFS spectra (k=0 > to > > 12) in only 250 datapoints? That would save us a lot of time! > > > > Best, Julian > > > > -----Urspr?ngliche Nachricht----- > > Von: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] Im > Auftrag > > von Carlo Segre > > Gesendet: Sonntag, 6. Mai 2018 01:07 > > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Betreff: Re: [Ifeffit] Energy Resolution > > > > > > Hi Julian: > > > > With an edge energy of 543 eV, your monochromator resolution should be at > > least 0.1 eV. If you are interested in XANES, you need to take data at > > this > > resolution or maybe even better. ONce past the edge, there is no need to > > keep that step size. If your beamline permits an EXAFS-type step scan > with > > steps in k-space, you want to use a dk of 0.05 which is what IFEFFIT > > interpolates to. Smaller step sizes are not really useful. > > > > Carlo > > > > On Sat, 5 May 2018, Julian Ehwald wrote: > > > > > Dear all, > > > > > > > > > > > > This might be a very general question, but: I was wondering what > > > energy resolution you typically use at beamlines to obtain your raw > data > > for exafs. > > > Since we have limited Beamtime only and other experiments that we want > > > to carry out, I was wondering what kind of resolution is common. Or > > > differently: Is it predictable what happens if I for example change > > > from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV > > > above Oxygen K, if that is of relevance. > > > > > > Best, Julian > > > > > > > > > > -- > > Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim > Chair, > > Department of Chemistry Director, Center for Synchrotron Radiation > Research > > and Instrumentation Illinois Institute of Technology > > Voice: 312.567.3498 Fax: 312.567.3494 > > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > >

1 0

Re: [Ifeffit] Athena programm for XAS data analysis
by Robert Gordon 08 May '18

08 May '18

changing colour: Preferences --> gnuplot --> col7 and Set a desired colour then apply and save....displayed "your value" might not update until you restart Athena, but the plot should. On Tue, May 8, 2018 at 3:07 AM, Stoll, Andreas (HIU) <andreas.stoll(a)kit.edu> wrote: > Hi Jonas, > > > first of all thank you very much for your quick answer! > > > unfortunately your suggestion is not working for my version of Athena. It > just worked for the older versions... > > > Is there another possibility? > > > Greetings > > > Andi > ------------------------------ > *Von:* Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> im Auftrag von > Wielinski, Jonas <Jonas.Wielinski(a)eawag.ch> > *Gesendet:* Dienstag, 8. Mai 2018 18:40 > *An:* XAFS Analysis using Ifeffit > *Betreff:* Re: [Ifeffit] Athena programm for XAS data analysis > > > Hi Andi, > > > > Using Athena under Windows, “Alt + J” and “Alt + K” move data groups > upwards and downwards. I hope that answers your question. > > > > Best, > > Jonas > > > > *From:* Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] *On > Behalf Of *Stoll, Andreas (HIU) > *Sent:* Dienstag, 8. Mai 2018 10:12 > *To:* ifeffit(a)millenia.cars.aps.anl.gov > *Subject:* [Ifeffit] Athena programm for XAS data analysis > > > > Hi, > > > > I´m using Athena Version 0.9.26 to analyse my XAS data. > > > > Is it possible to change the order of the imported data in the list after > importing them? Or at least change the colour of the plotted data? > Currently one of my standards is plotted in yellow and that is not really > good... > > > > Thanks in advance! > > > > Greetings > > > > Andi > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > >

2 1

Athena programm for XAS data analysis
by Stoll, Andreas (HIU) 08 May '18

08 May '18

Hi, I´m using Athena Version 0.9.26 to analyse my XAS data. Is it possible to change the order of the imported data in the list after importing them? Or at least change the colour of the plotted data? Currently one of my standards is plotted in yellow and that is not really good... Thanks in advance! Greetings Andi

2 2

Re: [Ifeffit] o exafs
by fred.mosselmans＠diamond.ac.uk 05 May '18

05 May '18

Hi Julian, First you'll do well to collect o k exafs to 500 evening, second exafs data is typically except on qexafs beamline collected in k space steps i.e. proportional to E squared spacing starting at the edge position. Hence 0.4 evening is a very small step for exafs NOT xanes. If your beamline doesn't do k space scanning you can simulate it with several fixed eV step regions the step increasing as you get further from the edge. Also normally you would increase the time per point as you get further from the edge as the xafs signal compared to the background dies off Best Regards Fred Sent from BlueMail<http://www.bluemail.me/r?b=12874> On 5 May 2018, at 18:02, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@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. Energy Resolution (Julian Ehwald) ________________________________ Message: 1 Date: Sat, 5 May 2018 12:01:26 +0200 From: "Julian Ehwald" <jehwald(a)gmail.com> To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Energy Resolution Message-ID: <000a01d3e458$086925c0$193b7140$(a)gmail.com> Content-Type: text/plain; charset="us-ascii" Dear all, This might be a very general question, but: I was wondering what energy resolution you typically use at beamlines to obtain your raw data for exafs. Since we have limited Beamtime only and other experiments that we want to carry out, I was wondering what kind of resolution is common. Or differently: Is it predictable what happens if I for example change from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV above Oxygen K, if that is of relevance. Best, Julian

1 0

IIT/APS XAFS School - still have openings
by Carlo Segre 04 May '18

04 May '18

Greetings, All some slots are still open for the APS/IIT 2018 XAFS Summer School, July 8-12, in Chicago: see attached description. If you wish to participate, please email bunker(a)iit.edu <mailto:bunker@iit.edu> with subject line "XAFS School 2018". Grant Bunker -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

1 0

Se reference XANES
by desmau 01 May '18

01 May '18

Hello everyone, would anybody have a reference XANES spectrum of Se in Selenocysteine or of Se in bacteria ? Thanks a lot in advance for your help. Best regards -- Morgane DESMAU Doctorant/PhD student Institut de Physique du Globe de Paris Équipe de Géochimie des Eaux 1, rue Jussieu - 75238 Paris cedex 05 Mail: desmau(a)ipgp.fr Phone: +33 1 83 95 77 33

2 1

Atoms with Z bigger than 94 are missing
by Kathy Dardenne 30 Apr '18

30 Apr '18

Hello, I just notice that feff6 in Athena from the last versions of Demeter (including the 0.9.26) did not accept Z value above 94 (Pu) anymore. I wanted to fit AM L3 data and got error message from FEFF that it was not possible. Changing Am Z to 94 solves the problem. Is it possible to get Am (Z=95) and Cm (Z=96) implemented in feff again? I am aware that using Z=94 for simulation of Am and Cm will likely yields similar results, by just replacing the Z in the atom output. But if it is possible without too much effort it will be nice to have. Thanks a lot. Cheers Kathy Dardenne

1 0

Reference spectrum
by Lorenzo Stievano 27 Apr '18

27 Apr '18

1 0

EXAFS fitting for regular & distorted monoclinic
by Ashwani Kumar 26 Apr '18

26 Apr '18

Hello everyone, I am new to the mailing list. i am Fitting data of regular and distorted ( from irradiation) NBS glass doped with Hafnium. Literature available Hafnia (monoclinic) data is taken as standard model to fit the data (monoclinic) of regular glass. Now i want to fit the distorted glass data with exafs result of regular glass data as standard model. or will it be ok , to also fit the distorted glass data with hafnia as standard model. . thanks A kumar

2 1

Cannot update Demeter to version 0.9.26 in MacPorts
by Fowler, Joseph W. (Assoc) 25 Apr '18

25 Apr '18

Hi Bruce, I’m posing this question to you in front of the whole mailing list, just in case someone out there can help us both. As you know, I’m the official Macports maintainer of the port demeter, in spite of my near-complete ignorance of how either Perl or Macports work. In February, I filed a Macports ticket to make their preferred perl (5.26) work with Demeter 0.9.25. It was a simple matter of adding the “-I.” argument, as you pointed out to me. They pulled my changes, or whatever they do over there. My next step is to update the Macports package information to upgrade from Demeter 0.9.25 to 0.9.26. I am having a problem when I try to build Demeter 0.9.26, however. The “./Build install” command says it cannot find or copy ‘src/Ifeffit.dylib’. Do the following give you any clues about why that might be? This might be too little information, but as you said, “ask early”. The following text shows how it goes when I try to build within the macports structure. I get the same error, though, when I clone the git repository, cd into it, run “perl -I. Build.PL”, and then try to run “sudo ./Build install”. It looks as if somehow an ifeffit directory variable is not being initialized properly in line 308 of DemeterBuilder.pm. If you or anyone can help me to solve this problem, then I ought to be able to change the Macports port to provide Demeter 0.9.26. Many thanks. Joe Fowler NIST Boulder Labs fowlerj@817jfmac:demeter-0.9.26$ ll /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.dylib -r-xr-xr-x 1 macports wheel 33008 Mar 5 09:05 /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.dylib fowlerj@817jfmac:demeter-0.9.26$ port installed ifeffit The following ports are currently installed: ifeffit @1.2.13_5+gcc7 (active) [Mac ports would normally run the following commands within its build script, of course. But I am isolating the failed command to see if makes more sense this way.] fowlerj@817jfmac:demeter-0.9.26$ pushd /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_demeter/demeter/work/demeter-0.9.26 fowlerj@817jfmac:demeter-0.9.26$ sudo ./Build install Use of uninitialized value $iffdir in pattern match (m//) at DemeterBuilder.pm line 308. Simple test for presence of gnuplot ---> found it! Using gnuplot with the wxt terminal. Building Demeter Can't copy('src/Ifeffit.dylib', 'blib/arch/auto/Ifeffit/Ifeffit.dylib'): No such file or directory at /opt/local/lib/perl5/vendor_perl/5.26/Module/Build/Base.pm line 5601.

1 0

Phase shift
by Julian Ehwald 20 Apr '18

20 Apr '18

Dear all, I have a very general question about the phase shift. I tried to fit a rather noisy sample of Li2IrO3, where I get a first main peak around 1 angstroem, according to FEFF calculation there should be something at 1.9 and not any closer. This phase shift seems a bit too big to be true, is there something like an upper bound for a reasonable phase shift? Best, Julian

2 2

Artemis Error
by Lê Ngọc Chính 19 Apr '18

19 Apr '18

Dear Demeter developer I have some trouble when using artemis. I have used artemis normally on windows 10, but recently I can't use it anymore. The error message appears after I click "FIT" button. I also have tried re-install the software, but nothing happened. Please provide me the way to fix it. Thank you so much -- Chính

2 1

Directory path in Larch
by Imad Ahmed 17 Apr '18

17 Apr '18

Hi Matt, I have a question about the working directory of Larch. So, as I run Larch from command line (OS=Unix), the default WD is the .larch/modules and that in anaconda, in which case running a Larch script means that I have to provide its full path. I wonder if there is a way to change the WD into the current project folder? Running *.lar is not a problem but is a rather less convenient. However, directing Larch to project directory seems important so that to avoid typing full path of data files within the *.lar script. ps. feffrunner.py allows flexible subfolder path but it assumes that the *.inp is located in that same folder. It would be helpful if the path of the *.inp can be allowed to vary, this would help organising project files into subfolders. Best wishes, Imad

1 0

Re: [Ifeffit] Larch python instructions
by Matt Newville 17 Apr '18

17 Apr '18

Hi Imad, On Sun, Apr 15, 2018 at 7:15 PM, Imad Ahmed <imad.ahmed(a)earth.ox.ac.uk> wrote: > Dear Matt, > > I am looking for some proper instructions on how to use Larch from python. > I have larch installed on Anaconda2 and trying to run the > /examples/feffit/doc_feffdat1.lar script from python. > I tried the python code below but still having issues to run it, > especially with Feffpath and some larch plugins. Could you please help? > > Best wishes, Imad > > > import sys, os > import numpy as np > from scipy.optimize import leastsq as scipy_leastsq > import larch > from larch import Group, Parameter > from larch_plugins.io import read_ascii > from larch_plugins.xafs import FeffPathGroup > from larch_plugins.xafs.feffit import (TransformGroup, > FeffitDataSet,feffit, feffit_report) > > fname = ‘~/xraylarch/examples/feffit/feff0001.dat' > path1 = FeffPathGroup(fname) > path2chi(path1) > show(path1) > newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', > ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, > title=r'$\chi(k)$ from %s' % fname) > path1.sigma2 = 0.002 > path2chi(path1) > plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') > > > Well, there are some differences between Larch and Python. With some small modifications, your scaript can become a valid Larch script like this: # larch from os.path import join, expanduser fname = join(expanduser(‘~'), '/xraylarch/examples/feffit/feff0001.dat') path1 = feffpath(fname) path2chi(path1) show(path1) newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, title=r'$\chi(k)$ from %s' % fname) path1.sigma2 = 0.002 path2chi(path1) plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') To do that from Python is a bit more involved. Each of the functions "feffpath", "path2chi", "show", "newplot", and "plot" need to be translated. As you probably say, "feffpath" is effectively `FeffPathGroup'. The others are less obvious, and many of the larch functions really want to be passed a "larch session" so that they can find other larch function or data sources. For example, FeffPathGroup needs a larch session in order to be able to look up atomic information. So in pure python that would be approximately: import os import os.path import matplotlib.pyplot as plt # using pyplot instead of build in plot commmands from larch import Interpreter from larch_plugins.xafs.feffdat import FeffPathGroup, _path2chi # need to create a Larch interpreter for each "session" _larch = Interpreter() fname = os.path.join(os.path.expanduser("~"), "Codes/xraylarch/examples/feffit/feff0001.dat") # note that many of the Larch functions will want a `_larch` instance passed in. path1 = FeffPathGroup(fname, _larch=_larch) _path2chi(path1, _larch=_larch) # show, approximately for attr in dir(path1): print(attr, getattr(path1, attr)) # plot, approximately plt.plot(path1.k, path1.chi*path1.k**2, label= r'$\sigma^2 = 0$') path1.sigma2 = 0.002 _path2chi(path1, _larch=_larch) plt.plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') plt.xlabel(r' $ k \rm\, (\AA^{-1})$') plt.ylabel(r'$ k^2\chi(k)$') plt.title(r'$\chi(k)$ from %s' % fname) plt.legend() plt.show() But also, since you have to build a Larch Interpreter, you could simply use it to execute the previous Larch script: from larch import Interpreter text = ''' # larch from os.path import join, expanduser fname = join(expanduser(‘~'), '/xraylarch/examples/feffit/feff0001.dat') path1 = feffpath(fname) path2chi(path1) show(path1) newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, title=r'$\chi(k)$ from %s' % fname) path1.sigma2 = 0.002 path2chi(path1) plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') ''' _larch = Interpreter() _larch.run(text) The latter approach is highly recommended. --Matt Newville

2 3

Beg for Athena install package
by zangyp＠mail.ustc.edu.cn 16 Apr '18

16 Apr '18

Sir/Madam： I am sorry to disturbe you! Here, I am a PHD of USTC, China and I want use the Anthena tool to analysis EXFAS data, my compute is 32-bites versions, so I beg for a Ifeffit-1.2.10.exe. Could you provide it for me? Very thanks! Zang, Y. P. zangyp(a)mail.ustc.edu.cn

2 1

Sulfur EXAFS k oscillations
by Miller, Elizabeth Christine 11 Apr '18

11 Apr '18

Hi all, I am analyzing some sulfur K-edge EXAFS data taken at 4-3 at SSRL. When I use a k-weight of k^3 to plot, my oscillations at high k reach over 100, which doesn't make sense to me. I have looked over the data with Riti, and it seems that while the XANES are rather self-absorbed due to high concentrations of sulfur-containing salt, the data can be normalized, and the EXAFS should contain some information. I've included screenshots in the attachment of plots of all of the k-weights as well as my parameters. The mixtures are solutions of organics (acetonitrile, 1,1,2,2-Tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether) with bis(trifluoromethane)sulfonimide lithium salt. I am also not hitting any other edges, as sulfur is the highest Z element in the solution. Any thoughts would be greatly appreciated! Thank you, Beth Elizabeth C. Miller, Ph.D. Postdoctoral Scholar Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory E-mail: ecmiller(a)slac.stanford.edu<mailto:ecmiller@slac.stanford.edu>

4 4

Re: [Ifeffit] [Ifeffit} Sulfur EXAFS k oscillations
by fred.mosselmans＠diamond.ac.uk 10 Apr '18

10 Apr '18

Dear Beth, Apart from the fact it looks like there is a trace Cl impurity in one of the samples (sharp line at ca. 9.5 k), it is hard to tell how a spline is going wrong without seeing the spline, thus posting the Athena file might get a better response. It may well be there is not much data beyond 10 k for soft scatterers at the S K-edge. Best wishes Fred J.F.W. Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 -- 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

1 0

Mac install issues
by Webb, Samuel M. 04 Apr '18

04 Apr '18

Hi all - I've run into a lot of problems with Mac installs in general with my compiled XAS programs as well, particularly with the latest High Sierra update. It's been pointed out to me by a few users that another potential work around is to use Wine 3.0 https://www.winehq.org as an emulator of sorts (and its free) to run a windows program within the MacOS environment. It's smaller and more compact than say Parallels or VMware as it doesn't do the whole operating system, hence the free part. Its seems easy to install, and also makes for one less OS to maintain a distribution for. It may not be the most elegant solution, but it could work for some... I may end up using this for myself rather than maintaining a native Mac distribution in the future. Sam

2 1

install for mac error
by Christopher Patridge 04 Apr '18

04 Apr '18

Hello everyone, I tried to install demeter on my mac (running high Sierra) and it appeared everything went well. However when I run either Athena or Artemis I get an error shown below about Demeter::Templates: showing a error and I am not sure how I can correct this error. Any help would be appreciated. Thanks in advanced, Chris -- Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Chemistry SASE 315 D'Youville College 320 Porter Ave., Buffalo, NY 14201 716-829-8096

5 8

Problem building latest demeter on Debian 32bit Stretch
by Al Kwiatkowski 30 Mar '18

30 Mar '18

Hello - We're trying to install demeter on a 32-bit system running Debian 9.2 Stretch. The 'perl Build.PL' and 'Build' run into no issues, but when we try running 'Build test' we get the following error messages: t/001_base.t ............ String found where operator expected at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" (Do you need to predeclare croak?) syntax error at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" Compilation failed in require at /home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244. Compilation failed in require at t/001_base.t line 22. BEGIN failed--compilation aborted at t/001_base.t line 22. # Looks like your test exited with 255 before it could output anything. t/001_base.t ............ Failed 24/24 subtests t/002_types.t ........... String found where operator expected at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" (Do you need to predeclare croak?) syntax error at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" Compilation failed in require at /home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244. The "croak" command not getting found appears to come from the "Carp" perl module - we have version 6.06-1 of the 'libcarp-clan-perl' package installed. Any suggestions as to what's causing this error? Again, the 'perl Build.PL' command shows no issues with the installed modules, but since most of them were installed from the Debian repository, maybe there's a discrepancy with the modules installed when we run './Build installdeps'? Thanks for any assistance - Al Kwiatkowski kwiatal(a)phys.iit.edu

3 5

Athena crashes on windows10
by Lisa Bovenkamp-Langlois 28 Mar '18

28 Mar '18

Hello. Me and other people running windows 10 have problems with Athena (demeter version 0.9.26). when switching to the LCF window the program crashes. I tested that indeed sometimes this happens when the list of data sets is long. However, it recently happened with only 3 data sets in the list. In one case Athena crashes at this same spot repeatedly. In other cases if works after restarting Athena or the PC. Is there a fix in sight or do I have to go back to windows7? Thanks, Lisa Lisa Bovenkamp-Langlois, PhD CAMD/LSU 6980 Jefferson Hwy Baton Rouge, LA 70806 Email: lbovenkamp(a)lsu.edu website: http://www.camd.lsu.edu/

3 2

Athena (Demeter 0.9.26) does not import all datapoints from ascci file
by Kathy Dardenne 28 Mar '18

28 Mar '18

Hello, I got a new trouble by importing datafile in Athena (Demeter 0.9.26). Athena from Demeter version 0.9.26 does not import all points from the datafile but some of them yielding a very poor resolution especially for the edge region. The given file has 275 points and only 143points are imported (see derivative after import with Athena(26) and with pymca were all points are imported). Importing data using Athena from an older version of Demeter and saving the file solved my import problem temporary. But there I notice that a priori only 202 instead 275 were imported but it was not obvious from the plot appearance that some points are missing . I joined some screenshots as well as Athena log file after importing the data (error message about a file not found but the name in stash is not the one Athena is looking for..?). I joined both Athena file (Demeter v26 and Demeter v19 after import of the same asci file) as well as the asci file. I got the problem of "partial import" with all my datafiles. Did somebody experienced this trouble too? Thanks a lot Kathy Dardenne Operating system : Windows 7 entreprise - Service pack 1 Programme : Demeter 0.9.26 last release Karlsruhe Institute of Technology (KIT) Institute for nuclear waste disposal (INE) Dr. Kathy DARDENNE Hermann-von-Helmholtz-Platz 1, Building 712 76344 Eggenstein-Leopoldshafen, Germany Tel. : +49 721 608-26669 Fax : +49 721 608-23927 E-mail : <mailto:kathy.dardenne@kit.edu> dardenne(a)kit.edu Internet : <http://www.kit.edu/> www.ine.kit.edu KIT - The Research University in the Helmholtz Association.

3 6

Larch 0.9.37 now available
by Matt Newville 27 Mar '18

27 Mar '18

Hi Folks, I'm happy to announce the release of Larch 0.9.37. It's been a while since I announced updates to Larch, and there has been steady progress on a number of areas over the past year. While much of the effort has been centered on X-ray fluorescence imaging and diffraction mapping work done at X-ray microprobes especially at GSECARS, there has also been been some work on XAFS and XANES. Larch now includes both Feff6l and Feff8l (that is, Feff85 for EXAFS-only calculations), with routines for running these from within Larch scripts or from Python. I want to draw your attention in particular to the program with the rather boring name "XAS Viewer" (formerly XYFit) that is included with Larch and may be of interest to several Ifeffit users. XAS Viewer is currently focussed on doing pre-edge peak fitting, but we do intend to add more XANES and EXAFS visualization and analysis tools. Feedback and suggestions of any kind would be helpful and greatly appreciated. Currently, XAS Viewer can read data from plain ASCII files or from recent "new-style" Athena Project files. Like Athena, it can merge groups and plot one or more XAFS spectra in various stages of the XAFS normalization process. XAS Viewer can also save data to Athena Project file, or save multiple data sets to CSV files. While XAS Viewer does basic XANES processing (normalization, etc) and visualization similar to Athena, its main emphasis is on fitting of pre-edge peaks. A dedicated panel helps the user first fit a baseline curve, then adds peaks (Gaussian, Lorentzian, Voigts, etc) and fits the entire model to the pre-edge region. Bounds and constraints can be placed on any of the parameters for the peaks, and full fit reports including uncertainties are generated. Fit models can be saved to a file and re-loaded. These saved models can be used from Python code. We will soon be generating fitting scripts for batch processing, but this is still work in progress. Some screenshots, and a bit more information are at https://xraypy.github.io/xraylarch/guis/xas_viewer.html Again, feedback or suggestions on this or any other aspects of Larch are most welcome. Larch can be installed with installers for Windows, Mac OSX, Linux. At the moment, these installers all assume 64-bit operating systems. If anyone needs to use Larch with 32-bit Windows please let me know, and I will try to build an installer for that platform. Larch can also be installed as a "conda package" for Anaconda Python, as with conda install -c GSECARS xraylarch Currently both Python 2.7 or 3.6 are supported. Finally, Larch can also be used as the "backend" for Athena/Artemis, and I strongly encourage all Athena/Artemis users to install Larch so that it can be used in place of the old and unsupported ifeffit library. --Matt Newville

1 0

synthesis of EXAFS via larch
by Katy Smith 20 Mar '18

20 Mar '18

Dear Colleagues, I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and I wonder if that would be the right way. I can synthesise the paths in Demeter/Artemis but I have no idea how to sum them in order to obtain a single EXAFS spectrum. Hence, the interest in Larch hoping that it can do what I am looking for. Best regards, Kate

4 8

Error in Atoms output
by Kaustubh Priolkar 20 Mar '18

20 Mar '18

Hello! We are trying to fit low temperature V K edge EXAFS data in V2O3. As per the cif files available (attached herewith – V2O3_10K data.cif) the structure is described by I2/a space group. When this file is read by ATOMS it gives an erroneous output ( attached herewith - feff.inp). In particular the values of V-O and V-V bond distances are not correct and do not match with bond distances reported in literature (Phys. Rev. B 2 (1970) 3771). Could anyone tell me where am I making a mistake. I am aware that I2/a is a non standard space group but I am not sure if I need to take any precaution while reading the cif file in ATOMS. Thanks and regards, Kaustubh Sent from Mail for Windows 10

3 3

Report a bug
by Zhengrui Xu 19 Mar '18

19 Mar '18

To whom it may concern, I found a bug when I am dealing with my data. I am using Windows system, and the software version is 0.9.26. I can plot my data in E, however, not in k, R and q. This problem happen to all of my data. My other three group members also have this problem. My raw data is attached for your review. We really appreciate your help. Best, Zhengrui Xu First-year PhD student Department of Chemistry Virginia Tech

3 4

2018 APS/IIT XAFS Summer School - schedule set
by Carlo Segre 19 Mar '18

19 Mar '18

Hello All: The APS/IIT XAFS Summer School will be held form July 8-12 on the Illinois Tech campus in Chicago. Please see attached flyer for details. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

1 0

Athena crushes
by Vasily Potapkin 16 Mar '18

16 Mar '18

Dear All, I am using latest version of Demeter package on Mac. I was working on unsaved project when Athena crushed for no apparent reason. Now when I restart Athena it suggest to me to recover project from autosave and couple of seconds later becomes unresponsive. Restarting the computer didn’t helped. Artemis works without issues. Does someone know the solution? warm wishes, Vasily

2 2

FeSe2 Se K-edge XANES request
by Robert Gordon 14 Mar '18

14 Mar '18

Hi Folks, Does anyone have a near-edge spectrum of FeSe2, Se K-edge, they could share? (Ideally with Se elemental reference measured simultaneous.) Thanks, -R.

3 3

Data Import Error
by Nathan Nakamura 12 Mar '18

12 Mar '18

Hello Everyone, I'm fairly new to XAS/Athena, and recently collected XAS data at the F3 beamline at CHESS. I have had trouble importing our data files into Athena for processing, and I did not see a plugin for this beamline. Has anyone experienced a similar problem and may be able to point me in the right direction? I've attached an example of one of our data files, as well as an image of the error I've been receiving. Thank you, -Nathan Nakamura

2 1

SSRL XAFS Summer School
by Ritimukta Sarangi 01 Mar '18

01 Mar '18

Hello, SSRL will host its annual summer school this year during the third week of August (13th-17th). The focus of the school will on EXAFS hands on data analysis. In addition, electronic structure determination from the XAS pre-edge analysis and advanced spectroscopies will be covered. Examples from a wide range of scientific applications will be covered, including metals in biology, chemical catalysis, heterogenous catalysis and materials. I will post more information here, as and when it becomes available (hopefully soon) and we hope that many of you can attend. Best Wishes, -Riti Sarangi

2 1

Error message "typo in Template.pm"
by Elizabeth Tomaszewski 26 Feb '18

26 Feb '18

Hello, I keep getting the error message ""Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.24/Text/Template.pm line 556, <DATA> line 236.” I located the Template.pm file but can not edit the template without changing permission in the terminal, which I don’t know how to do. Line 556 reads: local *SYM = *{"$ {dest}::$name”}; Line 236 reads: $cur_item .= '\\’; Athena will open when I type in the command window but I can only see the GUI for a second before the error message comes up and it has to shut down. Please help. Thanks, Elizabeth Tomaszewski

1 0

call for nominations for the IXAS Awards
by Matt Newville 16 Feb '18

16 Feb '18

Hi Folks, I realize that many of you will have received this from the IXAS mailing list, but I'd like to invite everyone here to consider nominations for the IXAS Awards too: The Awards Committee of the International X-ray Absorption Society (IXAS) seeks nomination for three awards. These awards will be presented at the XAFS17 Conference in Krakow, Poland. The three awards are: 1. The Edward Stern Outstanding Achievement Award: This is the highest award of the International X-ray Absorption Society. Nominations are invited across all disciplinary areas including both experimental andtheoretical studies of XAFS. Award: $1000 2. The Farrel Lytle Outstanding Young Scientist Award for Theory and Instrumentation: Nominee must have made remarkable contribution to the field of X-ray absorption spectroscopy. Nominee should be within 8 years of a Ph.D. (or equivalent) degree as of April 1, 2018. Award: $500 3. The Dale Sayers Outstanding Young Scientist Awards for Applications of XAFS: Nominee must have made remarkable contribution to the field of X-ray absorption spectroscopy. Nominee should be within 8 years of a Ph.D. (or equivalent) degree as of April 1, 2018. Award: $500 Nominations should include a CV with publications, a letter of recommendation and academic referees who can be contacted for further reference. The deadline for nomination is May 1, 2018. Please send nominations by email to IXAS vice chair Matthew Newville newville(a)cars.uchicago.edu Thanks, --Matt Newville

1 0

Job Posting
by Frejka, Jean M 16 Feb '18

16 Feb '18

Can you please post and/or upload the attached job posting? The position is for a Data Analysis Engineer at Brookhaven National Laboratory. I have attached a two pdf files: (1) short version for posting on a bulletin board and (2) a longer version to upload or email. If you have any questions, please contact me. Thank you for your assistance. Jeannie ************************************* Jean Marie Frejka Brookhaven National Laboratory Nuclear Science and Technology Department Building 817, 33 North Renaissance Road Upton, NY 11973 Phone: 631-344-2349 Fax: 631-344-2806 frejka(a)bnl.gov<mailto:frejka@bnl.gov>

1 0

Artemis having trouble
by Sheraz Gul 09 Feb '18

09 Feb '18

Can anyone please explain why Artemis is failing to open the fpj file I have attached? It doesn't respond anymore and screen look like the screenshot attached. It has happened to me multiple times now; I'm using Demeter version 0.9.25 on windows 10. Best regards, -- Sheraz Gul

4 12

XAFS short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 09 Feb '18

09 Feb '18

Dear subscribers: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course is open for applications at this web site: https://www.bnl.gov/exafs2017/ <https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5Kclqc…> The course will be useful for those scientists who are familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced methods. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis methods. The course instructors will use examples from their research during presentations. The topics covered will include: -Theory of XANES, -XANES data analysis, -Structural refinement using XANES, with emphasis on the following methods: -Molecular dynamics, -Reverse Monte Carlo. -Machine Learning methods During the data analysis practicum on November 3, participants will get an opportunity to work with research projects with the help of the course instructors. The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC). Best regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

4 7

larch warning that I don't understand
by Ravel, Bruce 08 Feb '18

08 Feb '18

Matt, When Larch starts, what is meant by warnings like this: No handlers could be found for logger "pyFAI.opencl.common" or No handlers could be found for logger "pyFAI.gui.matplotlib" The first one went away by installing python's opencl interface -- a rather sizable prerequisite! I haven't figured out how to make the second one happy. Thanks, 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

4 4

Demeter Mac install on High Sierra
by Alexandre Simionovici 05 Feb '18

05 Feb '18

Hi guyz, Trying to install Demeter on a Mac thru the Macports command: sudo port install xorg-server demeter neither demeter nor xorg-server is known ! Macs nowadays have XQuartz as X11 window manager so xorg is not needed but what about Zeus' wife ? Has someone managed to install it on High Sierra or even Sierra ? TIA, Alex -- _____________________________________________________________________ | Pr. Alexandre Simionovici | |Institut des Sciences de la Terre, UGA/CNRS tel. +33-(0)4.76.63.51.96 | |Observatoire des Sciences de l'Univers de Grenoble fax. +33-(0)4.76.51.40.58| |UMR 5275, Maison des Géosciences, alexandre.simionovici(a)univ-grenoble-alpes.fr| |CS 40700, 38058 Grenoble Cedex 9, FRANCE | |------------------------------------------------------------------------------------------------------------------|

1 0

Autosave; problem with Athena crashing on mac
by Astrid Avellan 16 Jan '18

16 Jan '18

All, I recently updated my mac OSX and had to change for iXAFS on my OSX 10.8 to the demeter servers on 10.12 It was runing fine, untill Athena crashed. When I was trying to restart it, it was frozen, asking me if I want to open the autosave file, but no being able to click anywhere. All the posts online says that you want to find the file athena.autosave in your Mac in the folder $home/.horae/stash The trick is that you CANNOT see these folders by default in your Mac. To show the hidden folders in your system, you have to type into your terminal $ defaults write com.apple.finder AppleShowAllFiles YES killall Finder Once you have done that, you can find the .horae folder ONLY manually in $home/.horae/stash. A search in your folder finder will NOT work. I deleted the Athena.autosave folder, AND open the Demeter.ini file (in $home/.horae/downloads) and chance “autosave=true” for “autosave=false”. Once you are done, you can hide the folders again by typing $ defaults write com.apple.finder AppleShowAllFiles NO killall Finder Now, everything is running smoothly. But I don’t have any autosave : I autosave myself regularly! Enjoy a long life with Athena! Best Astrid

1 0

Re: [Ifeffit] How to use Artemis with feff85L
by Bruce Ravel 12 Jan '18

12 Jan '18

Jose, I am unclear what you are sad about. The version of Feff has little to do with the quality of the analysis. See our recent paper: https://doi.org/10.1107/S1600577517011651 It is true that feff8l would simplify and streamline the code, making it easier to write and maintain. That's a bit incentive /for/ /me/ to do that work. But I think you are overstating the impact on the analysis you and others do with Artemis. B On 01/12/2018 07:15 AM, José Carlos Conesa wrote: > OK Bruce, I understand. (Sigh) > > Good luck in your actual job. > > JC > > > El 12/01/2018 a las 12:35, Bruce Ravel escribió: >> >> Yes. But I am pretty busy these with my new beamline. >> >> "Beamline scientist" is my actual job. "Software guy" is a side >> project. So the software work gets done when it gets done. >> >> B >> >> >> >> On 01/12/2018 05:25 AM, José Carlos Conesa wrote: >>> Dear Bruce, >>> >>> Do you foresee that (in a not far future) Artemis may be adapted so >>> that it can use the results of feff8.5L? >>> >>> All the best, >>> >>> >>> El 12/09/2017 a las 19:11, Bruce Ravel escribió: >>>> >>>> Feff8L is not properly integrated into Artemis yet. Sorry. I have >>>> a new beamline these days. It's hard to find time to work on the >>>> software. >>>> >>>> This is on my to do list, but it's going to take a while. >>>> >>>> B >>>> >>>> >>>> On 09/12/2017 12:54 PM, José Carlos Conesa wrote: >>>>> Hi, >>>>> >>>>> I should like to use feff85L within Artemis (from Demeter 0.9.25), >>>>> just to check in my system whether selfconsistency has a role in >>>>> unifying E0 values (with feff 6, allowing different E0 for each >>>>> scatterer leads to E0 differences >10 eV, which seems too much to >>>>> me). I find that after loading the EXAFS data (from Athena) and a >>>>> model (a .cif file containing Cu, Ce and O atoms), if I click Run >>>>> Atoms and then Run Feff with feff6 as executable I get the usual >>>>> set of paths that allow me doing a fit of the data, but if I try to >>>>> use the feff85L.exe that comes with the Demeter software (by >>>>> changing the feff executable in the File/Edit preferences menu), >>>>> after clicking the Run Feff button (without including the SCF card) >>>>> a bit of computation happens and after finishing it the path list >>>>> is empty. >>>>> >>>>> ¿Any idea of the possible reason why I get no path list? >>>>> >>>>> Thanks in advance >>>>> >>>> >>>> >>> >> >> > -- 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/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Re: [Ifeffit] How to use Artemis with feff85L
by Bruce Ravel 12 Jan '18

12 Jan '18

Yes. But I am pretty busy these with my new beamline. "Beamline scientist" is my actual job. "Software guy" is a side project. So the software work gets done when it gets done. B On 01/12/2018 05:25 AM, José Carlos Conesa wrote: > Dear Bruce, > > Do you foresee that (in a not far future) Artemis may be adapted so that > it can use the results of feff8.5L? > > All the best, > > > El 12/09/2017 a las 19:11, Bruce Ravel escribió: >> >> Feff8L is not properly integrated into Artemis yet. Sorry. I have a >> new beamline these days. It's hard to find time to work on the software. >> >> This is on my to do list, but it's going to take a while. >> >> B >> >> >> On 09/12/2017 12:54 PM, José Carlos Conesa wrote: >>> Hi, >>> >>> I should like to use feff85L within Artemis (from Demeter 0.9.25), >>> just to check in my system whether selfconsistency has a role in >>> unifying E0 values (with feff 6, allowing different E0 for each >>> scatterer leads to E0 differences >10 eV, which seems too much to >>> me). I find that after loading the EXAFS data (from Athena) and a >>> model (a .cif file containing Cu, Ce and O atoms), if I click Run >>> Atoms and then Run Feff with feff6 as executable I get the usual set >>> of paths that allow me doing a fit of the data, but if I try to use >>> the feff85L.exe that comes with the Demeter software (by changing the >>> feff executable in the File/Edit preferences menu), after clicking >>> the Run Feff button (without including the SCF card) a bit of >>> computation happens and after finishing it the path list is empty. >>> >>> ¿Any idea of the possible reason why I get no path list? >>> >>> Thanks in advance >>> >> >> > -- 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/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Some questions regarding running Larch code in Python
by Hanyu Zhang 09 Jan '18

09 Jan '18

Hello everyone, I'm trying to find radial distribution functions for materials with known concentrations of individual atoms by running Larch code through Python, but am having some difficulties with creating feffpaths: 1. I'm not quite understanding the feff.inp files stuff. Calling FeffRunner().run() with a input file that works with Atoms always throws the "rdinp not found exception". From what I'm understanding, feffrunner().run() calls the different modules to create a feffpath() group, but where are the rdinp, pot, xsph, etc codes/files? 2. Somewhat on the same line of thought, can someone give me an example of a valid feffNNNN.dat file to generate a feffpath() group? I went through feffdat.py and the parsing code in lines 88-102 (under __read()) looks like it only accepts very specific input formats. 3. What does "ipot" stand for in the "geom" variable? I understand that if I did pass in a valid file, I'd probably not have to know this, but I was just curious... Also, this might be a overly-general question, but is this the best way to approach the problem? The basic idea now is to get chi(k) values for a bunch of different paths/RDFs, and figure out which ones match experimental values the best. This is also the main reason I want to get past the Demeter GUI and Larch-specific interface: eventually I might throw the code on a supercomputer of some sort and have it crunch the numbers. The details still have to be worked out on my end, but I was wondering if there was a faster or better way to go about finding the RDF for compound materials with known concentrations of individual atoms. I've attached some of my Python code (with more specific versions of questions 1 and 2 inserted as comments) and the feff.inp file I've been testing with. (Simple file from http://cars9.uchicago.edu/~ newville/adb/search.html) I'm currently an undergrad exploring the field of XAFS, so sorry in advance if there is something obvious that I'm missing... Also, let me know if any clarifications are needed. Thank you for your time and sorry about the email being so long, Alice ---------- Hanyu (Alice) Zhang CWRU Class of 2018 | Engineering Physics major BS/MS program | Materials science *Minors:* Mathematics | Materials science *Honors societies:* National Society of Collegiate Scholars | Tau Beta Pi | Pi Mu Epsilon *Active Clubs:* Case Origami Circle | Case Rocket Team | CWRUbotix | Case Physics and Astronomy club | Math club

2 2

data table for larch data group
by Bruce Ravel 22 Dec '17

22 Dec '17

Matt, If I read an ascii file with read_ascii() like so: a = read_ascii(file) The "a" group has a data attribute which contains the entire data table as a 2D array. It also has 1D arrays for each column from the data table. Those 1D arrays have attribute names taken from the column labels. If I do something to change the data table, is there a function that I can call that repopulates the 1D arrays with the columns of the altered data table? For example: a = read_ascii(file) a.data is, say, array<shape=(5,500)> a.data = a.data[:, (0 .. 10)] now a.data is, say, array<shape=(5,11)> a.repopulate_arrays() # <---- the thing i am looking for.... Now a.energy, a.i0, etc should be array<shape=(11,)> Hope that's clear. 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/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

2 2

looking for β-Mo2C standard
by woschangqiang＠126.com 13 Dec '17

13 Dec '17

Hello, dear everyone. I am analysing some data about Mo K edge, but lack of standards. I searched many websites and mailing list, and only found the data from Carlo Segre. I am still need the data of β-Mo2C. Can anyone help sent me a data copy, if you have β-Mo2C. Thank you very much. Best regards, Qiang CHANG UCAS

1 0

Units for density in Athena's Booth self-absorption correction?
by John Christopher Lin 11 Dec '17

11 Dec '17

Dear XAFS community, I am trying to use the Booth algorithm to correct for self-absorption in Athena, and one of the input fields is for the density of the material. What units should be used for the density in that field? (I could not find the answer in Section 9.9 of the Athena documentation on self-absorption approximations.) Many thanks, John

2 2

how to import this kind of XAFS data
by woschangqiang＠126.com 11 Dec '17

11 Dec '17

Dear Bruce Ravel, Matt Newville and Carlo Segre, I am sorry to reply late. Thanks very much for your time and detailed explanations. Qiang CHANG Unversity of Chinese Academy of Sciences

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 178, Issue 9
by Christopher Thomas Chantler 10 Dec '17

10 Dec '17

Dear all The two best tests of any self-absorption correction are 1. that the resulting curve looks like an absorption curve, and the slope is consistent with one above the edge and 2. the pixels in a two-dimensional detector are consistent with such a pixel-dependent correction without excessive fitting parameters. That is, the pixel geometry is corrected for. It is not trivial to do this with a single channel, pixel or spectrum. Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS CIT, CCN President, 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, 11 December 2017 5:00:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 178, Issue 9 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. Units for density in Athena's Booth self-absorption correction? (John Christopher Lin) 2. Re: Units for density in Athena's Booth self-absorption correction? (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Sun, 10 Dec 2017 02:30:05 +0000 From: John Christopher Lin <jlin9(a)stanford.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Units for density in Athena's Booth self-absorption correction? Message-ID: <MWHPR02MB3358E7D14D4E058A9F44C79F8F360(a)MWHPR02MB3358.namprd02.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Dear XAFS community, I am trying to use the Booth algorithm to correct for self-absorption in Athena, and one of the input fields is for the density of the material. What units should be used for the density in that field? (I could not find the answer in Section 9.9 of the Athena documentation on self-absorption approximations.) Many thanks, John

1 0

how to import this kind of XAFS data
by woschangqiang＠126.com 08 Dec '17

08 Dec '17

Hello, dear everyone. I downloaded a XAFS data about mettalic Ru from the website of ixs.iit.edu. There are 4 groups of information in the data, and each ranges between ~67800 with ~63000 in energy. So how to import the data to Athena, and how this kind of data was produced? Does anyone come across this situation? Thanks for your time and help in advance. Q. CHANG Unversity of Chinese of Academy of Sciences

3 2

Hello
by Neama Imam 08 Dec '17

08 Dec '17

Dear Sir I am new user of Demeter, i would like to find he exact steps of Athena and Artemis. Best Regards Neama Imam : Post Doc. Position - XAFS beamline - Elettra-Sincrotrone Trieste S.C.p.A. Strada Statale 14, Km 163.5 Basovizza (Trieste), 34149 Trieste-Italia ( neama.imam(a)elettra.eu) and Lecturer : Atomic Energy Authority Nuclear Research Center Exp. Nuclear Phys. Dept. Solid State and Nanotechnology Lab. Cairo, Abou-Zabaal, Inshas , Egypt P.O. : 13759 Fax: 00-202-44520612 imam.eaea(a)gmail.com, nama_emam2018(a)yahoo.com

1 0

Re: [Ifeffit] Demeter 0.9.26 launch faillure
by Kirill Lomachenko 06 Dec '17

06 Dec '17

Dear Kathy and Robert, great, it works! Thanks a lot Kirill

1 0

Demeter 0.9.26 launch faillure
by Kirill Lomachenko 06 Dec '17

06 Dec '17

Dear Bruce, I have trouble running the Demeter 0.9.26_pre2 (64bit). When I start Artemis after installation of Demeter, it closes after showing nothing but the usual temple picture. Logfile is attached. The problem is analogous on both Win7 SP1 and Win8.1 and repeats also for Athena and Hephaestus. Could you please tell whether there is something I can do to fix it? Versions 0.9.25 and 0.9.24 start without problems. I know that 0.9.26 is a preview version, but I was installing it only to get the possibility to actually use the user-supplied value of epsilon_k for fitting multiple dataset. If it is difficult to make the version 0.9.26 available soon, maybe in 0.9.25 there is a possibility to set R-factor as a figure of merit for fitting rather than chi^2? That might also help. Thank you All the best, Kirill Lomachenko -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

3 2

Vanadium pre-edge peak fitting
by Will Bennett 06 Dec '17

06 Dec '17

Hi everyone, I've recently collected some V K-edge XANES spectra and am in the process of analysing the data. The pre-edge region has been shown to be quite useful for exploring the oxidation state and coordination geometry of vanadium in various samples. This approach requires the pre-edge peak area and centroid of unknowns to be compared with those of a suite of standards, with these parameters typically determined by fitting a peak (or peaks) to the pre-edge feature. The attached paper by Chaurand et al shows an example of how this is often done, but it raised a question in my mind that I wanted to clarify before proceeding to analyse my data in this way... Is it necessary to justify a particular selection of peak fitting parameters based on physical attributes? For example, Chaurand et al fits multiple pseudo-voigt peaks to the V pre-edge feature, with the Lorentzian contribution to this pseudo-voigt function constrained to be the same as the core-hole lifetime width at the V K-edge (i.e. 0.8 eV). The Gaussian contribution is allowed to vary, but the Lorentzian to Gaussian intensity ratio is set at 1:1. After justifying these parameters, the authors go on to say that *"It should be noted that width and height of the modeled pseudo-Voigt functions have little physical significance, being a convolution of two functions with significantly different width."* If this is the case, does it really matter what specific peak fitting parameters are used? If the goal is to simply obtain an accurate peak area and centroid of the pre-edge feature, wouldn't an empirical peak fitting approach provide comparable data? I'm not against fitting a series of pseudo-voigt functions constrained in a similar way, to my data, but I'd like to have a good justification for doing so. I'm quite new to the world of peak fitting in the context of XAS data analysis, so I'm looking forward to hearing the views of the mailing list. Thanks in advance. Will

3 2

Tenure track position in condensed matter physics
by Robert Meulenberg 01 Dec '17

01 Dec '17

Hello all, I hope I'm not overstepping any bounds here, but I know that this mailing list is populated with both experimentalists and theorists, so I figured the email could be of interest. The University of Maine is looking to hire a theoretical/computational condensed matter physicist for a tenure track Assistant Professor position. I have attached the ad and the link to the position can be found here: https://umaine.hiretouch.com/job-details?jobID=44990&job=assistant-professo… Please feel free to circulate as you see fit. Regards, Rob Meulenberg Robert W. Meulenberg Associate Professor of Physics Laboratory for Surface Science and Technology Department of Physics and Astronomy University of Maine Orono, ME 04469 phone: 207-581-2245 email: robert.meulenberg(a)maine.edu

1 0

Introduction to Synchrotron Radiation Course Online for Spring 2018
by Carlo Segre 29 Nov '17

29 Nov '17

Hello All: Illinois Tech's PHYS 570 (Introduction to Synchrotron Radiation) Course will be offered in the Spring semester of 2018 starting January 8, 2018. This is a graduate level course suitable for students in all science and engineering disciplines interested in learning more about synchrotron radiation production, instrumentation and experimental techniques. This is a for credit course which has both a live and online section. Lectures will be presented live on Tuesdays and Thursdays and will be posted for the online section within 12 hours through Illinois Institute of Technology's Blackboard system. A short description of the course is below. If you have an interest in this course, please contact me (Carlo Segre <segre(a)iit.edu>) for more details. PHYS 570 - Introduction to Synchrotron Radiation Term: Spring 2018, January 8, 2018 – May 5, 2018 Time: Tuesday & Thursday 13:50-15:05 Location: Live & Internet Instructor: Carlo U. Segre Description: This is a graduate course which introduces students to the production, manipulation and use of synchrotron radiation in research. The course will include visits to, and possibly hands-on experience with, beamlines at the Advanced Photon Source (APS) at Argonne National Laboratory but is not specific to the APS. Students will be expected to give presentations and write a General User Proposal to the APS as their final projects. Graduate students in any science or engineering program are welcome to register as are undergraduates with senior standing and permission of instructor. It is particularly recommended for students wishing to make use of synchrotron radiation in their research. The class meets Tuesdays and Thursdays 17:00-18:15 and the lectures are available online as an Internet section for students not on the IIT campus or outside the United States. Textbook: Elements of Modern X-Ray Physics, 2nd ed., Jen Als-Nielsen and Des McMorrow, (John Wiley & Sons, Ltd. 2011). Topics Covered: • X-rays and their interaction with matter • Sources of x-rays • Refraction and reflection from interfaces • Kinematical Diffraction • Diffraction by perfect crystals • Photoelectric absorption • Resonant scattering • Small angle scattering • Other topics as appropriate Course Organization: The grade will be based equally on homework assignments, student presentations and a draft General User Proposal to the Advanced Photon Source. There will be at least one field trip to the Advanced Photon Source for experiment demonstrations. -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

1 0

Athena: Data cannot be imported by using plugin PFBL12C
by 平岡　裕治 16 Nov '17

16 Nov '17

Dear all, I tried to import a data of multi-element detector at SPring-8 by using plugin PFBL12C to Athena, but it was not successful. if the number of rows in the file is about 2000[success.dat], it can be successfully imported. But for the data over about 4000 rows[fail.dat], it seems that several data at first of both converted energy and intensity are substituted by 0. column6.png shows intensity of ch6 vs energy_attained and I0.png shows intensity of I0 vs energy_attained. you can see this behavior. As a result, intensity cannot divide by I0, and data cannot be imported. if someone knows approach to solve this, could you teach me. Best regards, Yuji Hiraoka

4 4

current-amp recommendation
by Matthew Marcus 14 Nov '17

14 Nov '17

I've gotten involved with a project in which stabilization of the position of a monochromatic, soft X-ray beam is needed. The offending frequencies seem to be vibration frequencies like 57 and 116Hz. We have in mind to use a thin Au film with a gap in the middle, measuring the drain current from the films, much as people normally use the jaws of slits. Now, I'd like to find a couple of current amplifiers which are small enough so that they can be connected with very short cables to the BNC connectors on the air-side of this detector, and which would have decent frequency response and low noise with inputs of the order of 0.1-1nA. Although this topic is outside the realm of XAFS analysis with IFEFFIT, I figure that people on this group might have some good experience. mam

4 3

Re: [Ifeffit] Consult a few questions about XAS data analysis
by fred.mosselmans＠diamond.ac.uk 14 Nov '17

14 Nov '17

Hi Jun, Two points so Bruce doesn't get two upset. If you included the Athena project you used for the lcf and maybe an excel file of the results you got, then someone could Check what you did, as it is there is almost no way to offer an opinion on that. Bruce gave a course at Dimaond several years ago now, but most of what he shows is relatively as true as it was the day he said it. The videos can be found here. http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html The VLC media player works well with them. Regards Fred J.F.W. Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 [cid:image002.png@01D27563.28EDA240] -- 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

1 0

Consult a few questions about XAS data analysis
by Jun Ge 14 Nov '17

14 Nov '17

Hi Bruce I'm a learner for XAS data analysis because of the need of scientific research. I have been to SLAC in San Francisco three times last year and collected some XAS data of samples and models in Beamline 7-3. This summer, I began to learn how to analyze these XAS data. My professor used to use WinXAS to analyze data. But this time he asked me to learn Athena. He thinks use two different softwares can double check the result. After the data pro-processing, including background remove and data normalization, etc., I save each spectrum in the form .txt. However, *in the same energy range and same file of sample and models, the result of LCF performed by WinXAS and Athena was totally different!* I try to solve this problem for a long time but no progress was made. So I turn to you and Ressler (the author of WinXAS) for help. I guess may be the algorithm is different between your Athena with WinXAS, but I'm not sure. With great experience in XAS data analysis, I think it's easy for you to solve this problem, isn't it? By the way,* I don't know how to fit the Coordination Number in another software called Artemis* in the software package of Demeter. I was told by Artemis that the coordination number can only be a number not alphabet. So I have no idea how to do this (yeah, I'm really a noob orz). And I don't know how to set the parameter more correctly to run a excellent Feff fit. So could you please help me? Finally,* I want to learn XAS data analysis systematically. So could you please recommend me some references like books or papers?* Anyway, thanks a lot for your help and your precious time! Sincerely, Jun Ge

3 2

Re: [Ifeffit] Hephaestus: Absorption Data Source
by fred.mosselmans＠diamond.ac.uk 14 Nov '17

14 Nov '17

Hi Apologies for turning this into a social network, but Robert scanning Krause and Oliver, reminded me of when several decades ago, as a PhD student I typed all the K and L shell values from that paper into a table for Norman Binsted to use in his latest version of Excurve , probably Excurv88. Regards Fred -- 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

1 0

Hephaestus: Absorption Data Source
by Daniel Przyrembel 13 Nov '17

13 Nov '17

Dear All This might be a stupid question, but I have not been able to track this down myself: What is the data source of the "core-hole lifetimes" (i.e. the energy widths "gamma(ch)" in eV) of the "Absorption edges" in the "Absorption" panel of Hephaestus? As far as I could see these lifetimes/widths are not given in the 'Elam database'. Other XAS data tools based on the Elam database (like e.g. 'XrayDB') claim to be using values from 'O. Keski-Rahkonen and M. O. Krause, Atomic Data and Nuclear Data Tables 14, pp139-146 (1974) (http://dx.doi.org/10.1016/S0092-640X(74)80020-3)' for this. Because that reference does not give tabulated values but rough data plots only, it is difficult to compare those with the values in Hephaestus. If someone knows the respective data source used in Hephaestus, the answer/information is deeply appreciated! Best regards Daniel

4 8

E0 in Co3O4
by Jesús Eduardo Vega Castillo 30 Oct '17

30 Oct '17

Dear list, I enclose an Athena project with a XAFS spectrum of Co3O4 with a metallic Co reference. Athena by default has chosen E0 at the absolute maximun of the derivative curve (at 7727.8eV) which in my opinion is too high because it is at the white line zone. I believe that E0 should be the previous maximun in the derivative at around 7722eV, which would be at the rising edge. Am I wrong? I would appreciate some help with the criterion to determine the right value. Yours, Jesús

2 2

Re: [Ifeffit] iron carbide fitting with Artemis
by fred.mosselmans＠diamond.ac.uk 28 Oct '17

28 Oct '17

Dear Yunyun, I don't think Mike has written anything particularly incorrect , but he didn't point out why this approach is necessary. I believe there are two things you should definitely be aware of. An EXAFS dataset has a very limited amount of information. Approximately deltak.deltaR no of variables can be fitted To any spectrum as an absolute maximum and preferably quite a lot fewer than this (where deltak and deltaR are your fitted data range in k and R space respectively. Because of this if say you know you have N C atoms at ca G angstroms around your central atom. It is best not to use a variable for fit the degeneracy for that path but set it at the number you know is correct. And secondly because an EXAFS spectrum is effectively a collection of Sine waves there is a limited resolution, i.e. you cannot resolve paths of the same atom type that are less then Pi/2k(max) A apart, where k(max) is the maximum range of your dataset in k space, and Pi is Pi. Hence to separate two paths of the same atom that are 0.1 A apart you need about 15k worth of data. Regards Fred -- 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

2 1

iron carbide fitting with Artemis
by Yunyun Zhou 28 Oct '17

28 Oct '17

Hello All, I am having trouble fitting my sample with both Fe5C2 and Fe3O4 as standards. Hopefully somebody could help me out and I really appreciate it. My iron sample was mainly iron carbide in the core and iron oxide on the shell. Fe5C2 has a monoclinic structure and generated complicated FEFF paths. Many of the paths have similar distances. I have found some paper reported their results as follows, which apparently combined several paths together and assume they have similar path length. My first question is does someone know how they did it? It seems that combing similar paths makes fitting much easier, but I am not sure whether this is a correct way to do the fitting. My second question is regarding fitting with the two combined models of Fe5C2 and Fe3O4. I haven't fit with two models before. Is it just like what I did in the attached Artemis file? Shall there be any restrictions between the two models and do I have to fix some of the parameters? Thank you very much in advance for your help! Best, Yunyun Zhou Fe5C2 FEff paths: [image: Inline image 1] Literature reported results: [image: Inline image 2]

2 4

monoclinic elemental selenium data
by George Sterbinsky 26 Oct '17

26 Oct '17

Hello, I am trying to help someone locate XAFS data collected from the red allotrope (monoclinic) of elemental selenium. Does anyone have a data set they are willing to share? Thank you, George

1 0

flattened norm export issues
by Robert Gordon 22 Oct '17

22 Oct '17

Hi, Encountered a difference on export of normalised data. Flattening does not seem to be preserved when saving current group as norm(E) but is when saving marked group. Example in norm.prj attached. original data set normalised and flattened...displaying "Normalized" as current group or as marked group looks the same: current: marked: On saving current or marked group as norm(E), re-importing and plotting as mu(E) marked is still flattened, but the set exported using "save current group as" is not flattened. Similar difference saving "marked" versus saving "each marked" So it seems only "Save marked group as..." preserves flattening for norm(E). -R.

1 0

space group 224 & Atoms
by Robert Gordon 22 Oct '17

22 Oct '17

Hi, I was trying to simulate Cu2O...cubic...O tetrahedrally coordinated by Cu...Cu linearly coordinated by O. There are two origin choices for space group 224 (Pn-3m). If using origin choice 1, then atom positions would be O 0,0,0 Cu 0.25,0.25,0.25 If using origin choice 2, translate by -0.25,-0.25,-0.25 to get O 0.75,0.75,0.75 Cu 0,0,0 (or use the shift vector in Atoms...) My understanding is that Demeter defaults to the 2nd origin choice. Problem I am having is that neither gives me linearly coordinated copper using current Atoms. If I read in the attached atoms.inp (choice 2) and Run Atoms, the ATOMS list in the Feff output begins with: ATOMS * this list contains 87 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 cu1 0.00000 -1.06675 1.06675 1.06675 2 o1.1 1.84767 -1.06675 -1.06675 1.06675 2 o1.1 1.84767 1.06675 1.06675 -1.06675 2 o1.1 1.84767 -1.06675 -1.06675 -1.06675 2 o1.1 1.84767 2.13350 2.13350 0.00000 1 cu1.1 3.01722 I get 4-coordinate instead of 2-coordinate. If I try origin choice 1, almost the same result.... ATOMS * this list contains 83 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 cu1 0.00000 -1.06675 1.06675 1.06675 2 o1.1 1.84767 1.06675 -1.06675 1.06675 2 o1.1 1.84767 1.06675 1.06675 -1.06675 2 o1.1 1.84767 -1.06675 -1.06675 -1.06675 2 o1.1 1.84767 2.13350 2.13350 0.00000 1 cu1.1 3.01722 If I run choice 1 with the shift vector, I do reproduce the choice 2 result. If I use the old dos version of Atoms with origin choice 2, I do get linearly coordinated copper: ATOMS .00000 .00000 .00000 0 cu1 .00000 -1.06675 -1.06675 -1.06675 1 o1 1.84767 1.06675 1.06675 1.06675 1 o1 1.84767 .00000 -2.13350 2.13350 2 cu1 3.01722 SPECS: Demeter 0.9.26 (pre2) Win10x64 AMD64 -R.

1 0

Metal-Metal Peak Splitting in 5d Transition Metals
by Shoaib Muhammad 19 Sep '17

19 Sep '17

Dear All, I have a question that is not directly related to Athena or Artemis but it is more related with EXAFS theory. I work on lithium metal oxides and sometimes measure their XAS data. XAS data show typical trend, i.e; first prominent peak related with metal-oxygen co-ordination shell and second prominent peak is associated with metal-metal co-ordination shell in my materials. I have noticed that in similar crystal structures Li2MO3-type (where M is transition metal), if metal belongs to 3d transition metal groups I get a single prominent metal-metal peak but for 5d transition metals, the metal-metal peak splits and its intensity also drops. I could not figure out the reason for the splitting of metal-metal peak in case of 5d metals. I have attached a PDF file in which calculated EXAFS spectra for Li2RuO3 (4d transition metal) and Li2PtO3 (5d transition metal) are shown and metal-metal (Pt-Pt) peak in Li2PtO3 shows clear splitting whereas metal-metal peak for Li2RuO3 does not split even though their "ATOMS" input files are very similar. I would appreciate if anybody could briefly explain the reason for metal-metal peak splitting in 5d metals or point me towards any literature. Attachment can be downloaded from the below link as well. https://www.dropbox.com/s/1m3kf764junuukk/Metal-Metal%20Peak%20Splitting%20i n%205d.pdf?dl=0 Thanks, Shoaib Muhammad Department of Energy Science Sungkyunkwan University (South Korea)

2 1

Limit for number of data points in a file to be imported in Athena
by Kaustubh Priolkar 16 Sep '17

16 Sep '17

Hi! I have a QEXAFS data file with 12000 data points but Athena reads it only partially. Is there a limit on maximum number of data points in a file that Athena can import? Is there a way to increase the limit? Thanks in advance, Kaustubh Sent from Mail for Windows 10

1 0

[IFEFIT]Chi(E) in version 0.9.25
by Michael Stockenhuber 15 Sep '17

15 Sep '17

Dear mailing list, Is there any way to save data as Chi( E),i.e., energy one column and chi(E) in the 2nd column? This was possible in the past and it would be great to have that to be able to import into excurv. Thank you for all the help and great programs Cheers Michael Prof. Michael Stockenhuber Chemical Engineering, School of Engineering Faculty of Engineering and Built Environment The University of Newcastle T +61 2 4985 4433 F +61 2 4921 9095 M + 61 (0) 450352239 Michael.stockenhuber(a)newcastle.edu.au<mailto:Michael.stockenhuber@newcastle.edu.au> President Catalysis Society of Australia www.catalysis.org.au<http://www.catalysis.org.au> Co-chair ACEME 2018 https://www.aiche.org/aceme2018 Co-chair ISHHC 2018 http://www.ishhc17.org

3 3

How to use Artemis with feff85L
by José Carlos Conesa 14 Sep '17

14 Sep '17

Hi, I should like to use feff85L within Artemis (from Demeter 0.9.25), just to check in my system whether selfconsistency has a role in unifying E0 values (with feff 6, allowing different E0 for each scatterer leads to E0 differences >10 eV, which seems too much to me). I find that after loading the EXAFS data (from Athena) and a model (a .cif file containing Cu, Ce and O atoms), if I click Run Atoms and then Run Feff with feff6 as executable I get the usual set of paths that allow me doing a fit of the data, but if I try to use the feff85L.exe that comes with the Demeter software (by changing the feff executable in the File/Edit preferences menu), after clicking the Run Feff button (without including the SCF card) a bit of computation happens and after finishing it the path list is empty. ¿Any idea of the possible reason why I get no path list? Thanks in advance -- José C. Conesa Instituto de Catálisis y Petroleoquímica, CSIC Marie Curie 2, Madrid, Spain www.icp.csic.es Tel. (+34)915854766

4 6

1 Phd student and 2 postdocs positions are available at ROBL of ESRF
by Kristina Kvashnina 14 Sep '17

14 Sep '17

Dear Colleagues, We are looking for 2 postdocs and 1 PhD student to investigate the lanthanide/actinide oxides nanomaterials by X-ray absorption/emission spectroscopy and electronic structure calculations. Each contract is for 3 years. I will very much appreciate if you can share that information with anyone who might be interested. Thank you ! Kind regards, Kristina More information is here http://www.esrf.fr/Jobs/CRGJobs http://www.esrf.fr/files/live/sites/www/files/Jobs/giant/ROBL_phd_student_a… http://www.esrf.fr/files/live/sites/www/files/Jobs/giant/ROBL_Postdoc1.pdf http://www.esrf.fr/files/live/sites/www/files/Jobs/giant/ROBL_Postdoc2.pdf

1 0

Peak locations for Phosphorus in Carbon K-edge
by Kenneth Latham 28 Aug '17

28 Aug '17

Dear All, I have analysed some phosphoric acid activated carbons via NEXAFS and was wondering if anyone had come across any references or knew where the transition/peak for the C-O-P or C-P-O bonding arrangement occurs in the carbon K-edge region. The samples I am examining are a series at different heat treatment steps and lose a lot of oxygen functionality, so finding where C-O-P or C-P-O transitions occur would be very useful in understanding the chemical transitions that are occurring. Regards, Ken

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 174, Issue 8
by Carmelo Prestipino 18 Aug '17

18 Aug '17

Hi Hiroyuki, I done a small interface to Larch to work with a lot of files http://soonready.github.io/PrestoPronto/ It is not nice as Athena and it has not all its possibility but if you are used to Athena you should not get lost (the name of parameter is the same ). It is not fast how it should be but give a try, maybe could be useful Carmelo On Thu, Aug 17, 2017 at 7:00 PM, <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: How to use Larch as backend for Athena and Artemis on > Windows (Bruce Ravel) > 2. Re: How to use Larch as backend for Athena and Artemis on > Windows (ASAKURA, Hiroyuki) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Aug 2017 13:17:13 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] How to use Larch as backend for Athena and > Artemis on Windows > Message-ID: <1956f39f-85f4-7a92-a989-24a5436df426(a)bnl.gov> > Content-Type: text/plain; charset=utf-8; format=flowed > > > Hi Hiroyuki, > > Sorry I didn't respond yesterday. Yesterday was a bit of crazy day... > > I suppose that this is still a work in progress. I believe that Demeter > works with Larch on Windows, but it is certainly not as easy or > convenient yet as it should be. > > In the place where Demeter got installed on your computer, there is a > folder called \perl\site\bin -- you can look at the properties of the > Athena desktop icon to see where that is. In that folder is the > "dathena.bat" file which the Athena desktop icon points at. > > You should also find a file called "lathena.bat". Try running that or > pointing your desktop icon at it instead. > > The difference between "lathena.bat" and "dathena.bat" is line 25 that > sets an environment variable that Demeter uses to decide which of > ifeffit or larch to use. > > Obviously, there are number of other ways to get this environment > variable set. The bottom line is, yes, there is a switch. The switch > is the DEMETER_BACKEND environment variable. > > Unfortunately, that switch cannot be in the configuration files, > although what you tired in item 2 of your email was a sensible guess. > It turns out that the choice of larch/ifeffit has to made long before > the configuration files are read. > > Do let me know how you get on. While Demeter + larch should work, there > are still almost certainly problems. I need to get a new version of the > Demeter installer out soon, so it would be nice to get some feedback in > this area. > > As for using Demeter + larch + 100s of file -- it should work after a > fashion. But I worry that Athena's performance might not be what you > are hoping for. Athena does a lot of things that are more user-friendly > than performance-friendly.... > > > Cheers, > B > > > On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote: > > Dear all, > > > > I would like to use the latest Larch as backend for Athena and Artemis > > on Windows to handle hundreds of XAS data (, hopefully). > > But, I'm stuck. I would appreciate any comments and suggestions. > > > > Matt announced it is now possible on this list, but I still cannot do it > > on Windows. > > > > [Ifeffit] Larch 0.9.33 > > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017- > April/009091.html > > > >> The "server mode" for Athena and Artemis now works on all platforms and > I > >> strongly encourage everyone to use this over the ifeffit back end. > > > > Here is what I did. > > > > Environment: > > Windows 10 Pro (Japanese) > > Demeter 0.9.25 (via official website) > > Python 3.6 (official distribution) > > > > 1. Installation of the latest Larch > > > >> git clone https://github.com/xraypy/xraylarch.git (sha1: > >> 5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d) > >> cd xraylarch > >> python setup.py install > > # Some dependency related to XRD is not fulfilled. > > > > 2. Start Larch server > > > >> cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts > >> python larch_server start > > larch_server port=4966: started > > > > I found a parameter of peakfit backend in demeter.ini and changed to > > larch, but did not work (as expected). > > > > In the dathena.log, Athena still uses ifeffit as backend. > > > >> perl version: v5.18.2 > >> backend: ifeffit > > > > Should I compile Demeter package by myself to use the Larch backend? > > Or, is there any "switch" to use Larch? > > > > Thanks in advance, > > > > ASAKURA, Hiroyuki > > > > > > > -- > 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: Thu, 17 Aug 2017 18:21:51 +0900 > From: "ASAKURA, Hiroyuki" <asakura(a)moleng.kyoto-u.ac.jp> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] How to use Larch as backend for Athena and > Artemis on Windows > Message-ID: > <2d60a548-06bf-5cdf-02f7-154ab039924a(a)moleng.kyoto-u.ac.jp> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear Bruce, > > I do appreciate your prompt response! > > Now, I managed to run Athena with Larch backend on Windows 10 and handle > about 100 XAS data at once. > Athena with Ifeffit backend stalls when handling about 40 XAS spectra at > least in my case. > Unfortunately, there seems to be a bit severe performance issue with a > large number of spectra, as noted. > > Here is what I did. > > 0. Install an official Git package > 1-1. Download "64-bit Git for Windows Setup" via > https://git-scm.com/download/win > 1-2. Install Git with default options except for "Use Git from the > Windows Command Prompt" and "Use Windows' default console window" > Note: You can use any options you want. > > 1. Install an official Demeter package > 1-1. Download "Demeter 0.9.25 (32 bit)" via https://bruceravel.github.io/ > demeter/ > 1-2. Install Demeter with default options > Note: I cannot run 64 bit version with Larch. > > 2. Install an official Python package > 2-1. Download "Windows x86-64 web-based installer" via > https://www.python.org/downloads/release/python-362/ > 2-2. Custom Install Python with default options except for "Add Python > 3.6 to PATH" (checked) > > 3. Install unofficial Numpy and Scipy, Python libraries > 3-1. Download numpy?1.13.1+mkl?cp36?cp36m?win_amd64.whl and > scipy?0.19.1?cp36?cp36m?win_amd64.whl via http://www.lfd.uci.edu/~ > gohlke/pythonlibs/ > 3-2. pip install numpy-1.13.1+mkl-cp36-cp36m-win_amd64.whl > 3-3. pip install scipy?0.19.1?cp36?cp36m?win_amd64.whl > > 4. Install Larch and its dependencies > 4-1. Start a command prompt > 4-2. git clone https://github.com/xraypy/xraylarch.git > 4-3. cd xraylarch > 4-4. pip install lmfit > 4-5. pip install h5py > 4-6. pip install pillow > 4-7. pip install requests > 4-8. pip install sqlalchemy > 4-9. pip install matplotlib > 4-10. pip install pypiwin32 > 4-11. pip install wxpython > 4-12. pip install wxmplot > 4-13. pip install wxutils > 4-14. python setup.py install > 4-15. larch --version > 4-16. You will see "larch command-line version 0.2". > Note: I installed Larch dependencies except for pyFAI, CifFile, fabio, > tomopy, scikit-image. > > 5. Run Larch and Athena with Larch > 5-1. Start a new command prompt > 5-2. larch -rc > 5-3. Start another new command prompt > 5-4.cd %APPDATA%\DemeterPerl\perl\site\bin > 5-5. lathena.bat > > It works. > Athena is the most user-friendly XAS processing tool I have used. > > Thanks so much! > > Best regards, > > ASAKURA, Hiroyuki > > > On 2017/08/17 2:17, Bruce Ravel wrote: > > > > Hi Hiroyuki, > > > > Sorry I didn't respond yesterday. Yesterday was a bit of crazy day... > > > > I suppose that this is still a work in progress. I believe that Demeter > works with Larch on Windows, but it is certainly not as easy or convenient > yet as it should be. > > > > In the place where Demeter got installed on your computer, there is a > folder called \perl\site\bin -- you can look at the properties of the > Athena desktop icon to see where that is. In that folder is the > "dathena.bat" file which the Athena desktop icon points at. > > > > You should also find a file called "lathena.bat". Try running that or > pointing your desktop icon at it instead. > > > > The difference between "lathena.bat" and "dathena.bat" is line 25 that > sets an environment variable that Demeter uses to decide which of ifeffit > or larch to use. > > > > Obviously, there are number of other ways to get this environment > variable set. The bottom line is, yes, there is a switch. The switch is > the DEMETER_BACKEND environment variable. > > > > Unfortunately, that switch cannot be in the configuration files, > although what you tired in item 2 of your email was a sensible guess. It > turns out that the choice of larch/ifeffit has to made long before the > configuration files are read. > > > > Do let me know how you get on. While Demeter + larch should work, there > are still almost certainly problems. I need to get a new version of the > Demeter installer out soon, so it would be nice to get some feedback in > this area. > > > > As for using Demeter + larch + 100s of file -- it should work after a > fashion. But I worry that Athena's performance might not be what you are > hoping for. Athena does a lot of things that are more user-friendly than > performance-friendly.... > > > > > > Cheers, > > B > > > > > > On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote: > >> Dear all, > >> > >> I would like to use the latest Larch as backend for Athena and Artemis > on Windows to handle hundreds of XAS data (, hopefully). > >> But, I'm stuck. I would appreciate any comments and suggestions. > >> > >> Matt announced it is now possible on this list, but I still cannot do > it on Windows. > >> > >> [Ifeffit] Larch 0.9.33 > >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017- > April/009091.html > >> > >>> The "server mode" for Athena and Artemis now works on all platforms > and I > >>> strongly encourage everyone to use this over the ifeffit back end. > >> > >> Here is what I did. > >> > >> Environment: > >> Windows 10 Pro (Japanese) > >> Demeter 0.9.25 (via official website) > >> Python 3.6 (official distribution) > >> > >> 1. Installation of the latest Larch > >> > >>> git clone https://github.com/xraypy/xraylarch.git (sha1: > 5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d) > >>> cd xraylarch > >>> python setup.py install > >> # Some dependency related to XRD is not fulfilled. > >> > >> 2. Start Larch server > >> > >>> cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts > >>> python larch_server start > >> larch_server port=4966: started > >> > >> I found a parameter of peakfit backend in demeter.ini and changed to > larch, but did not work (as expected). > >> > >> In the dathena.log, Athena still uses ifeffit as backend. > >> > >>> perl version: v5.18.2 > >>> backend: ifeffit > >> > >> Should I compile Demeter package by myself to use the Larch backend? > >> Or, is there any "switch" to use Larch? > >> > >> Thanks in advance, > >> > >> ASAKURA, Hiroyuki > >> > >> > > > > > > -- > ASAKURA, Hiroyuki (Ph.D) > Program-Specific Assistant Professor (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/ > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 174, Issue 8 > *************************************** > -- Carmelo Prestipino Sciences Chimiques de Rennes, UMR 6226 Solid State and Materials Chemistry group (CSM) Campus de Beaulieu, Bât 10B, bureau 123 263 avenue du Général Leclerc F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959

3 3

How to use Larch as backend for Athena and Artemis on Windows
by ASAKURA, Hiroyuki 18 Aug '17

18 Aug '17

Dear all, I would like to use the latest Larch as backend for Athena and Artemis on Windows to handle hundreds of XAS data (, hopefully). But, I'm stuck. I would appreciate any comments and suggestions. Matt announced it is now possible on this list, but I still cannot do it on Windows. [Ifeffit] Larch 0.9.33 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html > The "server mode" for Athena and Artemis now works on all platforms and I > strongly encourage everyone to use this over the ifeffit back end. Here is what I did. Environment: Windows 10 Pro (Japanese) Demeter 0.9.25 (via official website) Python 3.6 (official distribution) 1. Installation of the latest Larch > git clone https://github.com/xraypy/xraylarch.git (sha1: 5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d) > cd xraylarch > python setup.py install # Some dependency related to XRD is not fulfilled. 2. Start Larch server > cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts > python larch_server start larch_server port=4966: started I found a parameter of peakfit backend in demeter.ini and changed to larch, but did not work (as expected). In the dathena.log, Athena still uses ifeffit as backend. > perl version: v5.18.2 > backend: ifeffit Should I compile Demeter package by myself to use the Larch backend? Or, is there any "switch" to use Larch? Thanks in advance, ASAKURA, Hiroyuki -- ASAKURA, Hiroyuki (Ph.D) T. Tanaka Lab., ESICB, Kyoto University, Japan asakura(a)moleng.kyoto-u.ac.jp http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/

3 3

How to use Larch as backend for Athena and Artemis on Mac (Re: Ifeffit Digest, Vol 174, Issue 8)
by Luke Higgins 17 Aug '17

17 Aug '17

Dear All, Following the excellent guide that Hiroyuki & Bruce gave for running larch on Demeter on Windows (Ifeffit Digest, Vol 174, Issue 8). The following steps worked for me to run larch/Demeter on MacOS (Sierra 10.12.6). 1) Install Demeter using the advice from: https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h… 2) Installed Anaconda and larch using the following guide: http://cars.uchicago.edu/xraylarch/installation/index.html (Python & larch from source is fine: but then use Hiroyuki’s step 3&4 advice [attached below]) 3) In a new terminal window check larch by: larch --version You should see "larch command-line version 0.2". 4) Running larch and Demeter, run in a new terminal window: larch --port=4966 –rc 5) Open Demeter.pm in a text editor (which for me was buried in: /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter.pm) and change line 44 to: $ENV{DEMETER_BACKEND} ||= 'larch'; 6) This has changed both Athena and Artemis to using larch – haven’t fully tested yet, but looks good. Best Wishes, Luke (from Hhiroyuki, installing python and larch from source files:) 3. Install unofficial Numpy and Scipy, Python libraries 3-1. Download numpy‑1.13.1+mkl‑cp36‑cp36m‑win_amd64.whl and scipy‑0.19.1‑cp36‑cp36m‑win_amd64.whl via http://www.lfd.uci.edu/~gohlke/pythonlibs/ 3-2. pip install numpy-1.13.1+mkl-cp36-cp36m-win_amd64.whl 3-3. pip install scipy‑0.19.1‑cp36‑cp36m‑win_amd64.whl 4. Install Larch and its dependencies 4-1. Start a command prompt 4-2. git clone https://github.com/xraypy/xraylarch.git 4-3. cd xraylarch 4-4. pip install lmfit 4-5. pip install h5py 4-6. pip install pillow 4-7. pip install requests 4-8. pip install sqlalchemy 4-9. pip install matplotlib 4-10. pip install pypiwin32 4-11. pip install wxpython 4-12. pip install wxmplot 4-13. pip install wxutils 4-14. python setup.py install 4-15. larch --version 4-16. You will see "larch command-line version 0.2". Note: I installed Larch dependencies except for pyFAI, CifFile, fabio, tomopy, scikit-image.

1 0

Artemis can't open project file and crashes
by Michelle Hammerton 11 Aug '17

11 Aug '17

Hello, I wonder if anyone can help me. Artemis (version 0.9.25) is unable to open the most recent project files that I have created and just crashes. These files also can't be opened on a different computer. I get the following message in the dartemis log file: You must define a method name at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\vendor\lib\Class\MOP\Mixin\HasMethods.pm line 96 Class::MOP::Mixin::HasMethods::has_method('Class::MOP::Class::Immutable::Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0xb49ab58)', '') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 424 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x10140bd0)', ' :') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 447 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x10140bd0)', 'space = I 41/a m d :2') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 382 Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x10140bd0)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 198 Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x10140bd0)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\racrw\atoms.inp') called at accessor Demeter::Atoms::file (defined at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 202) line 10 Demeter::Atoms::file('Demeter::Atoms=HASH(0x10140bd0)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Atoms\Xtal.pm line 667 Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x1afa1b38)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 1388 Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x1522a180)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp', 'CuCr2O4_I41-amd2_2006190') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis\Project.pm line 351 Demeter::UI::Artemis::Project::read_project('HASH(0xf7cdf60)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 996 Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x1522a180)', 'Wx::CommandEvent=SCALAR(0x15dc4558)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 440 Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x1522a180)', 'Wx::CommandEvent=SCALAR(0x15dc4558)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 50 eval {...} at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 50 So I guess I need to define a method name? What could it be and how do I define it? Thank you for your help (in advance!) Best wishes, Michelle *Michelle Hammerton Msc.* University of Amsterdam <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

Demeter on Windows with Inkscape (and possibly other programs)
by Bruce Ravel 10 Aug '17

10 Aug '17

Windows users: I got an interesting bug report today from a fellow who develops a popular open source program for vector graphics editing (Inkscape). Apparently, there is a problem in Demeter's installer that has an impact on the ability of that program (and possibly others) in accessing system font files. The issue with Inkscape is described here: https://github.com/bruceravel/demeter/issues/51 I mention this here on the mailing list in an effort to help the folks who maintain Inkscape. If you use Demeter and Inkscape on your Windows machine, there is a problem and it is my fault :( The simplest solution is to uninstall Demeter, then continue using Inkscape. If that's not true or if someone needs a better solution right now, post here and I will help you work out a solution. I think the real fix to the problem is simple and I will work on a new installer this month. Cheers, 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/

2 1

Athena Crashing on Mac
by Daniel Austin Sheffield Uni 04 Aug '17

04 Aug '17

Hi, I emailed relatively recently about Artemis crashing on my MacBook Pro. This is the email i sent: 'I was using Artemis on Mac and it crashed. Now when i try to reopen Artemis it attempts restore what i was doing from an autosave file but it becomes unresponsive and is just stuck on the screen posted below. Does anyone know how i can fix it? Do i have to uninstall and then reinstall the software? i have left it running for over an hour but it still hasn’t worked. Thanks for any help’ Now the exact same thing is occurring with Athena. One of the replies from the previous email instructed me to remove parts of the programme code. I did so an Artemis worked perfectly after, i just needed to save often. The full email that instructed me on this can be found below: Hi Daniel, I had a similar issue, but my solution hasn’t been put up yet on the list: With respect to the error that Katherine Davies reported (02/16/2016; RE: [Ifeffit] problem with Artemis crashing on mac), I came across the same problem when running Artemis on Mac. I believe this issue is caused by a piece of code found in “artemis.pm” (Demeter/UI/artemis.pm) line 512-521: 512 sub process_argv { 513 my ($app, @args) = @_; 514 if (Demeter->co->default("artemis", "autosave") and autosave_exists()) { 515 import_autosave(); 516 } elsif ($args[0]) { # and -e $args[0]) { 517 my $file = File::Spec->rel2abs( $args[0] ); 518 read_project(\%frames, $file) if Demeter->is_zipproj($file, 0, 'fpj'); 519 }; 520 }; I think the error is due to not shutting down the program correctly causing this code to fail. A fix is to comment out lines 514-516 & 519, save the file and reboot Artemis (to edit artemis.pm you will need to make the file writable)– thus getting you past startup and allowing you to turn off the autosave settings from within Artemis as suggested. Put the code back as it was after you have finished. Hope this helps. Best, Luke Higgins I tried searching for similar code in the Athena programme but couldn’t find it. Does anyone have a similar solution, or any solution, to this problem? Thank you so much

2 1

Artemis Crashing
by Daniel Austin Sheffield Uni 02 Aug '17

02 Aug '17

Hi, I was using Artemis on Mac and it crashed. Now when i try to reopen Artemis it attempts restore what i was doing from an autosave file but it becomes unresponsive and is just stuck on the screen posted below. Does anyone know how i can fix it? Do i have to uninstall and then reinstall the software? i have left it running for over an hour but it still hasn’t worked. Thanks for any help, Daniel

3 2

working at the lanthanide K-edges: question about amplitude reduction factors
by Bone, Sharon Elizabeth 28 Jul '17

28 Jul '17

Hello- I recently collected some Nd K-edge EXAFS at APS (~43 KeV). I've started fitting the data and am looking for S02 values in the literature to compare to my own (especially since my fitted S02 values- to two Nd reference materials for which I know coordination numbers- are outside of the typical range of 0.7 - 1), but I haven't found any reported. Has anyone worked at the lanthanide K-edges? Could you point me to a reference for S02? Thanks! Sharon

1 0

Postdoc
by mathieu le meur 24 Jul '17

24 Jul '17

Hello I am very interested with the postdoc doc position with Corwin H. Booth Unfortunately, the link is not working and I cannot apply. Can you help me? Thanks, Mathieu. Get Outlook for Android<https://aka.ms/ghei36>

2 1

LBNL Postdoctoral Fellow Position
by Corwin H. Booth 21 Jul '17

21 Jul '17

Greetings all! I have just posted for a new Postdoctoral Fellow position to work with me at LBNL on projects with the Actinide Chemistry Group here and with Prof. Eric Schelter at U. Penn. Most of the work is to perform and analyze XAFS data. Please take a look at the official posting and apply if you are interested and meet the minimum qualifications. Here is the posting: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=83928 <https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=83928> Very best, Corwin -- Corwin H. Booth Chemical Sciences Division Lawrence Berkeley National Laboratory MS 70A-1150 1 Cyclotron Rd. Berkeley, CA 94720-8175 voice: 510-486-6079 FAX: 510-486-5596 Email: chbooth(a)lbl.gov Web: http://lise.lbl.gov/chbooth/

1 0