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

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.

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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.

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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)

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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

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[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

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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

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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

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Peak locations for Phosphorus in Carbon K-edge
by Kenneth Latham 27 Aug '17

27 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

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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

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

17 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/

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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.

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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>

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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/

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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

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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

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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

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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>

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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/

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Trouble in running Artemis in Mac
by Chang-wook Lee 13 Jul '17

13 Jul '17

I’m using Artemis in Mac. I got a trouble on running the software. Once the Artemis shut down by accident, (during import .inp file), the problem occurred. When I reopen the Artemis, It tries to restore previous file but it never worked. I uninstalled and reinstalled it several times but I can only see same unlimited loading screen… Athena works well. Thanks, Changwook

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Help with running GUI
by Drew Syverson 07 Jul '17

07 Jul '17

Hello everyone, Every time I try to open gse_mapviewer via the terminal on Mac OSX, I keep getting the message: "This program needs access to the screen. Please run with a Framework build of python, and only when you are logged in on the main display of your Mac." I do not know how to get past this issue on my computer. Any help would be appreciated. -Drew ~~~~~~~~~~~~~~~~~~~~~~~~ Drew D. Syverson, PhD Postdoctoral Associate Department of Geology and Geophysics Yale University New Haven, CT, USA ph: +1 (612) 475-0575 email: drew.syverson(a)yale.edu https://sites.google.com/view/drewsyverson/home

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XAFS Tutorial
by Daniel Austin Sheffield Uni 07 Jul '17

07 Jul '17

Hello, I am currently trying to learn how to use the software through the tutorials on the User Manuals. For Athena I tried to download the practice fe.060 data from Github but the data won’t download. I have asked my supervisor and he can’t download it either. Can anyone suggest how i can successfully download it? I realise i may be missing something obvious. Alternatively, if someone has the practice file data already downloaded could they send it to me? Thanks you, Daniel

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Re: [Ifeffit] Ifeffit Digest, Vol 173, Issue 1
by Christopher Thomas Chantler 05 Jul '17

05 Jul '17

Thanks Fred and well suggested. I also encourage all interested. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS 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: Wednesday, 5 July 2017 8:21:22 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 173, Issue 1 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. Improving Data Quality in XAFS Spectroscopy Workshop - Q2XAFS 2017 - Reminder to Register & Deadline for Poster Abstracts (fred.mosselmans(a)diamond.ac.uk) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Jul 2017 10:14:17 +0000 From: <fred.mosselmans(a)diamond.ac.uk> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Improving Data Quality in XAFS Spectroscopy Workshop - Q2XAFS 2017 - Reminder to Register & Deadline for Poster Abstracts Message-ID: <CF65047C5B0562499EAFF9FBBC542D640105240B89@exchmbx01> Content-Type: text/plain; charset="iso-8859-1" [cid:image002.jpg@01D2974C.A644EF90]<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> Q2XAFS 2017 will bring together experts in the field of X-ray Absorption Spectroscopy to discuss aspects of the technique that affect data quality in XAFS experiments. The workshop will provide a forum for discussions with the goal of reviewing international standards and protocols, and developing revised recommendations for best practice when performing XAFS experiments. It will also look towards the first agreed data formats and standards for XAFS data and deposition. The workshop is hosted by Diamond Light Source<http://www.diamond.ac.uk/Home.html> and will take place on Monday 14th & Tuesday 15th August at Harwell Science and Innovation Campus, Didcot, UK. The full programme can be viewed on the website here - Q2XAFS 2017 Programme<http://www.q2xafs2017.com/Conference/Q2XAFS2017/Scientific-Programme.html>. Registration is ?220 standard and ?180 for students which includes access to 2 full days of scientific programme, a welcome reception (Sunday 13th August) a workshop dinner (Monday 14th) , optional facility tour and lunches and refreshments each day. The call for poster abstracts will remain open until the 7th July, please see the website for more details on submission<http://www.diamond.ac.uk/Conference/Q2XAFS2017/Participate/Abstract-Submiss…> poster presentation and for the abstract template. Visit the Q2XAFS 2017 website<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> to register and for details of the programme and further information. http://www.q2xafs2017.com/Conference/Q2XAFS2017.html We hope you can join us in August. Best wishes, Q2XAFS 2017 Local Organising Committee T: +44 (0) 1235 778384 E: q2xafs2017(a)diamond.ac.uk Sorry for this partial spam, but my excuse Is the "godfathers"(?) of this list Matt Newville ,in person, and Bruce Ravel, by videolink, will be presenting, and sometimes it is sunny in Oxfordshire. 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 http://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

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Improving Data Quality in XAFS Spectroscopy Workshop - Q2XAFS 2017 - Reminder to Register & Deadline for Poster Abstracts
by fred.mosselmans＠diamond.ac.uk 05 Jul '17

05 Jul '17

[cid:image002.jpg@01D2974C.A644EF90]<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> Q2XAFS 2017 will bring together experts in the field of X-ray Absorption Spectroscopy to discuss aspects of the technique that affect data quality in XAFS experiments. The workshop will provide a forum for discussions with the goal of reviewing international standards and protocols, and developing revised recommendations for best practice when performing XAFS experiments. It will also look towards the first agreed data formats and standards for XAFS data and deposition. The workshop is hosted by Diamond Light Source<http://www.diamond.ac.uk/Home.html> and will take place on Monday 14th & Tuesday 15th August at Harwell Science and Innovation Campus, Didcot, UK. The full programme can be viewed on the website here - Q2XAFS 2017 Programme<http://www.q2xafs2017.com/Conference/Q2XAFS2017/Scientific-Programme.html>. Registration is £220 standard and £180 for students which includes access to 2 full days of scientific programme, a welcome reception (Sunday 13th August) a workshop dinner (Monday 14th) , optional facility tour and lunches and refreshments each day. The call for poster abstracts will remain open until the 7th July, please see the website for more details on submission<http://www.diamond.ac.uk/Conference/Q2XAFS2017/Participate/Abstract-Submiss…> poster presentation and for the abstract template. Visit the Q2XAFS 2017 website<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> to register and for details of the programme and further information. http://www.q2xafs2017.com/Conference/Q2XAFS2017.html We hope you can join us in August. Best wishes, Q2XAFS 2017 Local Organising Committee T: +44 (0) 1235 778384 E: q2xafs2017(a)diamond.ac.uk Sorry for this partial spam, but my excuse Is the "godfathers"(?) of this list Matt Newville ,in person, and Bruce Ravel, by videolink, will be presenting, and sometimes it is sunny in Oxfordshire. 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

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Exporting Curves (as Data rather than Images)
by Felix E. Feiten 26 Jun '17

26 Jun '17

Dear all, I think the title is almost enough explanation. I would like to export the data corresponding to fits, chi(k), fourier-transform and back-transform to plot them with a different software. I couldn't figure out how, can someone please help me? With kind regards Felix

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Nearest neighbor statistics in a random alloy
by Felix E. Feiten 23 Jun '17

23 Jun '17

Dear all, I am fitting a Pt9Co1 foil sample. I assume the sample to be basically fcc platinum with every 10th atom randomly replaced by cobalt. Here are the assumptions I make: 1. every atom has 12 nearest neighbors 2. every Pt atom has (on average) 10.7 Pt nearest neighbors and 1.3 Co nearest neighbors 3. every Co atom has (on average) 11.7 Pt nearest neighbors and 0.3 Co nearest neighbors I have been told that assumptions 2 and 3 are not precise. Here is what I'm confused about: In order to determine the number of Pt or Co nearest neighbors I looked at an ensemble of 13 atoms: 1 absorber and 12 scatterers/nearest neighbors. I assume that the Pt/Co ratio in this ensemble is 9/1 and therefor, statistically, 1.3 out of those 13 atoms should be Co. That means that if Co is the central atom only 0.3 Co atoms are remaining for the 12 nearest neighbors. On the other hand, if Pt is the central atom, (all) 1.3 Co atoms are remaining for the 12 nearest neighbors. I have been told that the ratio of Pt/Co should be 9/1 in the 12 nearest neighbors, not in the 12 atoms including the central atom (quote: "because we have a bulk sample"). But I do not understand why. Can someone please explain the correct answer to me? With kind regards, Felix

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