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

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 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

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 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/

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