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

Question_Demeter installation on Mac with Apple Silicon M1
by 王茂林 23 Jan '22

23 Jan '22

Dear IFEFFIT members, Here I want to install Demeter in my Mac with M1 pro, I followed the processes in https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h… (First, install Xcode and Xcode command tool; Then install Macport). But when I type " sudo port install xorg-server demeter in the terminal and after agreeing to the terms, there came to a warning, shown in the attached figure. What should I do to install it on my mac? And the log file (also attached) seems like Demeter doesn't support the M1 with ARM architecture? I'm looking forward to your helpful reply! Best regards, Maolin Wang 确定

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The possibility of the defect concentration estimation by feff
by Iraida N. Demchenko 17 Jan '22

17 Jan '22

Dear All, Do I understand correctly that using feff calculations it is impossible to calculate the concentration of defects in a sample? I'll try to explain my question with an example. Let us assume that we have a (Ga,Mn)As sample, where Mn is a dopant. Comparing the experimental curve (Mn K edge) with the theoretical spectrum, we see that the experimental one is well described by a linear combination of two theoretical ones, namely, substitutional manganese in the position of gallium (Mn_Ga) and interstitial manganese (Mn_i) in proportions of 65 and 35%, respectively. Is it possible to recalculate these phases weights (I mean Mn_Ga and Mn_i) to the real concentration of the mentioned above defects in the sample? For example, for the Mn_Ga model, ONE manganese atom was considered per cluster of 900 atoms (FMS 7A). Does it make sense to recalculate the stoichiometry (using cluster size) and, subsequently, the weights of this model when compared to the experimental curve, which will eventually give the selected defect concentration at the low level (like ~0.2%). Do I understand it correctly? I will be very grateful for your help in understanding. Best, Iraida.

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Larch 0.9.58
by Matt Newville 16 Jan '22

16 Jan '22

Hi Folks, Larch version 0.9.58 has been released. It should now be installed by default using all installation mechanisms, and you may see a notice to update if running xas_viewer. Coming only 6 weeks after 0.9.57, and with the holidays in between, this is mostly a set of bug fixes, especially surrounding installation and errors associated with our use of deprecated features of silx and numpy. Thanks mostly to Mauro for this, and for updating the documentation for installation, especially for existing Anaconda Python users, and on Linux. FWIW, I checked that a fresh install works on Windows 10, MacOS 12, CentOS 7, CentOS 8 Stream, and that "auto-updates" work with "larch -u" or from XAS Viewer works on MacOS 12 and on Fedora 34. But, of course, let us know if you have suggestions, comments, or problems. There are a few fixes for reading some kinds of data files and with de-glitching XAS spectra. The plans discussed in the previous release message (see https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2021-December/010345.ht…) about saving more complex projects and how to think "reference spectra" have not had much work done on them. The request for suggestions and comments on these topics still stands. --Matt

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Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels
by Ming Zhang 14 Jan '22

14 Jan '22

sorry for the trouble, I forgot to register this email. -----原始邮件----- 发件人:"Ming Zhang" <mzhang17(a)zju.edu.cn> 发送时间:2022-01-13 14:41:04 (星期四) 收件人: ifeffit(a)millenia.cars.aps.anl.gov 抄送: 主题: Question--FEFF calclulated atom coordinates and labels Dear IFEFFIT members, I’m practicing EXAFS fitting with some standard crystal data. I GOT SOME QUESTIONS when I imported the CIF File into the FEFF calculation. 1)I’m confused with the atom label. The VESTA GUI shows that there are C1, C2, and C3 carbons in a unit cell. However, after FEFF calculation, they become C1.1 C2.1 C3.1, so do the other atoms like nitrogen and hydrogen. Since I need to set some geometry constraints, I have to figure out the nomenclature of the atom coordinates calculated by FEFF and link those atoms to real physical images. 2)I’m also confused with the calculated degeneracy, like the path of @ C1.1 @ (I have no idea about the atom C1.1 stands for). It’s a zinc absorber placed in a tetrahedron coordinated by the N atom of imidazole. Very intuitively, the degeneracy of @ N1.1 @ (row 1) is 4, and YES IT IS. But how comes the single scattering path (row 2) of the C atom next to N become 8? Also in row 5, degeneracy of @ N1.1 C2.1 @ is 8. Notably, we only got 3 C atoms in a coordinated molecule, so even treating closely located C atoms into the same one couldn’t help explain this. FEFF calculation VESTA GUI The CIF file is attached. I would appreciate it very much if you could help me out. Best regards Ming Zhang

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How do I launch Larch GUIs?
by Swanner, Elizabeth S [GE AT] 12 Jan '22

12 Jan '22

I use a Mac recently updated to Big Sur (11.6). I used the Binary Installer File for Larch and am a little stuck on what to do next. I was able to run the installer, and I have an xraylarch folder on my computer. However, I was hoping to use the XAS Viewer and do not see it within the folder. Should it be there? I had an old version of XAS Viewer I got while at APS but needed to replace that as it did not have all the modules. I did not check before removing that whether it was working on this OS. I am also not clear how to use Larch in general (i.e., the Basic Larch GUI). Do I need to install python? I see there is a python application in the folder but when I try to open that nothing happens. I’m not sure if these are issues with my OS or if I am missing something really basic about how to launch Larch. Best, Betsy Swanner

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Issues reinstalling Larch, error creating desktop shortcut for macOS
by Lauren N. Pincus 05 Jan '22

05 Jan '22

Hi Matt, I'm having an issue with reinstalling Larch. I'm using macOS Catalina 10.15.7. I had Larch previously installed and it was working well, but found I was no longer able to open up XAS Viewer. The application would start and then quit. So, I removed Larch from my system and tried to reinstall it. I first used the mac installer but would get an error that the "Installation failed. The installer encountered an error that caused the installation to fail." I then tried the installation using the script in terminal. This appeared successful, but no desktop shortcut was created. I tried to create a desktop shortcut using larch -m but get the following error: (base) laurenpincus@lnp24mbp2020 ~ % larch -m Traceback (most recent call last): File "/Users/laurenpincus/xraylarch/bin/larch", line 5, in <module> from larch.apps import run_larch File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/builtins.py", line 22, in <module> from . import io File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/__init__.py", line 39, in <module> from .specfile_reader import (str2rng_larch, read_specfile, open_specfile, File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/specfile_reader.py", line 26, in <module> from silx.io.convert import write_to_h5, _is_commonh5_group ImportError: cannot import name '_is_commonh5_group' from 'silx.io.convert' (/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/silx/io/convert.py) (base) laurenpincus@lnp24mbp2020 ~ % Thanks, Lauren Lauren Pincus, PhD NSF Earth Sciences Postdoctoral Fellow Princeton University Department of Geosciences

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Re: [Ifeffit] [Ext] Re: Problem in xrayLarch installation
by Jeffrey Terry 20 Dec '21

20 Dec '21

We’ve had to come up with a slightly different install plan for Windows users of our analysis package EXAFS Neo that is built on top of xrayLarch. We recommend a slightly different route using both conda and pip. You can read through out full recommended analysis route for xrayLarch in the Prerequisites section of our readme file at: https://github.com/laumiulun/EXAFS-Neo-Public We are pretty confident that the installation method given there works for xrayLarch installation on Mac, Windows, and Linux. Jeff Jeff Terry Interim Chair, Department of Social Sciences Professor of Physics Professor of Mechanical, Materials, and Aerospace Engineering Editor, Applied Surface Science Prairie Chapter Chair, AVS Illinois Institute of Technology 3101 S. Dearborn St. Chicago IL 60616 630-252-9708 Sent from my iPhone > On Dec 15, 2021, at 2:42 AM, Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> wrote: > Dear Latif, > > Thanks for reporting this. Unfortunately `pip` is not able to correctly install all dependencies of Larch. The way to go is to install those dependencies via `conda`. > > Under Windows, this is achieved by running the script `GetLarch.bat` (https://raw.githubusercontent.com/xraypy/xraylarch/master/installers/GetLar…) This script will download and install a minconda distribution, plus install Larch in it. > > Seen you already have Anaconda installed, you could simply run the following commands from your Anaconda prompt: > > conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw > pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch > > If this does not work, please, let me know. I have created a related Github issue in order to avoid such troubles in the future: > > https://github.com/xraypy/xraylarch/issues/333 > > Best, > Mauro > > On 2021-12-15 08:20, Latif Ullah Khan wrote: >> Dear Sir Madam, >> I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using “pip install xraylarch” . However, it is not installing and give me an following error: >> If you kindly help me in this regard, I will be grateful to you. >> Thank you in advance >> Best regards >> Latif >> _______________________________________________ >> 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

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Re: [Ifeffit] Ifeffit Digest, Vol 226, Issue 9_Problem in wavelet code
by Latif Ullah Khan 20 Dec '21

20 Dec '21

Dear Matt Newville and Mauro, Many thanks for the kind reply and great support in installation of the XrayLarch through window. Unfortunately, I could not install through Anaconda prompt using command " conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch" as suggested by Mauro. Fortunately I succeeded to install through window command prompt using the source code. Now I am using through VS Studio code. I just adopted the code for wavelet transformation written by Matt Newville, however, I faced some problem in plotting the 2D CCWT image, I am sharing the code with input data and also the code. Its showing some error in following syntax, probably "imopts" has problem: plt.imshow(f.wcauchy_mag, win=1, label='Wavelet Transform: Magnitude', **imopts) plt.imshow(f.wcauchy_re, win=2, label='Wavelet Transform: Real Part', **imopts) If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif -----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, December 15, 2021 6:08 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 226, 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. Re: Problem in xrayLarch installation (Matt Newville) 2. Re: Any coorelation about 'white line" in K-edge XAS with oxidation states? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2021 09:23:47 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "Ifeffit-request(a)millenia.cars.aps.anl.gov" <Ifeffit-request(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem in xrayLarch installation Message-ID: <CA+7ESbqCSsM+==XmUgzkjzjPHTOJjfLRGw8JRDqN5CGUxzJCuQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Latif, Sorry for the trouble. As Mauro said, some of the packages needed (and pymatgen is one of these) are not super-well supported for installing with pip. FWIW, I agree that the needed combination of conda and pip is sort of unfortunate. But most of the "problem packages" are either Windowing systems (wxPython: that have been challenging to have consistent binary support on Linux is very challenging) or packages of scientific code written by and for scientists, some with excellent engineering support and some (like us!) with "less" support. Conda is a popular option for many of these. We try to support the simpler / more ubiquitous pip where we can. Anyway, that's basically why we have the binary installers and installation scripts. But also: thanks for the report and we are trying to clean up or at least document some of these kinds of issues where we can: https://github.com/xraypy/xraylarch/issues/333 --Matt

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Any coorelation about 'white line" in K-edge XAS with oxidation states?
by Marco Wang 16 Dec '21

16 Dec '21

Dear everyone: Ihave some questions about the interpretation of "white line", from anarticle (https://doi.org/10.1038/s41467-021-27116-8) and the figure was attached. In the article, it is said that “the sample was fully reduced to Ni (0) state at ~480 °C judging from the edge position and ‘white-line’ profiles”. First, we assumed that the metal was coordinated with the same anion. We all know that K-edge transition in 3d and 4d metalis' spin forbidden, so it may be inappropriate to conclude that the intensity of the "white line" is correlated with metals' oxidation states. But in other words, the probability for s→d transition may be proportional to thenumber of empty d orbitals, so it seems like if the the intensity of "white line" is higher, the oxidation state is higher. So, how should we correctly interpret the “white line” and edge energy from XAS spectrum of metals’ K-edge and L-edge? Thank you in advance for your time. Marco Wang

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Problem in xrayLarch installation
by Latif Ullah Khan 15 Dec '21

15 Dec '21

Dear Sir Madam, I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using "pip install xraylarch" . However, it is not installing and give me an following error: If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif [cid:image001.png@01D7F194.F5C60C50]

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