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

Larch 2026.1.2
by Matthew Newville 11 Mar '26

11 Mar '26

Hi Folks, Larch 2026.1.2 is now available and will begin to appear for automatic updates. A more complete list of changes is at https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases/tag… . Highlights include: * There are several improvements and bug fixes to Larix and the Larch library from several contributors. Thanks to all those who reported and provided patches. * The binary and “GetLarch” installers have been updated and should resolve problems seen with installation on MacOS. * Support for “Dark Mode” on Windows and MacOS for Larix and the other GUIs is much improved. These will automatically adjust when the System Dark/Light mode changes. Unreadable dark text on dark backgrounds (or light text on light backgrounds) should be resolved. Please let us know if we have missed any such cases. I will say that for those using the GUIs on Linux desktops: we know that there are several problems (including “buttons are too large”) and will admit we have done essentially no testing of Dark Mode on desktop Linux. If anyone has feedback on using Larix on Linux desktops, please let us know. For those with a recent installation of Xray Larch that includes the shortcut to Jupyter Lab in the Larch desktop folder: you can update by launching Jupyter Lab, opening the “Terminal” from the “Launcher” window, and running pip install --upgrade xraylarch —Matt

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Issues opening Larch folder on a Mac
by odeluca＠barnard.edu 07 Mar '26

07 Mar '26

I used the Binary Installer File for Larch on my Mac and am running into issues launching Larch GUI. I ran the installer, and I have an xraylarch folder on my computer (which contains all the relevant code). However, I do not have a Larch folder that would contain the XAS Viewer (among other things). I opened a Terminal and typed ~/xraylarch/bin/larch -m to launch, but was met with the error "zsh: no such file or directory..." What should my next troubleshooting steps be? Should I try to uninstall and re-install? Best, Olivia

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Job Opening: Research Associate at Brookhaven National Laboratory, Upton NY USA (JR102274)
by atayal＠bnl.gov 06 Mar '26

06 Mar '26

Dear Colleagues, Brookhaven National Laboratory is seeking a Research Associate (JR102274) to develop machine learning methods for autonomous EXAFS analysis. This position will be of particular interest to those working in EXAFS/XAS data analysis, synchrotron-based spectroscopy, and the development of AI/ML approaches for advanced spectroscopy workflows. Details are available here: https://bnl.wd1.myworkdayjobs.com/en-US/Externa/details/Research-Associate_… Please feel free to share with anyone who may be interested. Thanks, Akhil Tayal atayal(a)bnl.gov

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Load chi.dat generated by FEFF8 directly into Larix?
by Bone, Sharon 06 Mar '26

06 Mar '26

Dear all, I am trying to fit a theoretical EXAFS spectrum (chi.dat) that was generated via FEFF8 from multiple snapshots from an AIMD trajectory. I can import the chi data into Athena, and from there into Artemis where I can fit it using the standard shell-by-shell routine. However, I cannot import the chi data into Larix and fit it in the FEFF fitting panel. I was able to load the file as XY data and (via the Larch buffer) assign k and chi so that Larix recognizes it in the EXAFS panel. I was also able to generate the Fourier transform (via the Larch buffer), but got no further. So my question is this: Is it possible to fit theoretical chi spectra generated by FEFF8 in Larix? It seems like it is necessary to use Larch directly? Are there any work arounds? Thanks, Sharon

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Re: error message when installing Larch on macbookpro M1
by Sebastian Kunze 25 Feb '26

25 Feb '26

Hi Nikita, using conda and pip together in one environment can sometimes lead to issues. I had this problem a lot, and not only with larch. What worked very well for me was using the pixi package manager ( https://urldefense.us/v3/__https://pixi.prefix.dev/latest/__;!!G_uCfscf7eWS… ). You can create one project environment for larch, set larix callable globally and never think about it again. Since then, all larch updates and installs work reliably across my win/lin and m3 devices, so it may also work for you. Best, Sebastian On Wed, 25 Feb 2026 at 15:00, <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 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: error message when installing Larch on macbookpro M1 > (Matthew Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 24 Feb 2026 16:11:21 +0000 > From: Matthew Newville <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Re: error message when installing Larch on > macbookpro M1 > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: Nikita Vostrov <nik.vostrov(a)gmail.com> > Message-ID: <MN6PR11MB821907E82A5C52338AA4C4E39674A(a)MN6PR11MB8219.nam > prd11.prod.outlook.com> > Content-Type: multipart/alternative; boundary="_000_MN6PR11MB821907 > E82A5C52338AA4C4E39674AMN6PR11MB8219namp_" > > Hi Nikita, > > Sorry for the trouble. I have not been able to reproduce this myself, and > I've seen others successfully install on a Macbook M1 (I am pretty sure the > details of the architecture do not matter) with the PKG installer and > GetLarch.sh script. I have also seen a few other broken installations, > too. The packages that come from the Materials Project (including spglib) > seem to be the most fragile. > > If you reach the point where 'spglib' fails to build, it is almost certain > you have a working conda Python environment that can be fixed in a Terminal > (under Applications->Utilities). I would suggest opening a Terminal window > and run > ~/xraylarch/bin/conda install -c conda-forge spglib pymatgen > > That may take some time, and it may install many more packages. But it > should work. > Then you can run > ~/xraylarch/bin/python -m pip install "xraylarch[larix]" > ~/xraylarch/bin/larch -m > > Again, each of those may take some time. And, at the time, the 'larch -m" > command will print out a lot of useless messages (only on MacOS, and on the > list of things to fix). > > --Matt > > > ________________________________ > From: Nikita Vostrov via Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Monday, February 23, 2026 11:23 AM > To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: Nikita Vostrov <nik.vostrov(a)gmail.com> > Subject: [Ifeffit] Re: error message when installing Larch on macbookpro M1 > > Hello, I still get the same error posted in this thread even with the > Python 3. 13. 10 installation script (also on m1 macbook). Sincerely, > Nikita. ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ > ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ > ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > > ZjQcmQRYFpfptBannerEnd > > Hello, > > I still get the same error posted in this thread even with the Python > 3.13.10 installation script (also on m1 macbook). > > Sincerely, > > Nikita. > > >

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error message when installing Larch on macbookpro M1
by Emmanuelle Montarges Pelletier 24 Feb '26

24 Feb '26

Hi I have recently tried to install xraylarch 26.1.1 version on my computer using the binary installer and/or the GetLarch.sh script. My computer is a macbookpro M1 running with Tahoe26.2 with the binary installer, when I open the « xraylarch » folder, I can not find the Larix application. listing the content of the xraylarch folder, there is a component python.app, but when I try to start it, nothing happens. ls xraylarch _conda envs libexec pkgs shell bin etc LICENSE.txt python.app ssl conda-meta include man sbin condabin lib micromamba share using the GetLarch.sh script , on the terminal window I had this error message : (and same message if I tried to update) 1 error generated. [24/31] Building C object _deps/spglib-build/CMakeFiles/Spglib_symspg.dir/src/refinement.c.o [25/31] Building C object _deps/spglib-build/CMakeFiles/Spglib_symspg.dir/src/spglib.c.o [26/31] Building C object _deps/spglib-build/CMakeFiles/Spglib_symspg.dir/src/spin.c.o [27/31] Building C object _deps/spglib-build/CMakeFiles/Spglib_symspg.dir/src/spacegroup.c.o [28/31] Building C object _deps/spglib-build/CMakeFiles/Spglib_symspg.dir/src/symmetry.c.o ninja: build stopped: subcommand failed. *** CMake build failed [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for spglib Failed to build spglib error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> spglib Is there anything I can do? as complementary information, I could use an older xraylarch version (from 2023 I think,not sure) thanks in advance for your help all the best Emmanuelle -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Emmanuelle Montargès-Pelletier Directrice de Recherche CNRS -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- LIEC - Laboratoire Interdisciplinaire des Environnements Continentaux CNRS Université de Lorraine 15 avenue du Charmois 54500 VANDŒUVRE-LES-NANCY FRANCE tel bureau +33 (0)3 72 74 47 30 tel mobile +33 (0)6 31 33 10 30 emmanuelle.montarges(a)univ-lorraine.fr -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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Problems with importing data in Athena
by Nicolò Orsingher - nicolo.orsingher＠studio.unibo .it 10 Feb '26

10 Feb '26

Dear all, I'm new to the XAS community and I'm currently struggling to solve an issue with the data import with Athena, The issue is simple enough but I didn't manage to solve it. My XAS data measure the fluorescence every 0.2 eV but when I import the files .dat in athena the plotted curve and the exported spectra norm(E).nor have one point every ~0.7/0.8 eV how can I fix this problem? I already tried importing the data in different format .dta, .txt and .csv Any help/tip is very much welcome

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Reminder: X-ray Larch Developer's / Topics in XAS Analysis meeting, Jan 29th
by Matthew Newville 28 Jan '26

28 Jan '26

Hi All, A reminder that we will have an X-ray Larch Developer’s / Topics in XAS Analysis meeting tomorrow, approximately 24 hours from now. Athar Khodabakhsh from Helmholtz-Zentrum Berlin will give a presentation on Machine Learning work with XAS. Time: January 29, at 1500 UTC (4 PM Paris, 9 AM Chicago) Topic: Athar Khodabakhsh, Helmholtz-Zentrum Berlin, Convolutional AutoEncoder for Anomaly Detection and Chemical State Identification in XAS Zoom link: available at https://millenia.cars.aps.anl.gov/xraylarch/meetings/ Hope to see some of you there, --Matt

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XAFS and Andrea Di Cicco on CNN
by Anatoly Frenkel 26 Jan '26

26 Jan '26

Hi all, It was a pleasant surprise to see that XAFS made it to the CNN Business Edition. Furthermore, it is nice to see that Andrea Di Cicco was prominently featured in the article (attached) as well. Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor and Deputy Chair Department of Materials Science and Chemical Engineering Affiliate Professor, Department of Chemistry * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973 Email: frenkel(a)bnl.gov https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… -------------------------------------------------------------------

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Numpy error during Upgrade to Larch 2026
by Danilo Oliveira de Souza 23 Jan '26

23 Jan '26

Dear Matt, I tried to upgrade my Larch version to this brand new one, but I faced some issues, which are reported below, concerning the NumPy version used for compilation (1.x) and that one I have installed in my PC (2.4.1). I ran the upgrade using the Anaconda prompt instead of the shortcut ("Update Larch") contained in the Larch folder. As you see on the top of the report, it was suggested to downgrade the Numpy present on my PC, but I'm wondering if there is a less conservative solution for that. Any clue? *A module that was compiled using NumPy 1.x cannot be run inNumPy 2.4.1 as it may crash. To support both 1.x and 2.xversions of NumPy, modules must be compiled with NumPy 2.0.Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.If you are a user of the module, the easiest solution will be todowngrade to 'numpy<2' or try to upgrade the affected module.We expect that some modules will need time to support NumPy 2.Traceback (most recent call last): File "C:\ProgramData\anaconda3\Lib\threading.py", line 1002, in _bootstrap self._bootstrap_inner() File "C:\ProgramData\anaconda3\Lib\threading.py", line 1045, in _bootstrap_inner self.run() File "C:\ProgramData\anaconda3\Lib\threading.py", line 982, in run self._target(*self._args, **self._kwargs) File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\wxxas\larix_app.py", line 58, in importer from larch.wxxas.xasgui import LarixFrame File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\wxxas\xasgui.py", line 28, in <module> from larch.io <https://urldefense.us/v3/__http://larch.io__;!!G_uCfscf7eWS!eDQ14v3BGN9E-bk… > import save_session, read_session File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\io\__init__.py", line 23, in <module> from .gse_mcafile import gsemca_group, GSEMCA_File File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\io\gse_mcafile.py", line 9, in <module> from larch.xrf import MCA, ROI File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\xrf\__init__.py", line 11, in <module> from .mca import MCA, isLarchMCAGroup, Environment, create_mca File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\xrf\mca.py", line 14, in <module> from ..math import interp, index_nearest File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\math\__init__.py", line 5, in <module> import lmfit File "C:\ProgramData\anaconda3\Lib\site-packages\lmfit\__init__.py", line 38, in <module> from .confidence import conf_interval, conf_interval2d File "C:\ProgramData\anaconda3\Lib\site-packages\lmfit\confidence.py", line 10, in <module> from .minimizer import MinimizerException File "C:\ProgramData\anaconda3\Lib\site-packages\lmfit\minimizer.py", line 41, in <module> from .parameter import Parameter, Parameters File "C:\ProgramData\anaconda3\Lib\site-packages\lmfit\parameter.py", line 13, in <module> from .jsonutils import decode4js, encode4js File "C:\ProgramData\anaconda3\Lib\site-packages\lmfit\jsonutils.py", line 15, in <module> from pandas import DataFrame, Series, read_json File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\pandas\__init__.py", line 62, in <module> from pandas.core.api import ( File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\pandas\core\api.py", line 28, in <module> from pandas.core.arrays import Categorical File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\pandas\core\arrays\__init__.py", line 1, in <module> from pandas.core.arrays.arrow import ArrowExtensionArray File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\pandas\core\arrays\arrow\__init__.py", line 5, in <module> from pandas.core.arrays.arrow.array import ArrowExtensionArray File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\pandas\core\arrays\arrow\array.py", line 64, in <module> from pandas.core.arrays.masked import BaseMaskedArray File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\pandas\core\arrays\masked.py", line 60, in <module> from pandas.core import ( File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\pandas\core\nanops.py", line 52, in <module> bn = import_optional_dependency("bottleneck", errors="warn") File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\pandas\compat\_optional.py", line 135, in import_optional_dependency module = importlib.import_module(name) File "C:\ProgramData\anaconda3\Lib\importlib\__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "C:\ProgramData\anaconda3\Lib\site-packages\bottleneck\__init__.py", line 7, in <module> from .move import (move_argmax, move_argmin, move_max, move_mean, move_median,AttributeError: _ARRAY_API not foundException in thread Thread-1 (importer):Traceback (most recent call last): File "C:\ProgramData\anaconda3\Lib\threading.py", line 1045, in _bootstrap_inner self.run() File "C:\ProgramData\anaconda3\Lib\threading.py", line 982, in run self._target(*self._args, **self._kwargs) File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\wxxas\larix_app.py", line 58, in importer from larch.wxxas.xasgui import LarixFrame File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\wxxas\xasgui.py", line 28, in <module> from larch.io <https://urldefense.us/v3/__http://larch.io__;!!G_uCfscf7eWS!eDQ14v3BGN9E-bk… > import save_session, read_session File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\io\__init__.py", line 23, in <module> from .gse_mcafile import gsemca_group, GSEMCA_File File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\io\gse_mcafile.py", line 9, in <module> from larch.xrf import MCA, ROI File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\xrf\__init__.py", line 11, in <module> from .mca import MCA, isLarchMCAGroup, Environment, create_mca File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\xrf\mca.py", line 14, in <module> from ..math import interp, index_nearest File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\math\__init__.py", line 28, in <module> from .pca import pca_train, pca_fit, nmf_train, save_pca_model, read_pca_model File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\math\pca.py", line 16, in <module> from sklearn.decomposition import PCA File "C:\ProgramData\anaconda3\Lib\site-packages\sklearn\__init__.py", line 82, in <module> from .base import clone File "C:\ProgramData\anaconda3\Lib\site-packages\sklearn\base.py", line 17, in <module> from .utils import _IS_32BIT File "C:\ProgramData\anaconda3\Lib\site-packages\sklearn\utils\__init__.py", line 19, in <module> from .murmurhash import murmurhash3_32 File "sklearn\utils\murmurhash.pyx", line 1, in init sklearn.utils.murmurhashValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObjectTraceback (most recent call last): File "C:\ProgramData\anaconda3\Lib\site-packages\wx\core.py", line 3425, in <lambda> lambda event: event.callable(*event.args, **event.kw <https://urldefense.us/v3/__http://event.kw__;!!G_uCfscf7eWS!eDQ14v3BGN9E-bk… >) ) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\wxxas\larix_app.py", line 62, in ShowMain from larch.wxxas.xasgui import LarixFrame File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\wxxas\xasgui.py", line 28, in <module> from larch.io <https://urldefense.us/v3/__http://larch.io__;!!G_uCfscf7eWS!eDQ14v3BGN9E-bk… > import save_session, read_session File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\io\__init__.py", line 23, in <module> from .gse_mcafile import gsemca_group, GSEMCA_File File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\io\gse_mcafile.py", line 9, in <module> from larch.xrf import MCA, ROI File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\xrf\__init__.py", line 11, in <module> from .mca import MCA, isLarchMCAGroup, Environment, create_mca File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\xrf\mca.py", line 14, in <module> from ..math import interp, index_nearest File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\math\__init__.py", line 28, in <module> from .pca import pca_train, pca_fit, nmf_train, save_pca_model, read_pca_model File "C:\Users\danil\AppData\Roaming\Python\Python311\site-packages\larch\math\pca.py", line 16, in <module> from sklearn.decomposition import PCA File "C:\ProgramData\anaconda3\Lib\site-packages\sklearn\__init__.py", line 82, in <module> from .base import clone File "C:\ProgramData\anaconda3\Lib\site-packages\sklearn\base.py", line 17, in <module> from .utils import _IS_32BIT File "C:\ProgramData\anaconda3\Lib\site-packages\sklearn\utils\__init__.py", line 19, in <module> from .murmurhash import murmurhash3_32 File "sklearn\utils\murmurhash.pyx", line 1, in init sklearn.utils.murmurhashValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject* Cheers, Danilo OLIVEIRA DE SOUZA

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