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

python accesses outlook PST files during X-ray larch binary installation on Windows 10 computer
by Voegelin, Andreas 06 Jun '23

06 Jun '23

Dear All I apologize for this question related to IT safety rather than science and the use of Larch. Today, I installed Larch for Windows on an institute computer using the latest Windows 64-bit binary installer (0.9.68). Now I got the following alert from our IT security: “The process c:\users\%USER%\appdata\local\xraylarch\python.exe accessed Outlook files. The user who ran the process was XXXX. The accessed files were: XXXX.pst, YYYY.pst”. It seems that during the installation of Larch, python.exe accessed some outlook archive files in another folder on the C drive, and I do not know if this should be a matter of concern. Has anyone experienced a similar behavior before, or does anyone with Larch/python skills have an explanation for this? Cheers, Andreas

2 2

calibrated Fe(CP)2 and beam effect
by Esmael Balaghi 26 May '23

26 May '23

Dear All, Does anyone happen to have a spectrum of bulk ferrocene (Fe K edge), by any chance? It would be even more helpful if it includes the spectrum of Fe foil or calibrated ferrocene. I'm trying to determine the extent of the beam effect, whether it caused reduction/oxidation or decomposition, during data acquisition. I would greatly appreciate any tips or tricks you may have for dealing with this situation. Thank you in advance. Esmael

1 0

Re: [Ifeffit] Problems with FEFF calculation using CIF file (Matt Newville)
by Volker, Anouk 26 May '23

26 May '23

Dear Matt, Thank you for the quick response. The first error gets indeed resolved by removing the atoms labeled with a B. I was not very clear in my first post that I had to do this to have the ATOMS window run properly in Artemis. The problem I am stuck on is that when I have them removed and then run the FEFF window, it seems to all work fine, until I try and drag the paths into the Path window in Artemis. At that point the paths seem to no longer exist. I hope this clears up my question a bit more. Kind regards, Anouk On Thu, May 25, 2023 at 7:02 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: Problems with FEFF calculation using CIF file (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 May 2023 12:29:01 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Problems with FEFF calculation using CIF file > Message-ID: > <CA+7ESbpH97zi+-xbK2R62m8ND-MG+6OgMB= > R16zSqXE2za7yCA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Anouk, > > I am not sure what is happening with that CIF file. When I try to read > that with pymatgen, I get > > >>> from pymatgen.io.cif import CifParser > >>> structs = CifParser('VOXZAJ.cif') > >>> structs.get_structures() > .../site-packages/pymatgen/io/cif.py:1145: UserWarning: Error is Species > occupancies sum to more than 1!. > warnings.warn(f"Error is {str(exc)}.") > .../site-packages/pymatgen/io/cif.py:1148: UserWarning: Issues encountered > while parsing CIF: Some occupancies ([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, > 2, 2, 2, 2, 2, 2, 2, 2]) sum to > 1! If they are within the > occupancy_tolerance, they will be rescaled. The current occupancy_tolerance > is set to: 1.0 > Species occupancies sum to more than 1! > warnings.warn("Issues encountered while parsing CIF: " + > "\n".join(self.warnings)) > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > .../site-packages/pymatgen/io/cif.py", line 1150, in get_structures > raise ValueError("Invalid cif file with no structures!") > ValueError: Invalid cif file with no structures! > > If you remove all the atomic sites that have a "B" in their name, that gets > resolved, but I do not know if that is still the correct structure - or > what the "B" means. > > CIF is complicated, but just from a practical point of view, I think we are > going to take `pymatgen` as the arbitrator of "valid CIF". > > > On Wed, May 24, 2023 at 11:30?AM Volker, Anouk <a.volker(a)student.rug.nl> > wrote: > > > Dear all, > > > > I hope this email finds you well. I have encountered a problem that I > have > > not been able to fix on my own. I have a specific CIF file (from the > CCDC > > database) that is attached to the e-mail. After removing the duplicate > > atoms in the file, the ATOMS window seems fine. The FEFF calculation will > > run without any errors and within the FEFF window the paths are displayed > > and can be plotted. The problem arises when I try to take some of the > paths > > from the FEFF window and drag them into the Path window. Now the paths > can > > no longer be plotted and when trying to use them to fit, it seems like > the > > paths are non-existent as well. > > > > Is there something wrong with the CIF file that causes this to happen and > > if so, what can be done to fix it? I have already tried to make a > feff.inp > > file from the xyz data (after opening the CIF file in any viewer), but > this > > gives the same problem. > > > > Thank you in advance, > > > > Kind regards, > > Anouk Volker > > > > Master student, Browne Group > > Stratingh Institute, University of Groningen > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > --Matt Newville <newville at cars.uchicago.edu> 630-327-7411 >

2 1

Problems with FEFF calculation using CIF file
by Volker, Anouk 24 May '23

24 May '23

Dear all, I hope this email finds you well. I have encountered a problem that I have not been able to fix on my own. I have a specific CIF file (from the CCDC database) that is attached to the e-mail. After removing the duplicate atoms in the file, the ATOMS window seems fine. The FEFF calculation will run without any errors and within the FEFF window the paths are displayed and can be plotted. The problem arises when I try to take some of the paths from the FEFF window and drag them into the Path window. Now the paths can no longer be plotted and when trying to use them to fit, it seems like the paths are non-existent as well. Is there something wrong with the CIF file that causes this to happen and if so, what can be done to fix it? I have already tried to make a feff.inp file from the xyz data (after opening the CIF file in any viewer), but this gives the same problem. Thank you in advance, Kind regards, Anouk Volker Master student, Browne Group Stratingh Institute, University of Groningen

2 1

Re: [Ifeffit] [Attachment Removed] Re: Low amplitude chi signal of first shell calculated by FEFF
by Matt Newville 24 May '23

24 May '23

Hi Fan, If you included an attachment, I did not see it. If so, can you send it some other way? I would not expect that the Sr K-edge of SrTiO3 needs much playing around with parameters in the feff.inp file prior to running Feff. I would advise against doing that unless you know what you are doing. Don't set Vi to be below 0. I would be more inclined to believe that the data treatment had problems or that the use of the feff paths had problems. Without knowing what you did, it is very hard to speculate what might be going wrong. On Tue, May 23, 2023 at 9:38 PM Dongxiao <dongxiaofan01(a)gmail.com> wrote: > An attachment on this email message was removed because it contained > potentially dangerous content. If you are expecting a file from the sender, > request that they provide access to it via a file sharing service. > ------------------------------ > > Hello, Matt, cc: who is interested, > > > > Thank you very much for your reply. > > The low amplitude chi signal is common when I calculated the A site EXAFS > signal of perovskite structure. > > Especially the chi signal of first single scattering path (A-O) is > unreasonable low. > > In my case (Sr K-edge EXAFS of SrTiO3), the intensity of calculated chi is > smaller than the low-temperature experimental chi. > > I have been struggling with this problem for some time. I am looking > forward to somebody who can give me some advice.. > > I attached the related files for your check. > > > > I try to vary Vr and Vi value and want to see how the amplitude change. > > If set the Vi to negative, it indeed can increase the amplitude, but I > don’t know if it is proper. > > Maybe the problem is caused by the bad muffin-tin potential, but I don’t > know how to improve it. > > > > Can you give me some advice? > > > > Best regards, > > Fan > > > > -----Original Message----- > > Matt Newville > <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=f…> > Fri, 12 May 2023 14:25:36 -0700 > <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=d…> > > > > Hi Fan, > > > > On Fri, May 12, 2023 at 9:56 AM <dx...(a)post.kek.jp> wrote: > > > > > Hi, All > > > > > > > > > > > > The problem I meet is the low amplitude chi signal of first shell > > > calculated by FEFF. > > > > > > The consequence of the fitting is large value of SO2 (1.5-2.0), which is > > > quite unacceptable. > > > > > > I tried to fit the dataset measured by different people at different > > > beamline, the consequence is same. > > > > > > > > > > > > My data is T-dependent Sr K-edge EXAFS of SrTiO3, path file generated by > > > FEFF10, fitting process by Larch+python. > > > > > > By check the email list, it seems the long shell distance (2.7 A) is the > > > origin of the problem. I am not sure for that. > > > > > > I also try to vary the Vi value to improve the amplitude, the change is > > > small. > > > > > > Can any body give me some advice? > > > > > > > I would not expect that a Sr-O distance of 2.7 to 2.8Ang would cause an > > amplitude problem. I would tend to expect that being off by a factor of 2 > > would > > imply normalization issues. You could try to vary Vi, but I would not > > guess that you need to do that. Why do you set Vi to 2 (eV)? > > > > Do you have data and/or analysis steps (script or Larch session file) you > > can share? > > > > > > > > > > > Best regards, > > > > > > Fan > > > > > > > > > > > > My feff.inp file is like: > > > > > > -------------------------------------------- > > > > > > * This feff8 file was generated by Demeter 0.9.26 > > > > > > * Demeter written by and copyright (c) Bruce Ravel, 2006-2019 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * space = 221 > > > > > > * a = 3.90500 b = 3.90500 c = 3.90500 > > > > > > * alpha = 90.00000 beta = 90.00000 gamma = 90.00000 > > > > > > * rmax = 9.00000 core = Sr > > > > > > * polarization = 0 0 0 > > > > > > * shift = 0 0 0 > > > > > > * atoms > > > > > > * # el. x y z tag > > > > > > * Sr 0.00000 0.00000 0.00000 Sr > > > > > > * Ti 0.50000 0.50000 0.50000 Ti > > > > > > * O 0.00000 0.50000 0.50000 O > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * total mu*x=1: 32.298 microns, unit edge step: 44.289 microns > > > > > > * specific gravity: 5.118 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * normalization correction: 0.00029 ang^2 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * Sr K edge energy = 16105 eV > > > > > > EDGE K > > > > > > S02 1.0 > > > > > > > > > > > > * pot xsph fms paths genfmt ff2chi > > > > > > CONTROL 1 1 1 1 1 1 > > > > > > > > > > > > PRINT 1 0 0 0 0 3 > > > > > > > > > > > > * ixc [ Vr Vi ] *** ixc=0 means to use Hedin-Lundqvist > > > > > > EXCHANGE 0 2 1 -1 > > > > > > *** Radius for self-consistent pots (2 shells is a good choice) > > > > > > * r_scf [ l_scf n_scf ca ] *** l_scf = 0 for a solid, 1 for > > > a molecule > > > > > > SCF 7 0 100 0.1 1 > > > > > > * kmax [ delta_k delta_e ] *** Upper limit of XANES > > > calculation. > > > > > > * XANES 4.0 > > > > > > * r_fms l_fms *** Radius for Full Mult. Scatt. l_fms = 0 > > > for a solid, 1 for a molecule > > > > > > * FMS 16.77392 0 > > > > > > * emin emax eimag *** Energy grid over which to calculate DOS > > > functions > > > > > > * LDOS -30 20 0.1 > > > > > > *** for EXAFS: RPATH 5.0 and uncomment the EXAFS card > > > > > > CRITERIA 0 0 > > > > > > * POLARIZATION 0 0 0 > > > > > > COREHOLE FSR > > > > > > RPATH 7.0 > > > > > > LDOS -30 20 0.1 > > > > > > EXAFS 20.0 > > > > > > > > > > --Matt

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 243, Issue 10
by Shuting Xiang 17 May '23

17 May '23

Thank you very much! We really appreciate it! Shuting On Wed, May 17, 2023 at 12:02 AM <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. In2O3 and In foil XAFS spectra in need (Shuting Xiang) > 2. Re: In2O3 and In foil XAFS spectra in need (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 16 May 2023 22:29:22 -0400 > From: Shuting Xiang <shuting.xiang(a)stonybrook.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov, "Li, Zhengyuan (li3zn)" > <li3zn(a)mail.uc.edu>, "Jimenez, Juan" <jjimenez1(a)bnl.gov> > Subject: [Ifeffit] In2O3 and In foil XAFS spectra in need > Message-ID: > < > CAPi4yra21_O6RT+KoZCJRUL8rk2ST-USoB_wMpRB7XFPyF5GZA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I hope this email finds you well. I am writing to inquire if any of you > might have the XAFS spectra of In oxide (In2O3) and In foil. We are in need > of these spectra as references for our ongoing research. If anyone would be > kind enough to share these spectra with us, we would greatly appreciate it. > > Please feel free to reach out to me if you are able to assist. Your support > would be greatly appreciated. > > Thank you very much for your attention and consideration. > > Best, > > Shuting Xiang > Department of Material Science and Engineering > Stony Brook University > Shuting.xiang(a)stonybrook.edu >

1 0

Question about EXAFS fitting of mixtures
by Soyoung Kim 17 May '23

17 May '23

Dear all, While fitting EXAFS for tiny Pt nanoparticles, a simple question occurred to me. For these two scenarios: 1. All Pt atoms are coordinated to 3 O atoms and 3 Pt atoms each. 2. Half of the Pt atoms are coordinated to 6 O atoms and half to 6 Pt atoms. If we fit only single-scattering paths, would it be possible to tell apart these two scenarios with EXAFS fitting? What about linear combination analysis of the XANES? Thank you, Soyoung

3 3

Not possible to install larch on actual system and Mac M1 system
by Mangold, Stefan (IPS) 17 May '23

17 May '23

Dear all, from binary package: can’t write to system partition by script and by anaconda I got the following message back: Collecting fabio Using cached fabio-2023.4.1.tar.gz (724 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... error error: subprocess-exited-with-error System ist 13.3.1, tried to install the newest version completely from scratch, because the update killed my larch version …. best regards Stefan

2 4

In2O3 and In foil XAFS spectra in need
by Shuting Xiang 17 May '23

17 May '23

Dear all, I hope this email finds you well. I am writing to inquire if any of you might have the XAFS spectra of In oxide (In2O3) and In foil. We are in need of these spectra as references for our ongoing research. If anyone would be kind enough to share these spectra with us, we would greatly appreciate it. Please feel free to reach out to me if you are able to assist. Your support would be greatly appreciated. Thank you very much for your attention and consideration. Best, Shuting Xiang Department of Material Science and Engineering Stony Brook University Shuting.xiang(a)stonybrook.edu

4 3

customized dead-time correction in Larch
by Esmael Balaghi 16 May '23

16 May '23

Dear Matt, Dear All, Is there a way to use our customized dead-time correction function in XAS viewer/Larch? Bests, Esmael

2 3