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

Phase shift
by Julian Ehwald 20 Apr '18

20 Apr '18

Dear all, I have a very general question about the phase shift. I tried to fit a rather noisy sample of Li2IrO3, where I get a first main peak around 1 angstroem, according to FEFF calculation there should be something at 1.9 and not any closer. This phase shift seems a bit too big to be true, is there something like an upper bound for a reasonable phase shift? Best, Julian

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Artemis Error
by Lê Ngọc Chính 19 Apr '18

19 Apr '18

Dear Demeter developer I have some trouble when using artemis. I have used artemis normally on windows 10, but recently I can't use it anymore. The error message appears after I click "FIT" button. I also have tried re-install the software, but nothing happened. Please provide me the way to fix it. Thank you so much -- Chính

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Directory path in Larch
by Imad Ahmed 17 Apr '18

17 Apr '18

Hi Matt, I have a question about the working directory of Larch. So, as I run Larch from command line (OS=Unix), the default WD is the .larch/modules and that in anaconda, in which case running a Larch script means that I have to provide its full path. I wonder if there is a way to change the WD into the current project folder? Running *.lar is not a problem but is a rather less convenient. However, directing Larch to project directory seems important so that to avoid typing full path of data files within the *.lar script. ps. feffrunner.py allows flexible subfolder path but it assumes that the *.inp is located in that same folder. It would be helpful if the path of the *.inp can be allowed to vary, this would help organising project files into subfolders. Best wishes, Imad

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Re: [Ifeffit] Larch python instructions
by Matt Newville 17 Apr '18

17 Apr '18

Hi Imad, On Sun, Apr 15, 2018 at 7:15 PM, Imad Ahmed <imad.ahmed(a)earth.ox.ac.uk> wrote: > Dear Matt, > > I am looking for some proper instructions on how to use Larch from python. > I have larch installed on Anaconda2 and trying to run the > /examples/feffit/doc_feffdat1.lar script from python. > I tried the python code below but still having issues to run it, > especially with Feffpath and some larch plugins. Could you please help? > > Best wishes, Imad > > > import sys, os > import numpy as np > from scipy.optimize import leastsq as scipy_leastsq > import larch > from larch import Group, Parameter > from larch_plugins.io import read_ascii > from larch_plugins.xafs import FeffPathGroup > from larch_plugins.xafs.feffit import (TransformGroup, > FeffitDataSet,feffit, feffit_report) > > fname = ‘~/xraylarch/examples/feffit/feff0001.dat' > path1 = FeffPathGroup(fname) > path2chi(path1) > show(path1) > newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', > ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, > title=r'$\chi(k)$ from %s' % fname) > path1.sigma2 = 0.002 > path2chi(path1) > plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') > > > Well, there are some differences between Larch and Python. With some small modifications, your scaript can become a valid Larch script like this: # larch from os.path import join, expanduser fname = join(expanduser(‘~'), '/xraylarch/examples/feffit/feff0001.dat') path1 = feffpath(fname) path2chi(path1) show(path1) newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, title=r'$\chi(k)$ from %s' % fname) path1.sigma2 = 0.002 path2chi(path1) plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') To do that from Python is a bit more involved. Each of the functions "feffpath", "path2chi", "show", "newplot", and "plot" need to be translated. As you probably say, "feffpath" is effectively `FeffPathGroup'. The others are less obvious, and many of the larch functions really want to be passed a "larch session" so that they can find other larch function or data sources. For example, FeffPathGroup needs a larch session in order to be able to look up atomic information. So in pure python that would be approximately: import os import os.path import matplotlib.pyplot as plt # using pyplot instead of build in plot commmands from larch import Interpreter from larch_plugins.xafs.feffdat import FeffPathGroup, _path2chi # need to create a Larch interpreter for each "session" _larch = Interpreter() fname = os.path.join(os.path.expanduser("~"), "Codes/xraylarch/examples/feffit/feff0001.dat") # note that many of the Larch functions will want a `_larch` instance passed in. path1 = FeffPathGroup(fname, _larch=_larch) _path2chi(path1, _larch=_larch) # show, approximately for attr in dir(path1): print(attr, getattr(path1, attr)) # plot, approximately plt.plot(path1.k, path1.chi*path1.k**2, label= r'$\sigma^2 = 0$') path1.sigma2 = 0.002 _path2chi(path1, _larch=_larch) plt.plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') plt.xlabel(r' $ k \rm\, (\AA^{-1})$') plt.ylabel(r'$ k^2\chi(k)$') plt.title(r'$\chi(k)$ from %s' % fname) plt.legend() plt.show() But also, since you have to build a Larch Interpreter, you could simply use it to execute the previous Larch script: from larch import Interpreter text = ''' # larch from os.path import join, expanduser fname = join(expanduser(‘~'), '/xraylarch/examples/feffit/feff0001.dat') path1 = feffpath(fname) path2chi(path1) show(path1) newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, title=r'$\chi(k)$ from %s' % fname) path1.sigma2 = 0.002 path2chi(path1) plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') ''' _larch = Interpreter() _larch.run(text) The latter approach is highly recommended. --Matt Newville

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Beg for Athena install package
by zangyp＠mail.ustc.edu.cn 16 Apr '18

16 Apr '18

Sir/Madam： I am sorry to disturbe you! Here, I am a PHD of USTC, China and I want use the Anthena tool to analysis EXFAS data, my compute is 32-bites versions, so I beg for a Ifeffit-1.2.10.exe. Could you provide it for me? Very thanks! Zang, Y. P. zangyp(a)mail.ustc.edu.cn

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Sulfur EXAFS k oscillations
by Miller, Elizabeth Christine 11 Apr '18

11 Apr '18

Hi all, I am analyzing some sulfur K-edge EXAFS data taken at 4-3 at SSRL. When I use a k-weight of k^3 to plot, my oscillations at high k reach over 100, which doesn't make sense to me. I have looked over the data with Riti, and it seems that while the XANES are rather self-absorbed due to high concentrations of sulfur-containing salt, the data can be normalized, and the EXAFS should contain some information. I've included screenshots in the attachment of plots of all of the k-weights as well as my parameters. The mixtures are solutions of organics (acetonitrile, 1,1,2,2-Tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether) with bis(trifluoromethane)sulfonimide lithium salt. I am also not hitting any other edges, as sulfur is the highest Z element in the solution. Any thoughts would be greatly appreciated! Thank you, Beth Elizabeth C. Miller, Ph.D. Postdoctoral Scholar Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory E-mail: ecmiller(a)slac.stanford.edu<mailto:ecmiller@slac.stanford.edu>

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Re: [Ifeffit] [Ifeffit} Sulfur EXAFS k oscillations
by fred.mosselmans＠diamond.ac.uk 10 Apr '18

10 Apr '18

Dear Beth, Apart from the fact it looks like there is a trace Cl impurity in one of the samples (sharp line at ca. 9.5 k), it is hard to tell how a spline is going wrong without seeing the spline, thus posting the Athena file might get a better response. It may well be there is not much data beyond 10 k for soft scatterers at the S K-edge. Best wishes 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 -- 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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Mac install issues
by Webb, Samuel M. 04 Apr '18

04 Apr '18

Hi all - I've run into a lot of problems with Mac installs in general with my compiled XAS programs as well, particularly with the latest High Sierra update. It's been pointed out to me by a few users that another potential work around is to use Wine 3.0 https://www.winehq.org as an emulator of sorts (and its free) to run a windows program within the MacOS environment. It's smaller and more compact than say Parallels or VMware as it doesn't do the whole operating system, hence the free part. Its seems easy to install, and also makes for one less OS to maintain a distribution for. It may not be the most elegant solution, but it could work for some... I may end up using this for myself rather than maintaining a native Mac distribution in the future. Sam

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install for mac error
by Christopher Patridge 04 Apr '18

04 Apr '18

Hello everyone, I tried to install demeter on my mac (running high Sierra) and it appeared everything went well. However when I run either Athena or Artemis I get an error shown below about Demeter::Templates: showing a error and I am not sure how I can correct this error. Any help would be appreciated. Thanks in advanced, Chris -- Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Chemistry SASE 315 D'Youville College 320 Porter Ave., Buffalo, NY 14201 716-829-8096

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Problem building latest demeter on Debian 32bit Stretch
by Al Kwiatkowski 30 Mar '18

30 Mar '18

Hello - We're trying to install demeter on a 32-bit system running Debian 9.2 Stretch. The 'perl Build.PL' and 'Build' run into no issues, but when we try running 'Build test' we get the following error messages: t/001_base.t ............ String found where operator expected at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" (Do you need to predeclare croak?) syntax error at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" Compilation failed in require at /home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244. Compilation failed in require at t/001_base.t line 22. BEGIN failed--compilation aborted at t/001_base.t line 22. # Looks like your test exited with 255 before it could output anything. t/001_base.t ............ Failed 24/24 subtests t/002_types.t ........... String found where operator expected at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" (Do you need to predeclare croak?) syntax error at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" Compilation failed in require at /home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244. The "croak" command not getting found appears to come from the "Carp" perl module - we have version 6.06-1 of the 'libcarp-clan-perl' package installed. Any suggestions as to what's causing this error? Again, the 'perl Build.PL' command shows no issues with the installed modules, but since most of them were installed from the Debian repository, maybe there's a discrepancy with the modules installed when we run './Build installdeps'? Thanks for any assistance - Al Kwiatkowski kwiatal(a)phys.iit.edu

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