April 2018 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 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. Re: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > 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: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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SSRL EXAFS School- Application Open!
by Ritimukta Sarangi 19 May '18

19 May '18

Hello Friends, SSRL will host its annual summer school this year during the third week of August (13th-16th). The application page is now open. Please hit the "apply" button on: http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2018/index.html Note that seats are limited and we will have to choose from the application pool. Please apply soon to help us with the process. If selected, you will receive an email to register for the school. This year, we will drill down into Artemis based EXAFS analysis. Hope to see many of you here! Best Wishes, -Riti Sarangi

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Atoms with Z bigger than 94 are missing
by Kathy Dardenne 30 Apr '18

30 Apr '18

Hello, I just notice that feff6 in Athena from the last versions of Demeter (including the 0.9.26) did not accept Z value above 94 (Pu) anymore. I wanted to fit AM L3 data and got error message from FEFF that it was not possible. Changing Am Z to 94 solves the problem. Is it possible to get Am (Z=95) and Cm (Z=96) implemented in feff again? I am aware that using Z=94 for simulation of Am and Cm will likely yields similar results, by just replacing the Z in the atom output. But if it is possible without too much effort it will be nice to have. Thanks a lot. Cheers Kathy Dardenne

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Reference spectrum
by Lorenzo Stievano 27 Apr '18

27 Apr '18

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EXAFS fitting for regular & distorted monoclinic
by Ashwani Kumar 26 Apr '18

26 Apr '18

Hello everyone, I am new to the mailing list. i am Fitting data of regular and distorted ( from irradiation) NBS glass doped with Hafnium. Literature available Hafnia (monoclinic) data is taken as standard model to fit the data (monoclinic) of regular glass. Now i want to fit the distorted glass data with exafs result of regular glass data as standard model. or will it be ok , to also fit the distorted glass data with hafnia as standard model. . thanks A kumar

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Cannot update Demeter to version 0.9.26 in MacPorts
by Fowler, Joseph W. (Assoc) 25 Apr '18

25 Apr '18

Hi Bruce, I’m posing this question to you in front of the whole mailing list, just in case someone out there can help us both. As you know, I’m the official Macports maintainer of the port demeter, in spite of my near-complete ignorance of how either Perl or Macports work. In February, I filed a Macports ticket to make their preferred perl (5.26) work with Demeter 0.9.25. It was a simple matter of adding the “-I.” argument, as you pointed out to me. They pulled my changes, or whatever they do over there. My next step is to update the Macports package information to upgrade from Demeter 0.9.25 to 0.9.26. I am having a problem when I try to build Demeter 0.9.26, however. The “./Build install” command says it cannot find or copy ‘src/Ifeffit.dylib’. Do the following give you any clues about why that might be? This might be too little information, but as you said, “ask early”. The following text shows how it goes when I try to build within the macports structure. I get the same error, though, when I clone the git repository, cd into it, run “perl -I. Build.PL”, and then try to run “sudo ./Build install”. It looks as if somehow an ifeffit directory variable is not being initialized properly in line 308 of DemeterBuilder.pm. If you or anyone can help me to solve this problem, then I ought to be able to change the Macports port to provide Demeter 0.9.26. Many thanks. Joe Fowler NIST Boulder Labs fowlerj@817jfmac:demeter-0.9.26$ ll /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.dylib -r-xr-xr-x 1 macports wheel 33008 Mar 5 09:05 /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.dylib fowlerj@817jfmac:demeter-0.9.26$ port installed ifeffit The following ports are currently installed: ifeffit @1.2.13_5+gcc7 (active) [Mac ports would normally run the following commands within its build script, of course. But I am isolating the failed command to see if makes more sense this way.] fowlerj@817jfmac:demeter-0.9.26$ pushd /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_demeter/demeter/work/demeter-0.9.26 fowlerj@817jfmac:demeter-0.9.26$ sudo ./Build install Use of uninitialized value $iffdir in pattern match (m//) at DemeterBuilder.pm line 308. Simple test for presence of gnuplot ---> found it! Using gnuplot with the wxt terminal. Building Demeter Can't copy('src/Ifeffit.dylib', 'blib/arch/auto/Ifeffit/Ifeffit.dylib'): No such file or directory at /opt/local/lib/perl5/vendor_perl/5.26/Module/Build/Base.pm line 5601.

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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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