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:
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> 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.)
>
Dear IFEFFIT Experts,
My colleagues and I are working on preparing Python scripts which:
1) run about 20,000 cif files from MD simulations through Atoms,
2) produce feff.inp files,
3) run feff.inp files through Feff (for XANES),
4) average all the XANES spectra.
We are having trouble opening the stand alone Atoms program through Python
– we can get Athena and Artemis to open, but for some reason Atoms will
not.
A snipet of our code which includes the file path is attached below.
*Code:*
###
def openAtoms():
try:
subprocess.run([r"C:\Users\ADIAZ\AppData\Roaming\DemeterPerl\perl\site\bin\datoms.bat"])
except:
print('Error')
openAtoms()
###
We have searched the Ifeffit archive for some answers but came up short,
and we were wondering if anybody on the list has any suggestions for a
potential fix to this problem?
Additionally, has anybody prepared a similar series of scripts (in Python)
to generate XANES spectra from MD simulations? We note that Marcus
Karolewski did discuss something similar in a past post:
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02744.html
Thanks in advance,
Dave
--
----------------------------------------------------------------------------------
David J. Sprouster, Ph.D.
Assistant Research Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
222 Old Engineering
Stony Brook, NY 11794
Phone: (631) 294-8983
web: http://stonybrook.edu/emrel
----------------------------------------------------------------------------------
