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Today's Topics:
1. Re: Scattering paths in Artemis (Matt Newville)
2. Re: Stand Alone Atoms (Matt Newville)
3. Re: Issue with Larch interacting with other software
(Matt Newville)
----------------------------------------------------------------------
Message: 1
Date: Thu, 13 Apr 2023 12:57:16 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Scattering paths in Artemis
Message-ID:
<CA+7ESbriDraZ4TvE7afH_gFj_Aa9R_Hyw64d9WY+0j22wa4v2Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Jyoti,
The scattering paths are held in the "feffNNNN.dat" files, and do not
necessarily need the feff.inp file that was used to generate them. It is
fine to move those around, rename them, etc. That just means that you are
then taking charge of managing and organizing them instead of letting
Artemis (or, say XAS Viewer) do that for you.
You can definitely use different scattering paths from multiple
calculations, including those done elsewhere.
On Thu, Apr 13, 2023 at 10:30?AM Jyoti Pandey <jyotipandey51092@gmail.com>
wrote:
> Hello everyone,
>
> I have a question regarding the scattering paths.
> Can we manually feed the scattering paths in artemis or it will only read
> from the feff input file.
>
> Thank you.
>
>
>
> With Best Regards
>
> Dr. Jyoti Pandey, Ph.D.
> Postdoctoral Researcher
> Department of Physics
> Central Michigan University, MI, USA
> Mobile No. +1-9282650599
> .....................................
>
> _______________________________________________
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--
--Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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Message: 2
Date: Thu, 13 Apr 2023 15:07:00 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Stand Alone Atoms
Message-ID:
<CA+7ESbpFs4_BmeBXEuEGxQ2nuWtfgvTni2bPxE3Xv_v=HfeAog@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Yasin,
On Thu, Apr 13, 2023 at 7:20?AM Yasin Deep <yasindeep@gmail.com> wrote:
> Dear All,
>
> I want to calculate bond lengths of the SrFe2As2 parent compound for E//ab
> and E//c polarization with stand-alone atoms pack of the Demeter. How can I
> calculate bond lengths for these two different polarizations? There is a
> panel for polarization vector I guess that panel I should adjust. I should
> put (0,0,1) for E//c and E//ab (1,1,0) is this correct? What should I put
> let's say for 30 degrees of polarization? Thank you in advance,
>
The bond lengths won't depend on the polarization, of course, though the
interaction of that crystal with X-rays will.
Setting the polarization vector as with
POLARIZATION 0 0 1
would put the polarization vector (not the electric field) along the `c`
axis, and
POLARIZATION 1 1 0
will put it at 45 degrees (tau/8) between the `a` and `b` axes.
If I'm not mistaken, put it at 30 degrees (tau/12) from the "a" axis toward
the "c" axis you would say
POLARIZATION 0.866 0.000 0.500
Hopefully, someone will correct me if that is not correct ;).
> Dr. Yasin HACISALIHOGLU
> _______________________________________________
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--
--Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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Message: 3
Date: Thu, 13 Apr 2023 15:28:21 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Issue with Larch interacting with other
software
Message-ID:
<CA+7ESbrV6_t8NDhRJkdF2CokLYv4nh463XtHwg57AS6oPLee-w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Luke,
On Thu, Apr 13, 2023 at 5:58?AM Luke Townsend <l.townsend@sheffield.ac.uk>
wrote:
> Hi All,
>
> Apologies if this has been brought up previously but I wanted to see if
> anyone else has had some issues with other software installed on the
> computer interacting with Larch (particularly XAS Viewer) and resulting in
> Larch no longer functioning. A couple of colleagues/students have been
> running into this issue with the SEM software AZtec.
>
> The error code that has been reported is (I'm not sure how helpful this
> is):
>
> 'Entry Point Not Found - The procedure entry point H5Literate could not be
> located in the dynamic link library C:\Program Files\Oxford Instruments
> NanoAnalysis\AZtec\x64\HDF5_hl.dll.'
>
> If anyone has any suggestions for resolving this (without having to run
> two separate computers for each software which is our current work around)
> it'd be thoroughly appreciated.
>
Hmm, Sorry for the trouble. I don't know what would cause that. It *should
be* that (by default) Larch installs its own Python interpreter and a full
stack of libraries and never looks or notices if there happens to be some
other Python environment installed. You *can* install it into an
existing Python environment -- that is allowed and not even really
discouraged, but it is sort of "advanced usage" in that it at least opens
up the possibility of conflicts.
That error message looks like Python is somehow seeing the HDF5 library
files from the Oxford AZtec installation. I don't know why it would find
that. I might suggest a few things in the "testing why this could be" and
a couple in the "workaround" category.
First, to track down why this happens, If you open a Python interpreter (or
even a "Larch CLI buffer", if that can run) you could try this:
import h5py
print(h5py.__version__)
print(h5py.__file__)
For "workaround", first can you confirm what the Larch installation folder
is? Like, did you install from the installer to
C:\Users\<UserName>\AppData\xraylarch
or something similar? Have you tried re-installing Larch? I'm not
certain that will help....
You might also check if there is some environmental variable that points or
that AZtec folder. I think that H5PY does not use environmental variables,
so I'm not sure what to look for here. But, you might just check what
"PATH" is, and maybe adjust that (maybe removing references to AZtec, at
least temporarily, or for a "launcher batch file" for Larch / XAS Viewer).
I hope that gives a few things to try that will help,
--Matt
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