[Ifeffit] about WebAoms

[Park Gyuchul]

Hi Bruce Ravel,

I appreciate for your precious comments. Your suggestion makes my life easier!  Is "distance" column is not required information in feff.inp format? (please find the part of the feff file attached. This is what I got from WebAtoms (typical cif file is used here).

Sincerely,
Gyuchul Park
Graduate Research Assistant
School of Materials Enginnering
Purdue University
________________________________
From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov> on behalf of Ravel, Bruce <bravel at bnl.gov>
Sent: Wednesday, November 20, 2019 4:16 PM
To: ifeffit at millenia.cars.aps.anl.gov <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] about WebAoms


Hi,

I am wondering whether you are thinking about your problem in the most
straight-forward way.  Atoms is a tool to expand crystal data into a
cluster.  From lammps, you already have a cluster, you just don't have
your cluster expressed in a form that Feff knows how to read.

Unless I am significantly misunderstanding your question, I dont think
Atoms is your best tool.  You just need to take some (or all) of the
atoms from the output cluster from your MD simulation and wrap it up in
the correct dressing for Feff.

Here is what I mean, explained for a much smaller problem (in terms of
number of atoms):

https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples?slide=11

Note what I say on the next page -- the absorber DOES NOT need to be at
(0,0,0) and the absorber does not need to be the first item in the list.

You can just edit (or write a short script/program) your lammps output
to cut out the atomic coordinates, assign unique potential indeces to
all the atoms, and put the correct boilerplate at the top of the file.
Voila!  You have a feff input file.

While it is true that you can, in principle, convert your lampps file to
a CIF file, it just doesn't seem like a necessary or helpful step.  I'd
really recommend taking the time to understand how to move the MD output
into the proper form for feff input.

HTH,
B


On 11/19/19 9:27 PM, Park Gyuchul wrote:
> Hi All,
>
> I am trying to simulate the EXAFS spectrum of pure molybdenum through
> FEFF9 software. I got the atomic configurations of molybdenum from
> molecular dynamics simulations, and I'd like to import it into FEFF 9.
> In order to do that, I converted lammps file into cif file, and I am
> trying to convert cif file into feff.inp. I am using Webatoms to convert
> cif file into feff.inp. The default value of cluster size and longest
> path is 8 and 5, respectively (in angs). However, when I try to increase
> the cluster size and the longest path to 10, it stops working, and I got
> the internal error. I am working with 1024 atoms (8x8x8 cells, bcc
> crystal structure). Are 1024 atoms too many to deal with in webatoms? or
> is there other ways to convert cif file into feff.inp?
> I don't have any problems when I use the ideal cif file (not from
> molecular dynamics simulations).
>
> Sincerely,
> Gyuchul Park
>
>
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--
  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Beamline:    https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/

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