[Ifeffit] Writing a Script for MD Simulations / Scripting Atoms

David Sprouster david.sprouster at stonybrook.edu
Tue Jul 28 09:29:33 CDT 2020

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

A snipet of our code which includes the file path is attached below.



def 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:

Thanks in advance,


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
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