[Ifeffit] Strategy to obtain cofigurationally averaged EXAFS fromMD simulations

Frenkel, Anatoly frenkel at bnl.gov
Mon Apr 11 15:46:55 CDT 2011

The answer depends, really, on what you want to accomplish.
There are several approaches:
1. Full atom-by-atom calculations of EXAFS following an MD trajectory: Riscioni, et al, PRB 83, 115409 (2011). This is required if you have disordered clusters, for example, and your electronic contributions to EXAFS change from atom to atom and you cannot factor them out. 
2. Full atom-by-atom calculation of structural (geometric) contributions to EXAFS only, factoring out the electronic contributions: Yevick, Frenkel, PRB 81, 115451 (2010).
In the second approach, the advantage is also that if you have small disorder you can calculate it independently from your MD simulations and add it to the structural term that you will obtain from the average coordinates only. Thus, in principle, you will use atom-by-atom calculations only to see if your configurational disorder is something less trivial than a Gaussian, and you would not know without such calculations. Either approach would allow you to match theory to the data without any fitting parameter.


From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of Francisco Garcia
Sent: Mon 4/11/2011 4:18 PM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] Strategy to obtain cofigurationally averaged EXAFS fromMD simulations

Dear users,

I want to compute the "average EXAFS spectra" usin 500 snapshots of
atomic coordinates from my MD simulations. The idea is to compute the
EXAFS spectra for each snapshot and then average the spectra over all
snapshots (the so-called "MD EXAFS" approach).  I know how to use
Artemis to generate the EXAFS spectrum of a single snapshot. However,
generating the EXAFS data for each of the 500 snapshots individually
will be too time consuming and messy (this is essentially a
book-keeping approach). I was wondering if there is a time-saving
strategy/script for computing the average EXAFS instead of the
snapshot-by-snapshot approach. For example, is it possible to include
the coordinates of all the snapshots in a single feff.inp file and
feed it to Artemis? Or if I have the feff.inp file for each snapshot,
is it possible to write a script for Artemis that will compute each
EXAFS spectra individually and dump them in a specified directory?

Thank you very much.

Ifeffit mailing list
Ifeffit at millenia.cars.aps.anl.gov

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110411/3d71a920/attachment.html>

More information about the Ifeffit mailing list