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. Anatoly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of Francisco Garcia Sent: Mon 4/11/2011 4:18 PM To: ifeffit@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit