[Ifeffit] Dynamic XAFS Simulations?

Wed Jan 23 17:04:11 CST 2019

Dear Hunter,

I also recommend you to join the mailing list for the ultrafast laser community: dyna at listes.epfl.ch [to subscribe: dyna-subscribe at listes.epfl.ch]

Best,

Cecilia Gentle 
PhD Candidate, Department of Chemistry
University of Illinois at Urbana-Champaign
https://www.vanderveen-lab.com/ 

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Today's Topics:

   1. Dynamic XAFS Simulations? (Hunter Allison)
   2. Re: Dynamic XAFS Simulations? (Robert Gordon)

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Message: 1
Date: Wed, 23 Jan 2019 13:26:21 -0800
From: Hunter Allison <hgalliso at uci.edu>
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] Dynamic XAFS Simulations?
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	<CAH6J0e_vk1n4viX8H5A4vX=SRL0e5NQHmSZGEQ43wVxBzpwo5Q at mail.gmail.com>
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Hi,

        I'm a graduate student at the University of California, Irvine.
Firstly, thank you for all the copious resources. It is a treasure trove of information and a beacon of light for someone just starting out.

       Let's begin with some brief background. In my research group, we intend to perform pump-probe spectroscopy with attosecond x-ray probes. The Professor says that we can use XAFS to study how the electrons move on these very short timescales. While the system is being setup and other experiments are being conducted, my Professor wants me to figure out how to do simulations of XAFS. This is a bit of a daunting order, since I've never simulated anything before and only have basic programming knowledge. The only direction I have is, "Try Google.".

       So, today, I've been "trying Google" and found my way to here.
Since, I don't really know what I'm doing, I thought I try asking and finding out if anyone else does this sort of thing:
How/where does one do simulations of dynamic XAFS? Where would I get started?
(Please forgive me if this question has been answered somewhere else or if it seems profoundly dumb or too broad. I'm really just looking for some more direction. Perhaps, it could be that nobody does this and, in that case, I need to figure out how to model this myself. Wow! That thought seems daunting.)

       For example, let's say I want to find out how the x-ray adsorption of a carbon foil like Graphene would change on attosecond time scales as it's heated by a femtosecond laser and electrons move. Is there a program or code out there that people use to model this sort of thing?
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Message: 2
Date: Wed, 23 Jan 2019 14:53:04 -0800
From: Robert Gordon <ragordon at alumni.sfu.ca>
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Dynamic XAFS Simulations?
Message-ID: <3ecd57b0-1f86-a15d-9bcc-c5d585bdf5aa at alumni.sfu.ca>
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Hi,

Welcome to XAFS and all the excitement, thrills and adventure that implies!

First, since you are new to the subject, I would strongly recommend you take a course on XAFS. Many synchrotron facilities offer such - e.g. The APS/IIT Summer school was held last July; the SSRL course was last August, and NSLS2 had theirs in November. Any schools being held this year will likely also be announced on this iFeffit mailing list.

Some other resources for learning the basics can be found here:
https://www.ixasportal.net/ixas/index.php?option=com_content&view=article&id=46&Itemid=136
Matt's introduction is a good place to start.

For "dynamic XAFS" searches, you should consider "pump probe xafs" or "time-resolved xafs"
as search terms. Searching for pump probe xafs for me easily yielded this article
https://link.springer.com/chapter/10.1007/978-3-319-43866-5_9

As for simulation of XAFS, one program is FEFF, developed by the Rehr Group at the University of Washington http://feff.phys.washington.edu/
FEFF9 (8, 7) requires a license and modest fee for academic use, and is widely used for simulating both the near edge and extended fine structure. Bruce Ravel's Demeter suite of programs for XAFS processing and analysis includes an earlier version (FEFF6). Demeter is free - mostly a labour of love by Bruce, and he likes beer and maple syrup if you happen to run into him at a conference.

FDMNES (Yves Joly group, Institut Neel) is another program for simulating the near-edge. I find it works quite well. It allows for tweaking of the starting electronic configuration as well (with cautionary notes) that might be useful for simulating excited systems (I haven't checked literature to see if anyone has done so).

An additional program of note for fitting and simulation is GNXAS (DiCicco group, U. Camerino) but I haven't used it myself.

I am probably overlooking others, but these should get you going. I strongly recommend you take a course on the basics before plunging into any of these.

cheers,
Robert

On 2019-01-23 1:26 p.m., Hunter Allison wrote:
> Hi,
>
> ? ? ? I'm a graduate student at the University of California, Irvine. 
> Firstly, thank you for all the copious resources. It is a treasure 
> trove of information and a beacon of light for someone just starting out.
>
> ? ?? Let's begin with some brief background. In my research group, we 
> intend to perform pump-probe spectroscopy with attosecond x-ray 
> probes. The Professor says that we can use XAFS to study how the 
> electrons move on these very short timescales. While the system is 
> being setup and other experiments are being conducted, my Professor 
> wants me to figure out how to do simulations of XAFS. This is a bit of 
> a daunting order, since I've never simulated anything before and only 
> have basic programming knowledge. The only direction I have is, "Try 
> Google.".
>
> ? ?? So, today, I've been "trying Google" and found my way to here. 
> Since, I don't really know what I'm doing, I thought I try asking and 
> finding out if anyone else does this sort of thing:
> How/where does one do simulations of dynamic XAFS? Where would I get 
> started?
> (Please forgive me if this question has been answered somewhere else 
> or if it seems profoundly dumb or too broad. I'm really just looking 
> for some more direction. Perhaps, it could be that nobody does this 
> and, in that case, I need to figure out how to model this myself. Wow!
> That thought seems daunting.)
>
> ? ?? For example, let's say I want to find out how the x-ray 
> adsorption of a carbon foil like Graphene would change on attosecond 
> time scales as it's heated by a femtosecond laser and electrons move.
> Is there a program or code out there that people use to model this 
> sort of thing?
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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