From: Ifeffit <ifeffit-bounces@millenia.cars.aps.anl.gov> On Behalf Of Matt Newville
Sent: Friday, July 12, 2024 10:36 AM
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] problem Generating feffNNNN.dat with Larch in python

Hi Anis, Sorry for the trouble. I'm not certain what you are seeing. Can you attach one of the feff. inp files generated? You did attach a Feff input file, but that says it was generated by Atoms. As Kaifeng suggests, the default version

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Dear All, I am trying to generate the path files of a DFT structure using larch in python. I will briefly describe the methodology I am following in hope it might help shed some light to the problem I am facing. I start from a .cif file of

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Dear All,

 

I am trying to generate the path files of a DFT structure using larch in python. I will briefly describe the methodology I am following in hope it might help shed some

light to the problem I am facing.

I start from a .cif file of the relaxed  DFT structure of 64-atoms GeSn. Then, I try to evaluate all the possible .inp file of the corresponding absorbing atoms (Sn and Ge). I am attaching the .inp file of one site0 for Sn ( tested it through Artemis and it works fine). Then I try to call the FeffRunner module to extract the corresponding feffNNNN.dat path files that will be used to build the EXAFS spectra.

It is in this step that I am facing an issue. It seems that FeffRunner is working but it doesn’t generate the corresponding feffNNNN.dat path files. (I am attaching an image of what is produced when I run the FeffRunner module).

Below is the python script I used to generate the .inp file as well as the paths via Larch.

“

from larch.xafs import FeffRunner

from larch.xrd.struct2xas import Struct2XAS

 

# read .cif DFT data with ase

DFT_path = '/home/ml-dell/Documents/Simulation/exafs/DFT/'

cif_file = f'{DFT_path}CIF-00010-T300K.xyz'

mat_obj = Struct2XAS(file = cif_file, abs_atom="Ge")

 

for site in range(mat_obj.nabs_sites):

    mat_obj.set_abs_site(site)

 

    #to get information on the coordination environment around absorber atom

    mat_obj.get_coord_envs_info()

    mat_obj.get_coord_envs()

 

    # use feff to generate .inp

    mytemplate = None

    mypath = DFT_path

    mat_obj.make_input_feff(radius=9.0, template=mytemplate, parent_path=mypath)

 

    # now we can run feff to generate the paths via larch

    feff_inp = f"{mat_obj.outdir}/feff.inp"

    session = Interpreter()

    sim = FeffRunner(feff_inp,_larch=session)

    sim.run()

 

”

 

I will be thankful for any suggestions on how to fix this issue.

 

Best regards,

Dr. Anis Attiaoui,   Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://mcintyre.stanford.edu

 

 

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