Thank you so much, Kaifeng. Your suggestions fixed the problem!
Best regards,
A.
From: Ifeffit On Behalf Of Kaifeng Zheng
Sent: Friday, July 12, 2024 9:19 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] problem Generating feffNNNN.dat with Larch in python
Dear Dr. Anis, If you want to print feffNNNN. dat files, you may need to modify the print level in your PRINT card. Please try the following card. The 6th number in the PRINT card needs to be 3. Best, Kaifeng Zheng, Stony Brook UniversityStony
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Dear Dr. Anis,
If you want to print feffNNNN.dat files, you may need to modify the print level in your PRINT card. Please try the following card. The 6th number in the PRINT card needs to be 3.
[cid:image001.png@01DAD448.DE65AC70]
Best,
Kaifeng Zheng,
Stony Brook University
Stony Brook, NY 11794
Department of Materials Science and Chemical Engineering
Tele: +1(213)512-8539
Email: kaifeng.zheng@stonybrook.edumailto:kaifeng.zheng@stonybrook.edu
Structure and Dynamics of Applied Nanomaterials Group
Chemistry Division
Brookhaven National Laboratory
Email: kzheng@bnl.govmailto:kzheng@bnl.gov
On Fri, Jul 12, 2024 at 11:59 AM Anis Attiaoui mailto:anatt@stanford.edu> wrote:
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
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