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.
[image: image.png]
Best,
Kaifeng Zheng,
Stony Brook University
Stony Brook, NY 11794
Department of Materials Science and Chemical Engineering
Tele: +1(213)512-8539
Email: kaifeng.zh...@stonybrook.edu
Structure and Dynamics of Applied Nanomaterials Group
Chemistry Division
Brookhaven National Laboratory
Email: kzh...@bnl.gov
On Fri, Jul 12, 2024 at 11:59 AM Anis Attiaoui <an...@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
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> This message came from outside your organization.
>
> ZjQcmQRYFpfptBannerEnd
>
> 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(6**50)485-0501*
>
> Web:
> https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!ZVgulPXWZhwL3i4SjGXL7h__rqqmZ1AV_0e-Nu-hK7ESOw_u3RICr8n46KeOMWG7xrfV4uyA4e8sj-wji2iofIesF3yhv1490ecSFFxn0nk$
>
> <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!ctJ0zkFWwNTPEk_U5zx5-qfJjm6WqCH7qtEznlj8S2bokHYuqm_yn6Pb0sjuqt4Uu6thKR-GDWDAKlrxtN1OJav3q5rQYe0$>
>
>
>
>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit__;!!G_uCfscf7eWS!ZVgulPXWZhwL3i4SjGXL7h__rqqmZ1AV_0e-Nu-hK7ESOw_u3RICr8n46KeOMWG7xrfV4uyA4e8sj-wji2iofIesF3yhv1490ecSihKrm9s$
>
> Unsubscribe:
> https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options/ifeffit__;!!G_uCfscf7eWS!ZVgulPXWZhwL3i4SjGXL7h__rqqmZ1AV_0e-Nu-hK7ESOw_u3RICr8n46KeOMWG7xrfV4uyA4e8sj-wji2iofIesF3yhv1490ecS918xe8Q$
>
>
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
