problem Generating feffNNNN.dat with Larch in python
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://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!ct... <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!c... >
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.zheng@stonybrook.edu
Structure and Dynamics of Applied Nanomaterials Group
Chemistry Division
Brookhaven National Laboratory
Email: kzheng@bnl.gov
On Fri, Jul 12, 2024 at 11:59 AM Anis Attiaoui
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!ZV... https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!c...
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Thank you so much, Kaifeng. Your suggestions fixed the problem!
Best regards,
A.
From: Ifeffit
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 of feff run by FeffRunner (Feff 8) needs 6 values for the
CONTROL and PRINT statements, not 4. But that is what should be produced
when creating the Feff.inp files.
Since you are using CIFs as input, have you tried using the
cif2feff function? That might work here.
On Fri, Jul 12, 2024 at 10:59 AM Anis Attiaoui
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!Zb... https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!c...
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinfo... Unsubscribe: https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options/...
-- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411
Thank you Matt for the suggestion, you and Kaifeng were correct. Adjusting the PRINT statement seemed to make it work, and I now have access to the feffNNNN.dat files.
Best regards,
A.
From: Ifeffit
participants (3)
-
Anis Attiaoui -
Kaifeng Zheng -
Matt Newville