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,
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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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