Writing a Script for MD Simulations / Scripting Atoms
Dear IFEFFIT Experts, My colleagues and I are working on preparing Python scripts which: 1) run about 20,000 cif files from MD simulations through Atoms, 2) produce feff.inp files, 3) run feff.inp files through Feff (for XANES), 4) average all the XANES spectra. We are having trouble opening the stand alone Atoms program through Python – we can get Athena and Artemis to open, but for some reason Atoms will not. A snipet of our code which includes the file path is attached below. *Code:* ### def openAtoms(): try: subprocess.run([r"C:\Users\ADIAZ\AppData\Roaming\DemeterPerl\perl\site\bin\datoms.bat"]) except: print('Error') openAtoms() ### We have searched the Ifeffit archive for some answers but came up short, and we were wondering if anybody on the list has any suggestions for a potential fix to this problem? Additionally, has anybody prepared a similar series of scripts (in Python) to generate XANES spectra from MD simulations? We note that Marcus Karolewski did discuss something similar in a past post: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02744.html Thanks in advance, Dave -- ---------------------------------------------------------------------------------- David J. Sprouster, Ph.D. Assistant Research Professor Department of Materials Science and Chemical Engineering Stony Brook University 222 Old Engineering Stony Brook, NY 11794 Phone: (631) 294-8983 web: http://stonybrook.edu/emrel ----------------------------------------------------------------------------------
Are you specifying arguments for datoms.bat?
datoms [--output format] [--rmax #] [--cif --rec=#] [--wx] mydata.inp
If no input or CIF file is specified at the command line, F
Dear IFEFFIT Experts,
My colleagues and I are working on preparing Python scripts which: 1) run about 20,000 cif files from MD simulations through Atoms, 2) produce feff.inp files, 3) run feff.inp files through Feff (for XANES), 4) average all the XANES spectra.
We are having trouble opening the stand alone Atoms program through Python – we can get Athena and Artemis to open, but for some reason Atoms will not.
A snipet of our code which includes the file path is attached below.
* *
*Code:*
###
def openAtoms():
try:
subprocess.run([r"C:\Users\ADIAZ\AppData\Roaming\DemeterPerl\perl\site\bin\datoms.bat"])
except:
print('Error')
openAtoms()
###
We have searched the Ifeffit archive for some answers but came up short, and we were wondering if anybody on the list has any suggestions for a potential fix to this problem?
Additionally, has anybody prepared a similar series of scripts (in Python) to generate XANES spectra from MD simulations? We note that Marcus Karolewski did discuss something similar in a past post: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02744.html
Thanks in advance,
Dave
-- ---------------------------------------------------------------------------------- David J. Sprouster, Ph.D. Assistant Research Professor Department of Materials Science and Chemical Engineering Stony Brook University 222 Old Engineering Stony Brook, NY 11794 Phone: (631) 294-8983 web: http://stonybrook.edu/emrel ----------------------------------------------------------------------------------
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participants (2)
-
David Sprouster -
Robert Gordon