[Ifeffit] Writing a Script for MD Simulations / Scripting Atoms

Robert Gordon ragordon at alumni.sfu.ca
Tue Jul 28 12:28:29 CDT 2020


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<atoms.inp>
in the current working directory will be used, if available.

If the C<--wx> flag for running the GUI is given, all other command
line arguments are ignored.


for cif input
.../datoms.bat --c "yourfile.cif"

  I put the cif file in the bin directory for testing...don't have the 
bin directory in my $path

The log file (datoms.log) in appdata/roaming/demeter indicates it did 
the calculation



On 2020-07-28 7:29 a.m., David Sprouster wrote:
> 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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