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

[Robert Gordon]

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

[David Sprouster]

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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