Exporting electron density etc to XYZ file for plotting in other software

[serhan]

Thank you very much.

Cheers,
Serhan

[serhan]

Hi all,

I'm trying to export electron density to file using the script given in this thread. I need to extract electron densities of lots of .nc files.

If the exportED.py is like this

Code:

scf=restoreSelfConsistenCalculation('/home/master/atk/1.nc')
electron_density=calculateElectronDensity(scf)
from export3d import *
export3D(electron_density)

And I execute this file as

/home/master/atk/atk /home/master/atk/exportED.py > /home/master/atk/electronDensity1.dat &

then, a file named electrondensity1.dat is successfully created in the directory. The code is excellent. However, I have dozens of .nc files of which the electron densities are to be extracted as:

1.nc -> electronDensity1.dat
2.nc -> electronDensity2.dat
.
.
.

etc. How can I achieve this as a batch mode instead of executing

/home/master/atk/atk /home/master/atk/exportED.py > /home/master/atk/electronDensity1.dat & (when 1.nc is pointed in exportED.py)
/home/master/atk/atk /home/master/atk/exportED.py > /home/master/atk/electronDensity2.dat & (when 2.nc is pointed in exportED.py)
.
.

etc. Any help is greatly appreciated  

Cheers,
Serhan

[Nordland]

Dear Serhan.

I would do it like this.

import glob
import sys
from export3d import *
nc_files = glob.glob('*.nc')

for nc_file in nc_files:
    sys.stdout = file('electronDensity'+nc_file[:-3]+'.dat','w')
    scf=restoreSelfConsistenCalculation(nc_file)
    electron_density=calculateElectronDensity(scf)
    export3D(electron_density)
    sys.stdout.close()

Copy this script (call it serhan.py ) into the folder with all the nc-files in, and run it using atk serhan.py in that folder,
and wolla! No shell scripts needed

Edit: Ups - correct an error in the script.

[Anders Blom]

There are a couple of ways to approach this.

You can handle the many files within the script itself, using the "glob" module. This is a bit more complex, however, so I'd recommend using simple bash looping.

To do this, first we need to modify the code slightly, so that we can pass the name of the NC file on the command line:

Code:

import sys
scf=restoreSelfConsistenCalculation(sys.argv[2])

Then, we execute the script as

for i in *.nc ; do atk exportED.py $i > electronDensity$i.dat ; done

You need to add paths etc. This has the slight disadvantage that the files will be called "electronDensity1.nc.dat". If you can live with that, all ok. If you prefer the filename "electronDensity1.dat", we just need to change it a bit:

for i in *.nc ; do j=`echo $i | sed 's/.nc//g'` ; atk exportED.py $i > $j.dat ; done

[serhan]

Thank you very much for your answers. I could do it now.

Cheers,
Serhan

[Nordland]

Serhan, I have correct a bug in my script, if you are using my script, look above for the modification.