[ase-users] EOF Error Vibrational Modes Espresso

[Lance Kavalsky]

Hello,


Below is the traceback. It reaches this point and then hangs. I am running the script with mpirun on 4 processors (mpirun -np 4 python trans_ase.py).


As for the pseudopotentials, I am using Na.pbe-mt_fhi.UPF and P.pbe-mt_fhi.UPF which were obtained from the Quantum Espresso webpage.


Writing vib.log.0x+.pckl
Writing vib.log.eq.pckl
Writing vib.log.0y-.pckl
Writing vib.log.0x-.pckl
Writing vib.log.0y+.pckl
Writing vib.log.0z+.pckl
Writing vib.log.1x-.pckl
Writing vib.log.0z-.pckl
Writing vib.log.1z-.pckl
Writing vib.log.1y+.pckl
Writing vib.log.1y-.pckl
Writing vib.log.1x+.pckl
Traceback (most recent call last):
  File "trans_ase.py", line 23, in <module>
    vib.summary(log='vib.txt')
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 292, in summary
    hnu = self.get_energies(method, direction)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 256, in get_energies
    self.read(method, direction)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 210, in read
    fplus = load(name + '+.pckl')
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 195, in load
    f = pickleload(fl)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 1384, in load
Traceback (most recent call last):
  File "trans_ase.py", line 23, in <module>
    vib.summary(log='vib.txt')
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 292, in summary
    hnu = self.get_energies(method, direction)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 256, in get_energies
    self.read(method, direction)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 210, in read
    fplus = load(name + '+.pckl')
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 195, in load
    f = pickleload(fl)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 1384, in load
Traceback (most recent call last):
  File "trans_ase.py", line 23, in <module>
    vib.summary(log='vib.txt')
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 292, in summary
    hnu = self.get_energies(method, direction)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 256, in get_energies
    self.read(method, direction)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 210, in read
    fplus = load(name + '+.pckl')
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py", line 195, in load
    f = pickleload(fl)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 1384, in load
    return Unpickler(file).load()
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 864, in load
    return Unpickler(file).load()
    return Unpickler(file).load()
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 864, in load
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 864, in load
    dispatch[key](self)
    dispatch[key](self)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 886, in load_eof
    dispatch[key](self)
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 886, in load_eof
  File "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py", line 886, in load_eof
    raise EOFError
    raise EOFError
EOFError
    raise EOFError
EOFError
EOFError



Thanks,

Lance



________________________________
From: Ask Hjorth Larsen <asklarsen at gmail.com>
Sent: Saturday, December 2, 2017 7:42:51 AM
To: Lance Kavalsky
Cc: ase-users at listserv.fysik.dtu.dk
Subject: Re: [ase-users] EOF Error Vibrational Modes Espresso

Hi,

2017-12-01 18:39 GMT+01:00 Lance Kavalsky via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> Hello,
>
>
> My end goal is to calculate the vibrational energies (and subsequently ZPE
> and TS) of an adatom on a fixed substrate using ase.vibrations.
>
>
> As a test case, I have been trying to reduce my system to only 2 atoms (1 P
> and 1 Na) to ensure my script is functioning properly (attached). The script
> successfully reads from the Quantum Espresso input file, and vib.run() will
> write the pckl displacement files, but it returns EOFError when trying to
> execute vib.summary().
>
>
> Any advice or guidance would be very much appreciated.

I don't know if I can help with vibrations, but in case someone can,
could you give the full stack trace please?  It would be useful to
know what it was reading when it caused EOF.

The pseudopotentials and version numbers might also prove useful.

Best regards
Ask

>
>
> Thanks,
>
> Lance Kavalsky
>
> HBSc., MASc. Student
>
> Dept. of Materials Science and Engineering
>
> University of Toronto
>
>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
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