[gpaw-users] gpaw-users Digest, Vol 9, Issue 11

[Misha Monder]

Hello Andrew,

I faced the same problem a few months back and that thread is linked below:
https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2010-June/000178.html

Also see:
https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2010-June/000179.html

Do let us know if the above does not fix it.

Cheers,
Misha Monder




----- Original Message ----
From: "gpaw-users-request at listserv.fysik.dtu.dk" 
<gpaw-users-request at listserv.fysik.dtu.dk>
To: gpaw-users at listserv.fysik.dtu.dk
Sent: Thu, October 14, 2010 6:00:01 AM
Subject: gpaw-users Digest, Vol 9, Issue 11

Send gpaw-users mailing list submissions to
    gpaw-users at listserv.fysik.dtu.dk

To subscribe or unsubscribe via the World Wide Web, visit
    https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
or, via email, send a message with subject or body 'help' to
    gpaw-users-request at listserv.fysik.dtu.dk

You can reach the person managing the list at
    gpaw-users-owner at listserv.fysik.dtu.dk

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gpaw-users digest..."


Today's Topics:

   1. Dipole correction breaks restart (Andrew Peterson)


----------------------------------------------------------------------

Message: 1
Date: Wed, 13 Oct 2010 15:33:09 -0700
From: Andrew Peterson <andy.peterson at stanford.edu>
Subject: [gpaw-users] Dipole correction breaks restart
To: gpaw-users at listserv.fysik.dtu.dk
Message-ID: <4CB633A5.10003 at stanford.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi again,

I've discovered that implementing the dipole correction breaks the 
restart function of the GPAW calculator. I've attached a simple script 
that has a dipole correction. Trying to use restart('calc.gpw') on the 
output file results in the below error. (This doesn't happen on the same 
script if the dipole parts are removed.)

thanks,
Andy

===== Error message from gpaw.restart:
>>> from gpaw import restart
>>> atoms, calc = restart('calc.gpw')

  ___ ___ ___ _ _ _ 
|   |   |_  | | | |
| | | | | . | | | |
|__ |  _|___|_____|  0.7.6383
|___|_|            

User: aap at suncat0073
Date: Wed Oct 13 15:31:34 2010
Arch: x86_64
Pid:  6584
Dir:  /afs/slac/g/suncat/vol1/gpawv3/install/lib64/python/gpaw
ase:   /afs/slac/g/suncat/vol1/gpawv3/ase/ase  version:  3.4.1
numpy: 
/afs/slac/g/suncat/vol1/gpawv3/numpy-1.4.1/build/lib.linux-x86_64-2.4/numpy
units: Angstrom and eV
Memory usage: 23.12 MB
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File 
"/afs/slac/g/suncat/vol1/gpawv3/install/lib64/python/gpaw/__init__.py", 
line 261, in restart
    calc = Class(filename, **kwargs)
  File 
"/afs/slac/g/suncat/vol1/gpawv3/install/lib64/python/gpaw/paw.py", line 
116, in __init__
    self.initialize()
  File 
"/afs/slac/g/suncat/vol1/gpawv3/install/lib64/python/gpaw/paw.py", line 
580, in initialize
    par.external)
  File 
"/afs/slac/g/suncat/vol1/gpawv3/install/lib64/python/gpaw/hamiltonian.py", 
line 69, in __init__
    self.poisson.set_grid_descriptor(finegd)
  File 
"/afs/slac/g/suncat/vol1/gpawv3/install/lib64/python/gpaw/poisson.py", 
line 52, in set_grid_descriptor
    self.operators = [Laplace(gd, scale, self.nn, allocate=False)]
  File 
"/afs/slac/g/suncat/vol1/gpawv3/install/lib64/python/gpaw/fd_operators.py", 
line 154, in Laplace
    return NewGUCLaplace(gd, scale, n, dtype, allocate)
  File 
"/afs/slac/g/suncat/vol1/gpawv3/install/lib64/python/gpaw/fd_operators.py", 
line 270, in __init__
    coefs = [laplace[n][0] * a_d.sum()]
IndexError: list index out of range



===== Input script:
#!/usr/bin/env python

from ase.data.molecules import molecule
from ase.visualize import view

from gpaw import GPAW
from gpaw.poisson import PoissonSolver
from gpaw.dipole_correction import DipoleCorrectionPoissonSolver

atoms = molecule('H2O')
atoms.set_cell([12.,12.,12.])
atoms.center()

p = PoissonSolver()
calc = GPAW(txt='H2O.txt',
            poissonsolver=DipoleCorrectionPoissonSolver(p, 2),
           )

atoms.set_calculator(calc)

energy = atoms.get_potential_energy()

calc.write('calc.gpw')




------------------------------

_______________________________________________
gpaw-users mailing list
gpaw-users at listserv.fysik.dtu.dk
https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users

End of gpaw-users Digest, Vol 9, Issue 11
*****************************************