[ase-users] AssertionError upon running slab calculation

[Offermans Willem]

Dear ASE friends,

Can someone help me to solve the following problem?

My input file is:

<snip>j

       import numpy as np
       import math

       from ase import Atoms
       from ase.calculators.abinit import Abinit
       from ase.io.trajectory import Trajectory
       from ase.optimize import BFGS
       from ase.units import Ha
       from ase.units import Angstrom

       a = 2.789 * Angstrom

       unitcell = [
               [ 2.00000,  0.0000000000,  0.000000000000000],
               [ 1.00000,  math.sqrt(3),  0.000000000000000],
               [ 0.00000,  0.0000000000,  10*math.sqrt(2/3)]
               ]

       unitcell = np.multiply(unitcell, a)

       scal_pos = [
               [0.0000000000000000,  0.0000000000000000,  0.3000000000000000],
               [0.5000000000000000,  1.0000000000000000,  0.3000000000000000],
               [0.0000000000000000,  0.5000000000000000,  0.3000000000000000],
               [0.5000000000000000,  0.5000000000000000,  0.3000000000000000],
               [0.1666666666666667,  0.1666666666666667,  0.4000000000000000],
               [0.6666666666666667,  0.1666666666666667,  0.4000000000000000],
               [0.1666666666666667,  0.6666666666666667,  0.4000000000000000],
               [0.6666666666666667,  0.6666666666666667,  0.4000000000000000],
               [0.3333333333333333,  0.3333333333333333,  0.5000000000000000],
               [0.8333333333333333,  0.3333333333333333,  0.5000000000000000],
               [0.3333333333333333,  0.8333333333333333,  0.5000000000000000],
               [0.8333333333333333,  0.8333333333333333,  0.5000000000000000],
               [0.5000000000000000,  0.5000000000000000,  0.6000000000000000],
               [0.0000000000000000,  0.5000000000000000,  0.6000000000000000],
               [0.5000000000000000,  1.0000000000000000,  0.6000000000000000],
               [1.0000000000000000,  1.0000000000000000,  0.6000000000000000],
               [0.6666666666666666,  0.6666666666666666,  0.7000000000000000],
               [0.1666666666666667,  0.6666666666666666,  0.7000000000000000],
               [0.6666666666666667,  0.1666666666666667,  0.7000000000000000],
               [0.1666666666666667,  0.1666666666666667,  0.7000000000000000]
               ]

       slab = Atoms(scaled_positions=scal_pos,
               symbols='Pd20',
               cell=unitcell,
               pbc=[True,True,False]
               )

       WorkingDirectory = '/data/users/Public/woffermans/abinit/Pd/Pd_surface_GGA_PBE_PAW/Pd111/5M5V2x2/'

       intKpoints = 14
       intEcut = 30
       intPawEcut = 40

       calc = Abinit(command='./abinit.zip/abinit < PREFIX.files > pd.log',
             label='pd',
             ixc=11,
             xc='PBE',
             pps='pawxml',
             chksymbreak=0,
             occopt=3,
             tsmear=0.005
             )

       # one can specify abinit keywords also using set
       calc.set(toldfe=1.0e-6)  # warning - used to speedup the test
       calc.set(ecut=intEcut * Ha)  # warning - used to speedup the test
       calc.set(pawecutdg=intPawEcut * Ha)
       calc.set(kpts=[intKpoints, intKpoints, intKpoints])

       slab.set_calculator(calc)

       dyn = BFGS(slab)
       dyn = BFGS(slab, trajectory='Pd111_5M5V2x2.traj',restart='Pd111_5M5V2x2.pckl')
       dyn.run(fmax=0.05,steps=10)

</snip>

Upon running this python script, I got following error:

<snip>
….
   pbc=[True,True,False]
 File "/home/woffermans/.local/lib/python2.7/site-packages/ase/atoms.py", line 217, in __init__
   assert self.number_of_lattice_vectors == 3
AssertionError
….
</snip>

I assume that something is wrong with the slab definition. However I don’t know what.

Can someone help me out?




Met vriendelijke groeten,
Mit freundlichen Grüßen,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]

Indien u VITO Mol bezoekt, hou aub er dan rekening mee dat de hoofdingang voortaan enkel bereikbaar is vanuit de richting Dessel-Retie, niet vanuit richting Mol, zie vito.be/route.<http://www.vito.be/route>
If you plan to visit VITO at Mol, then please note that the main entrance can only be reached coming from Dessel-Retie and no longer coming from Mol, see vito.be/en/contact/locations.<http://www.vito.be/en/contact/locations>
VITO Disclaimer: http://www.vito.be/e-maildisclaimer
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20180821/aca43f15/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: vito.jpg
Type: image/jpeg
Size: 15232 bytes
Desc: vito.jpg
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20180821/aca43f15/attachment-0001.jpg>