[gpaw-users] STM simulations

[Vladislav Ivanistsev]

Please provide some more comments on symmetries used in STM simulations:
https://wiki.fysik.dtu.dk/gpaw/exercises/stm/stm.html

When trying to simulate STM for Gold with an organic adsorbate or ever for
a simple Gold surface I receive:
  File "/home/vladislav/ase/ase/dft/stm.py", line 69, in
get_averaged_current
    self.calculate_ldos(width)
  File "/home/vladislav/ase/ase/dft/stm.py", line 59, in calculate_ldos
    ldos += ldos.transpose((1, 0, 2)).copy()
ValueError: operands could not be broadcast together with shapes
(92,64,104) (64,92,104) (92,64,104)

Sincerely yours,
Vladislav Ivanistsev

Script:
from gpaw import GPAW
from gpaw import Mixer
from gpaw.poisson import PoissonSolver

name='RPBE'

# Define geometry of slab:
slab = fcc111('Au', size=(5, 4, 2),orthogonal=True)
# Fix second and third layers:
mask = [atom.tag > 0 for atom in slab]
#print mask
slab.set_constraint(FixAtoms(mask=mask))
top = fcc111('Au', size=(5, 4, 1),orthogonal=True)
add_adsorbate(slab,top,2.5,position='fcc', mol_index=0)
slab.center(axis=2, vacuum=6)

# Initial state:
calc = GPAW(h=0.16,
            mixer=Mixer(0.12, 5, weight=100.0),
            basis='dzp',
            kpts=(4,4,1),
            txt=name+'.txt',
            parallel={'sl_auto':True},
            xc=name,
            poissonsolver=DipoleCorrection(PoissonSolver(relax='GS'), 2)
           )

slab.set_calculator(calc)
qn=QuasiNewton(slab,trajectory=name+'.traj')
qn.attach(calc.write,1,name+'.gpw')
qn.run(fmax=0.05)
calc.write(name+'.gpw',mode='all')
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