[gpaw-users] Error of STM Simulation in GPAW

[Shuang Leung]

Dear gpaw-users,

I tried to use GPAW to do some STM simulations, but I got a trobule and may
need your help.
I firstly did a STM simulation of clean Ag(111) surface(3x3x1 surpercell)
and it worked. My gpaw run_script is:
******************************
from gpaw import *
from gpaw import GPAW
from ase.io import read
from ase.dft.stm import STM
import matplotlib.pyplot as plt
import numpy as np

name = 'Ag111'
atoms = read(name+'.cif')

calc = GPAW(mode=PW(800),
            xc='PBE',
            kpts=(3, 3, 3),
            symmetry='off',
            txt='Ag111-log')
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
calc.write('Ag111-wav.gpw', 'all')

#STM_simulation
atoms,calc = restart('Ag111-wav.gpw',txt=None)
stm = STM(atoms)
z = 8.0
bias = -0.6
c = stm.get_averaged_current(bias, z)
x, y, h = stm.scan(bias, c, repeat=(5, 5))

#STM-image_constant height
plt.figure()
plt.gca(aspect='equal')
x, y, I = stm.scan2(bias, z, repeat=(5, 5))
plt.contourf(x, y, I, 100)
plt.colorbar()
plt.savefig('2d_I.png')
*************************

But when I applied the same run_script (only changed the file names and z
value)to another adsorption system: Ag(110)/Tetracene, an error appeared
(as shown below ), even though the output file showed .gpw had been wirrten
successfully.
------------------------------------------------------------------------------------------------
rank=33 L00: Traceback (most recent call last):
rank=33 L01:   File
"/usr/local/python3/lib/python3.6/site-packages/gpaw/__init__.py", line
200, in main
rank=33 L02:     runpy.run_path(gpaw_args.script, run_name='__main__')
rank=33 L03:   File "/usr/local/python3/lib/python3.6/runpy.py", line 263,
in run_path
rank=33 L04:     pkg_name=pkg_name, script_name=fname)
rank=33 L05:   File "/usr/local/python3/lib/python3.6/runpy.py", line 96,
in _run_module_code
rank=33 L06:     mod_name, mod_spec, pkg_name, script_name)
rank=33 L07:   File "/usr/local/python3/lib/python3.6/runpy.py", line 85,
in _run_code
rank=33 L08:     exec(code, run_globals)
rank=33 L09:   File "Ag-2dSTM.py", line 24, in <module>
rank=33 L10:     calc = GPAW('Ag111-Org_wav.gpw')
rank=33 L11:   File
"/usr/local/python3/lib/python3.6/site-packages/gpaw/calculator.py", line
146, in __init__
rank=33 L12:     atoms, **kwargs)
rank=33 L13:   File
"/usr/local/python3/lib/python3.6/site-packages/ase/calculators/calculator.py",
line 359, in __init__
rank=33 L14:     self.read(restart)  # read parameters, atoms and results
rank=33 L15:   File
"/usr/local/python3/lib/python3.6/site-packages/gpaw/calculator.py", line
226, in read
rank=33 L16:     self.wfs.read(reader)
rank=33 L17:   File
"/usr/local/python3/lib/python3.6/site-packages/gpaw/wavefunctions/pw.py",
line 768, in read
rank=33 L18:     spin=kpt.s, collinear=self.collinear)
rank=33 L19:   File
"/usr/local/python3/lib/python3.6/site-packages/gpaw/wavefunctions/arrays.py",
line 166, in __init__
rank=33 L20:     data = data.view(float)
rank=33 L21: AttributeError: 'NDArrayReader' object has no attribute 'view'
GPAW CLEANUP (node 33): <class 'AttributeError'> occurred.  Calling
MPI_Abort!
application called MPI_Abort(MPI_COMM_WORLD, 42) - process 1
----------------------------------------------------------------------------------------------

Can someone correct this error？ Thanks a lot！

PS: I have attched my atomic coordinate file in this letter.

Shuang Leung
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