[ase-users] ase-users Digest, Vol 114, Issue 11

[Ask Hjorth Larsen]

Hi,



2018-01-18 15:24 GMT+01:00 fabian <Fabian.T89 at web.de>:
> Hi,
>
> If i use this code :
>
> import numpy as np
> from ase import Atoms
> from ase.io import read
> from ase.visualize import view
> from ase.constraints import FixAtoms
> from ase.io import write
> from ase.utils.geometry import wrap_positions
>
>
> atoms = read('POSCAR')  # The first one in the previous mail
> indices = np.arange(len(atoms))
> indices[38] = 0
> indices[0] = 38
> atoms[indices]
> print(atoms)
> write('POSCAR_NEW', atoms, vasp5=True, sort=True,
> direct=True,long_format=True, format='vasp')
>
> to generate the case were the Co atom is first, i get this error:
>
>
> CURRENTPATH>shuffleatoms.py
> Traceback (most recent call last):
>   File "CURRENTPATH\shuffleatoms.py", line 14, in <module>
>     atoms[indices]
>   File "PYTHONPATH\Python27\lib\site-packages\ase\atoms.py", line 877, in
> __getitem__
>     con.index_shuffle(self, i)
>   File "PYTHONPATH)\Python27\lib\site-packages\ase\constraints.py", line
> 133, in index_shuffle
>     for new, old in slice2enlist(ind, len(atoms)):
>   File "PYTHONPATH\Python27\lib\site-packages\ase\constraints.py", line 22,
> in slice2enlist
>     return enumerate(range(*s.indices(n)))
> AttributeError: 'numpy.ndarray' object has no attribute 'indices'

OK.  The script works for me in master.  So the problem should
disappear soon when the next ASE is out.  Please feel free to confirm
this, and thanks for reporting the problem.

Best regards
Ask

>
>
> I abbreviated some pathes as they are really long...
> Can this be related to the fact that i use an older version of ASE on my PC?
> Ifi add
>
> atoms.set_constraint(None)
>
> before
>
> indices = np.arange(len(atoms))
>
> It works but the constraints are gone.
>
> Al the best
>
> fabian
>
>
>
> Am 18.01.2018 um 14:26 schrieb Ask Hjorth Larsen:
>>
>> Hi,
>>
>> 2018-01-18 11:13 GMT+01:00 fabian <Fabian.T89 at web.de>:
>>>
>>> Dear Ask
>>>
>>>
>>> Here are two example files in POSCAR format to illustrate my problem:
>>>
>>> The initial file looks like this and i want to move the Atom with the
>>> number
>>> 138 ( Co ) and Nr 28 (Ag) to the
>>> top position. I want to do this for core level calculations in VASP. Line
>>> 1
>>> , 6 and 7 need to
>>> be changed accordingly. The constraints should be kept.
>>>
>>> This is the original file:
>>
>> (snip)
>>
>> Okay, so I try to do an arbitrary permutation, e.g.:
>>
>> from ase.io import read
>> import numpy as np
>>
>> atoms = read('POSCAR')  # The first one in the previous mail
>> indices = np.arange(len(atoms))
>> indices[6] = 0
>> indices[0] = 6
>> atoms[indices]
>> print(atoms)
>>
>> The above works for me and keeps the constraints.  Which exact
>> permutation causes the problem?
>>
>> Best regards
>> Ask
>
>