Indexing Atoms broken on __getitem__

[pmrv]

s = Atoms(...)
s[0]

triggers the exception below. Setting values is unaffected.

File ~/software/pyiron_atomistics/pyiron_atomistics/atomistics/structure/atoms.py:2122, in Atoms.__getitem__(self, item)
   2112     return Atom(
   2113         element=element,
   2114         position=position,
   (...)
   2118         **new_dict,
   2119     )
   2121 new_array = super(Atoms, self).__getitem__(item)
-> 2122 new_array.dimension = self.dimension
   2123 if isinstance(item, tuple):
   2124     item = list(item)

AttributeError: 'Atom' object has no attribute 'dimension'

[skatnagallu]

I am using a pyiron structure for atom probe simulations. I am also running into same error.

However, strangely I am unable to reproduce the error when I just do this.

from pyiron_atomistics import Atoms
s = Atoms('N2', [(0, 0, 0), (0, 0, 1.5)])
s[0]

The above code block runs perfectly fine in my simulation environment. But, when I am trying to run my simulations I get the error. afaik the only difference is that I have a simulation class instance, whose attribute is pyiron structure.

a = MySimulation()
print(a.structure[0].number)

This gives me error.

[skatnagallu]

I was able to reproduce the error now. strangely, when index is of dtype np.int64 it gives an error.

from pyiron_atomistics import Atoms
import numpy as np
s = Atoms('N2', [(0, 0, 0), (0, 0, 1.5)])
a = 0
print(type(a))
print(s[a])
a = np.int64(a)
print(type(a))
print(s[a])

This gives the following output

<class 'int'>
Atom('N', [0.0, 0.0, 0.0], index=0)
<class 'numpy.int64'>

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[24], line 9
      7 a = np.int64(a)
      8 print(type(a))
----> 9 print(s[a])

File ~/.venv/lib/python3.11/site-packages/pyiron_atomistics/atomistics/structure/atoms.py:2122, in Atoms.__getitem__(self, item)
   2112     return Atom(
   2113         element=element,
   2114         position=position,
   (...)
   2118         **new_dict,
   2119     )
   2121 new_array = super(Atoms, self).__getitem__(item)
-> 2122 new_array.dimension = self.dimension
   2123 if isinstance(item, tuple):
   2124     item = list(item)

AttributeError: 'Atom' object has no attribute 'dimension'

Not sure if this helps.

[pmrv]

Zhenyu and I figured out a hint for this (on a different problem). Can you check whether anywhere in Atoms.__getitem__ there is a check of the form isinstance(..., int)? If so replace int by numbers.Integral and it might work.