The old way for modification of ZVAL in the POTCAR is unavailable

[yuyuanjingxuan]

Hi all,

I am carrying out a vasp calculation with potentiostat method. Thus, I use potential_file_creator to modify the ZVAL of one element of a structure provided. Take an example which add 0.01e to the 1st Ne atom of struc. What I used to do is

from pyiron_mpie.electrochemistry.potential_ramp import potential_file_creator
Ne_new= potential_file_creator(element="Ne", charge=0.01)
struct[0] = Ne_new

The type of struc here is pyiron_atomistics.atomistics.structure.atoms.Atoms, while the type of Ne_new is pyiron.atomistics.structure.periodic_table.ChemicalElement.

I am confused that the code above works one month ago. However, when I run the same code today, it is unavailable.

pyiron Version and Platform
python 3.7.9
pyiron 0.4.0

What I expect
0.01e was successfully added to the 1st Ne atom of struc.

Actual Behavior

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/u/system/SLES12/soft/pyiron/dev/anaconda3/lib/python3.7/site-packages/pyiron_atomistics/atomistics/structure/atoms.py in __setitem__(self, key, value)
   2205                 el = value
   2206             else:
-> 2207                 raise TypeError("value should either be a string or a ChemicalElement.")
   2208             if el != old_el:
   2209                 new_species = np.array(self.species).copy()

TypeError: value should either be a string or a ChemicalElement.

Could you please tell me how to avoid the issue here? Many thanks.

[sudarsan-surendralal]

This is very strange. Can you check if

from pyiron_atomistics.atomistics.structure.periodic_table import ChemicalElement

print(isinstance(Ne_new, ChemicalElement)

returns True?

[yuyuanjingxuan]

Unfortunately, it returns False here.
Does that means pyiron_atomistics.atomistics.structure.periodic_table.ChemicalElement and pyiron.atomistics.structure.periodic_table.ChemicalElement are not the same object?

[sudarsan-surendralal]

Unfortunately, it returns False here.
Does that means pyiron_atomistics.atomistics.structure.periodic_table.ChemicalElement and pyiron.atomistics.structure.periodic_table.ChemicalElement are not the same object?

Yes you are right! We have updated pyiron.atomistics to pyiron_atomistics.atomistics but unfortunately, these changes are not made in the pyiron_mpie repository which you use. I've opened a pull request for this (https://github.com/pyiron/pyiron_mpie/pull/39). Can you try using this branch?

[yuyuanjingxuan]

Thanks Sudarsan. It works when I load the refactor branch from pyiron_mpie.