plot3d with select_atoms does not work anymore

[ahmedabdelkawy]

If you try to plot3d() from a generated structure with select_atoms showing subset of atoms:

from pyiron import Project
pr = Project('test')
struc = pr.create.structure.bulk('Fe', cubic=True)
struc.plot3d(select_atoms=[0])

you will end up with the error:

File /u/system/SLES12/soft/pyiron/dev/anaconda3/lib/python3.10/site-packages/structuretoolkit/visualize.py:310, in _plot3d(structure, show_cell, show_axes, camera, spacefill, particle_size, select_atoms, background, color_scheme, colors, scalar_field, scalar_start, scalar_end, scalar_cmap, vector_field, vector_color, magnetic_moments, view_plane, distance_from_camera)
    308 if select_atoms is not None:
    309     select_atoms = np.array(select_atoms, dtype=int)
--> 310     elements = elements[select_atoms]
    311     atomic_numbers = atomic_numbers[select_atoms]
    312     positions = positions[select_atoms]

TypeError: only integer scalar arrays can be converted to a scalar index

The current structure.plot3d() currently works as follows:

1. plot3d() Inside pyiron_atomistics/atomistics/structure/atoms.py calls and passes pyiron_to_ase(self): self=structure to
2. plot3d() inside /structuretoolkit/visualize.py
3. Which passes the element list as a list and not numpy array
4. However plot3d() inside visualize.py explicitly changes the select_atoms into a numpy: select_atoms = np.array(select_atoms, dtype=int)
5. You end up trying to index a list with a numpy array which does not work:

s = ['A', 'B', 'C', 'D']
ind = np.array([1])
s[ind]

If you try to use plot3d() directly from visual.py and pass the structure to it, it works because elements is an array no pyiron_to_ase was imposed.

from structuretoolkit.visualize import _plot3d
_plot3d(struc, select_atoms=[0])

Proposed solutions:

1. remove pyiron_to_ase(self) and just pass (self) in plot3d() in atoms.py
2. explicitly change elements list to numpy similar to select_atoms in plot3d() in visual.py: elements= np.array(elements)

Both are tested and work locally. However, I am not sure if they affect other functionalities.

[ahmedabdelkawy]

This is now fixed by #104