Fix orbital values when an orbital is completely outside of the unit cell

[pfebrer]

The orbital values computation was failing if there were orbitals that were completely outside of the unit cell.

[pfebrer]

E.g. I tested one case where rx,ry,rz was slice(354, 300, None), slice(0, 4, None), slice(8, 12, None)

which resulted in:

File ~/webDevelopement/sislGUI/sisl/src/sisl/_core/geometry.py:3825, in Geometry._orbital_values(self, grid_shape)
   3822     warn(f"Atom '{atom}' does not have a wave-function, skipping atom.")
   3823     continue
-> 3825 idx = sphere_grid_index(grid, ia_xyz, R)
   3827 if len(idx) == 0:
   3828     continue

File ~/webDevelopement/sislGUI/sisl/src/sisl/_core/geometry.py:3765, in Geometry._orbital_values.<locals>.sphere_grid_index(grid, center, R)
   3761 rz = slice(cmin[2], min(cmax[2], grid.shape[2]))
   3763 print(rx, ry, rz)
-> 3765 indices = np.mgrid[rx, ry, rz].reshape(3, -1).T
   3767 return indices

File ~/miniconda3/envs/simulationspy311/lib/python3.11/site-packages/numpy/lib/index_tricks.py:173, in nd_grid.__getitem__(self, key)
    170     nn = [_nx.arange(_x, dtype=_t)
    171           for _x, _t in zip(size, (typ,)*len(size))]
    172 else:
--> 173     nn = _nx.indices(size, typ)
    174 for k, kk in enumerate(key):
    175     step = kk.step

File ~/miniconda3/envs/simulationspy311/lib/python3.11/site-packages/numpy/core/numeric.py:1764, in indices(dimensions, dtype, sparse)
   1762     res = tuple()
   1763 else:
-> 1764     res = empty((N,)+dimensions, dtype=dtype)
   1765 for i, dim in enumerate(dimensions):
   1766     idx = arange(dim, dtype=dtype).reshape(
   1767         shape[:i] + (dim,) + shape[i+1:]
   1768     )

ValueError: negative dimensions are not allowed

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.68%. Comparing base (52d83bd) to head (9ea4768).
Report is 4 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #836   +/-   ##
=======================================
  Coverage   86.68%   86.68%           
=======================================
  Files         402      402           
  Lines       51886    51887    +1     
=======================================
+ Hits        44979    44980    +1     
  Misses       6907     6907           

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[zerothi]

Removed np.maximum I think they were too heavy for such small arrays. Will merge once coveraged.

[zerothi]

Thanks @pfebrer