Generated, decoded structures all seem to be of P(1) symmetry

[sgbaird]

e.g.

Structure Summary
Lattice
    abc : 3.5100414781297133 3.515196078431373 3.5448717948717947
 angles : 59.64705882352941 59.959276018099544 59.93891402714934
 volume : 30.820712660051388
      A : 3.0385369088434473 0.0 1.7571808762296304
      B : 1.0068399538873045 2.861393772226697 1.7763171049499542
      C : 0.0 0.0 3.5448717948717947
PeriodicSite: Ag (0.4705, 0.1010, 1.2526) [0.1431, 0.0353, 0.2647]
PeriodicSite: Cr (1.0788, 0.7294, 1.6928) [0.2706, 0.2549, 0.2157]
PeriodicSite: H (0.1329, 0.0898, 0.1213) [0.0333, 0.0314, 0.0020]
PeriodicSite: H (0.0654, 0.0842, 0.2814) [0.0118, 0.0294, 0.0588]
PeriodicSite: He (0.0278, 0.0112, 0.0416) [0.0078, 0.0039, 0.0059]

Tried with a looser symprec tolerance, which threw an error at 0.2 and higher.

structures[0].get_space_group_info(symprec=0.2)

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\Miniconda3\envs\xtal2png-docs\lib\site-packages\pymatgen\core\structure.py", line 1013, in get_space_group_info
    return a.get_space_group_symbol(), a.get_space_group_number()
  File "C:\Users\sterg\Miniconda3\envs\xtal2png-docs\lib\site-packages\pymatgen\symmetry\analyzer.py", line 97, in get_space_group_symbol
    return self._space_group_data["international"]
TypeError: 'NoneType' object is not subscriptable

[sgbaird]

materialsproject/pymatgen#1764 mentioned same issue.

Looking a bit closer at the structures, probably has to do with the presence of distances less than 0.2 between differing sites, causing atoms to "collide".

structures[0].distance_matrix

array([[0.        , 0.97919993, 1.18065832, 1.05236272, 1.2924594 ],
       [0.97919993, 0.        , 1.94263668, 1.85350771, 2.08496016],
       [1.18065832, 1.94263668, 0.        , 0.17392385, 0.15348728],
       [1.05236272, 1.85350771, 0.17392385, 0.        , 0.25348576],
       [1.2924594 , 2.08496016, 0.15348728, 0.25348576, 0.        ]])

Note that these small distances are localized to $H$ and $He$.

structures[0].atomic_numbers

(47, 24, 1, 1, 2)

[sgbaird]

Looping through all 16 generated samples

Interestingly with the higher symprec of 0.1 instead of 0.01 more None-s are produced

space_group = []
for s in structures:
    try:
        space_group.append(s.get_space_group_info(symprec=0.1)[1])
    except Exception as e:
        space_group.append(None)
        pass
print(space_group)

[1, None, None, None, 1, 1, None, None, 1, None, None, 1, None, 1, 1, None]

[sgbaird]

Better now, but still not great:

[1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1]

with relax_on_decode, decode_as_primitive, and 127k iterations.

The formulas:

which seem somewhat better.

The images (sample-127.png):

[sgbaird]

from Kevin:

yes, also in your case, if you'd encode the space group in the image, you could write components for the loss that penalize mismatching angles. In other contexts, I have seen such extra loss terms to help a lot