[Code scan] Use dictionary special-token ids for UniMol v1 atomic representations

This issue is a result of a Codex global repository scan.

## Summary
UniMol v1 atomic representation filtering hard-codes token ids 0, 1, and 2 as BOS/EOS/PAD. The Dictionary actually initializes [CLS]=0, [UNK]=1, [PAD]=2, [SEP]=3. As a result, [SEP] is kept as a fake atom and unknown atoms are dropped from atomic representations.

## Code references
https://github.com/deepmodeling/unimol_tools/blob/4596596aa8f73eb462d5cc5a921d79966d0465da/unimol_tools/models/unimol.py#L255-L283
https://github.com/deepmodeling/unimol_tools/blob/4596596aa8f73eb462d5cc5a921d79966d0465da/unimol_tools/data/dictionary.py#L19-L33

## Impact
return_atomic_reprs=True can return an extra [SEP] entry and omit legitimate unknown atoms, so atomic symbols, coordinates, and representations no longer align with the molecule atoms.

## Suggested fix
Build the filter mask from self.dictionary.bos(), self.dictionary.eos(), and self.dictionary.pad(). Do not filter self.dictionary.unk(), because unknown atom tokens still correspond to atom positions.