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Datasets:
andreasburger
/
HIP-UMA-OMol25

Tasks:
Graph Machine Learning
Tags:
atomistic
molecular-dynamics
hessian
uma
omol25
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The dataset viewer is not available for this split.
Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code:   StreamingRowsError
Exception:    ValueError
Message:      Dataset 'atomic_numbers' has length 800 but expected 401
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/utils.py", line 147, in get_rows_or_raise
                  return get_rows(
                      dataset=dataset,
                  ...<4 lines>...
                      column_names=column_names,
                  )
                File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
                  return func(*args, **kwargs)
                File "/src/services/worker/src/worker/utils.py", line 127, in get_rows
                  rows_plus_one = list(itertools.islice(safe_iter(ds, dataset=dataset), rows_max_number + 1))
                File "/src/services/worker/src/worker/utils.py", line 483, in safe_iter
                  yield from ds.decode(False) if ds.features else ds
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2840, in __iter__
                  for key, example in ex_iterable:
                                      ^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2373, in __iter__
                  for key, pa_table in self._iter_arrow():
                                       ~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2398, in _iter_arrow
                  for key, pa_table in self.ex_iterable._iter_arrow():
                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 536, in _iter_arrow
                  for key, pa_table in iterator:
                                       ^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 419, in _iter_arrow
                  for key, pa_table in self.generate_tables_fn(**gen_kwags):
                                       ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 76, in _generate_tables
                  num_rows = _check_dataset_lengths(h5, self.info.features)
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 355, in _check_dataset_lengths
                  raise ValueError(f"Dataset '{path}' has length {dset.shape[0]} but expected {num_rows}")
              ValueError: Dataset 'atomic_numbers' has length 800 but expected 401

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HIP-UMA-OMol25

Snapshot of completed UMA-S-1.2 (uma-s-1p2) predictions on a uniform sample of OMol-1 train geometries, using the omol task.

This snapshot contains only validated, complete HDF5 shards. Checkpoint files (*.partial.h5) are intentionally excluded.

Current snapshot (2026-08-21): 10846 complete shards, about 25 GB, 4.3 million samples. The full 10M campaign is still running (41911 shards planned).

Shard files are grouped to stay under Hugging Face's 10,000-files-per-directory limit:

shards/000/shard_00000.h5 … shards/010/shard_10xxx.h5

Contents

Each HDF5 file contains variable-size molecular configurations with:

  • atomic_numbers, coords, and natoms
  • charge, spin, spin_multiplicity, and unrestricted
  • energy, forces, and dense hessian_flat
  • atom_ptr and hessian_ptr for reconstructing variable-size arrays
  • OMol matching fields: omol_index, source, data_id, sid, reference_source, and composition
  • optional OMol reference labels: dft_energy, dft_forces, and has_dft_labels

The teacher labels are float32:

  • energy: eV
  • forces: eV/Angstrom
  • Hessian: eV/Angstrom^2

The Hessian is dense, symmetrized, and has shape (3N, 3N) after reconstruction from hessian_flat.

Reproducing UMA inputs

Use task_name=omol, UMA-S-1.2, FP32, and a 120 Angstrom molecular cell. The OMol25 spin field is the spin multiplicity. Charge and spin are required conditioning inputs and must be passed through the equivalent of r_data_keys=["spin", "charge"].

Provenance

  • Parent dataset: OMol-1 train, release 260123
  • Sampling: fixed-seed uniform sample, seed 20260729
  • Model: uma-s-1p2
  • Hessian mode: loop
  • Precision: float32

omol_index is the index into the parent OMol-1 train ASE-LMDB. The additional identity fields and molecular geometry are included to support cross-checking and use without the parent dataset.

Format

HDF5 is the canonical release format. It preserves random access and variable-size dense Hessians without padding. FairChem graph/training caches should be generated locally from these files because their exact representation depends on FairChem version and training configuration.
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