Dataset Viewer
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: Illegal slicing argument for scalar dataspace
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/utils.py", line 99, in get_rows_or_raise
return get_rows(
^^^^^^^^^
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 77, in get_rows
rows_plus_one = list(itertools.islice(ds, rows_max_number + 1))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2815, in __iter__
for key, example in ex_iterable:
^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2352, in __iter__
for key, pa_table in self._iter_arrow():
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2377, in _iter_arrow
for key, pa_table in self.ex_iterable._iter_arrow():
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 536, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/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/python3.12/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 87, in _generate_tables
pa_table = _recursive_load_arrays(h5, self.info.features, start, end)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 273, in _recursive_load_arrays
arr = _recursive_load_arrays(dset, features[path], start, end)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 275, in _recursive_load_arrays
arr = _load_array(dset, path, start, end)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 242, in _load_array
arr = dset[start:end]
~~~~^^^^^^^^^^^
File "h5py/_objects.pyx", line 56, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 57, in h5py._objects.with_phil.wrapper
File "/usr/local/lib/python3.12/site-packages/h5py/_hl/dataset.py", line 879, in __getitem__
selection = sel2.select_read(fspace, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/h5py/_hl/selections2.py", line 101, in select_read
return ScalarReadSelection(fspace, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/h5py/_hl/selections2.py", line 86, in __init__
raise ValueError("Illegal slicing argument for scalar dataspace")
ValueError: Illegal slicing argument for scalar dataspaceNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Hessian-OMol
This dataset contains recalculated Hessians for selected molecules from the THEMol Hessian data, using the hessian_0.h5 source shard. The files here are the Hessians calculated so far for the comparison study in THEMol; the full original THEMol source HDF5 shards are not included in this upload.
Contents
- HDF5 Hessian files: 201
- Unique source samples: 57
- Atom count range: 3 to 50 atoms
- Total uploaded HDF5 size: 21.02 MB
- Manifest:
metadata/manifest.csv - Method summary:
metadata/method_summary.csv
File Layout
Files are organized by calculation engine and method:
hessians/
ml/uma_s_1p2_omol/
orca/wb97m_d4_def2_qzvppd/
orca/wb97m_d4_def2_tzvpd/
pyscf/ccsd_t_cbs/
pyscf/wb97m_v_def2_tzvpd/
pyscf/wb97m_v_def2_tzvpd_density_fit/
semiempirical/g_xtb/
semiempirical/gfn2_xtb/
metadata/
manifest.csv
method_summary.csv
summary.json
Each Hessian file is named hessian_0_sample_<zero-padded sample id>.h5. The path and original_path columns in metadata/manifest.csv map uploaded names back to the local calculation outputs.
HDF5 Schema
Each .h5 file contains one molecule group keyed by the original THEMol sample key. Within that group, the common datasets are:
atomic_numbers: atomic numbers, shape(N, 1)coords: coordinates, shape(N, 3)energy: scalar energy from the method in that fileforce: force array, shape(N, 3)gradient: gradient array, shape(N, 3)hessian: flattened Cartesian Hessian, shape(3N, 3N)hessian_4d: Hessian as atom/axis blocks, shape(N, N, 3, 3)when presentreference_hessian: source THEMol Hessian copied fromhessian_0.h5when presentmetadata_json: calculation metadata, including source sample id and method details
Methods
g_xtb: 40 files, g-xTBgfn2_xtb: 10 files, GFN2-xTBorca_wb97m_d4_def2_qzvppd: 37 files, ORCA wB97M-D4/def2-QZVPPDorca_wb97m_d4_def2_tzvpd: 45 files, ORCA wB97M-D4/def2-TZVPDpyscf_ccsd_t_cbs: 2 files, PySCF RCCSD(T)/CBSpyscf_wb97m_v_def2_tzvpd: 28 files, PySCF wB97M-V/def2-TZVPDpyscf_wb97m_v_def2_tzvpd_density_fit: 9 files, PySCF wB97M-V/def2-TZVPD with density fittinguma_s_1p2_omol: 30 files, UMA-S-1.2 OMol autograd Hessian
Notes
The calculations were run on samples from data/hessians/hessian_0.h5 in the local THEMol workflow. The original source THEMol shard is referenced in metadata but is not uploaded here.
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