[chrisiacovella]

Pull Request Summary

This primarily focuses on making it easier to examine a trained model after the fact.

Key changes

Notable points that this PR has either accomplished or will accomplish.

• When loading an hdf5 file, we store the name of the record; this quantity is available within the TorchDataset. To get the name associated with an individual index in the torch_dataset, we can call the _get_datapoint function that will return the name and then the normal output from the iterator.
• Adds in a helper function to setup an instance of the DataModule directly from a config .toml file, making it easier to exactly replicate splitting and any filtering that was done during training.
• Adds in a helper function to perform batch evaluation of a subset of the dataset (in the DataModule instance). This will perform some aggregation as well, adding in the name, model output, and associated metadata.
• Fixes doc string in geom qm9.
• Adds in a notebook to show how to use the helper functions.

Associated Issue(s)

• Make it easier to evaluate trained models. #446
• GEOM QM9: "dft_total_energy" contains GFN2-xTB energies, not r2SCAN-3c DFT #445

Pull Request Checklist

• Issue(s) raised/addressed and linked
• Includes appropriate unit test(s)
• Appropriate docstring(s) added/updated
• Appropriate .rst doc file(s) added/updated
• PR is ready for review

[Copilot]

🟡 Changes recommended

evaluate_batch maps batched results to the wrong records for subset="train" because the train dataloader shuffles by default while the code assumes fixed indices order.

6 open issues

• Typo in comment: "reocrds" should be "records". · New
• The return type annotation is incorrect: __getitem__ returns a BatchData, not a torch.Tensor,… · New
• Typo in docstring: "torch_datset" should be "torch_dataset". · New
• For subset="train", dm.train_dataloader() is called with its default shuffle=True, so the… · New
• per_atom_properties.append("atomic_numbers") runs on every batch iteration instead of only once.… · New
• Leftover debug print in a test. This PR removes similar stray prints elsewhere (e.g. in… · New

What changed in this PR

This PR adds tooling to make it easier to examine a trained model after the fact. It propagates each record's name from the hdf5 file through the TorchDataset (exposed via a new _get_datapoint), adds initialize_datamodule_from_config to rebuild a DataModule from a training .toml, and adds evaluate_batch to run batched inference over a dataset subset while aggregating name/output/metadata per original index. It also hardens hdf5 processing against records with zero valid conformers and corrects the GEOM QM9 energy-level-of-theory docstrings (GFN2-xTB, not r2SCAN-3c DFT) per issue #445.

Changes:

• Track and expose record names through the dataset; add _get_datapoint, initialize_datamodule_from_config, and evaluate_batch helpers.
• Guard _from_hdf5 so records with no valid configurations are skipped, and align the names list accordingly; replace stray prints with log.debug.
• Fix GEOM QM9 docstrings to reflect xtb energies, bump curation version to 1.1, and add an evaluation example notebook/tests.

File	Description
modelforge/​potential/​potential.py	Adds evaluate_batch for batched subset evaluation; has a train-subset ordering bug and a redundant per-batch append.
modelforge/​dataset/​dataset.py	Adds name tracking, _get_datapoint, initialize_datamodule_from_config, zero-conformer guard, and cache-validation update.
modelforge/​tests/​test_potentials.py	New test_batch_evaluation covering only the test subset.
modelforge/​tests/​test_dataset.py	Tests name access via _get_datapoint; includes a leftover debug print.
modelforge-curate/​.../​geom_qm9_curation.py	Corrects energy level-of-theory docstring to xtb.
modelforge-curate/​.../​scripts/​curate_geom_qm9.py	Corrects docstring and bumps dataset version to 1.1.
modelforge-curate/​.../​sourcedataset.py	Uses OrderedDict for records to preserve order.
notebooks/​evaluating_models.ipynb	New example demonstrating the evaluation helpers.
modelforge-curate/​.../​examples/​*.ipynb	Notebook metadata version bumps only.

_{Review effort: Balanced}