Small non-periodic C9H4 dataset (21 structures), trains Lorem model
for 2 epochs on energy and forces. Runs in ~45 seconds.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- models/__init__.py: wrap bec/mlip imports in try/except
- mlip.py, bec.py: use _masked from backbone instead of direct
  marathon.utils import

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

The calculator had broken imports (nonexistent SetUpEwald, get_batch)
and wrong field access patterns. Rewired to use lorem.batching directly,
added from_model() classmethod for easy construction without checkpoints.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Also fixes the i-PI driver command name (loremjax-install-ipi-driver
-> lorem-install-ipi-driver) to match pyproject.toml.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Previously these were hardcoded to None and always auto-detected from
folder structure. Now settings.yaml can override them while keeping the
folder-based fallback as default.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Wire up the Calculator → i-PI BEC data path: extract "apt" from
LoremBEC model output, reshape to (3*natoms, 3), and expose as "BEC"
for i-PI's driven_dynamics module. Implement LOREMCalculator as a
proper Calculator subclass and clean up the i-PI driver (remove buggy
compute_structure override that operated on JSON strings).

Add md-ipi example with input.xml (eda-nve, bec mode="driver"),
run.sh, start.xyz, and README.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

The model predicts the virial (stress * volume) as a 3x3 tensor.
Convert to ASE convention: divide by cell volume and return as
Voigt 6-element array.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

jax-pme moved halfspace handling into prepare(), so get_batch no
longer accepts this parameter.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Update BEC tests to use "born_effective_charges" key and (N,3,3) shape
  to match the ASE-compatible calculator output
- Export LOREMCalculator alias from __init__.py
- (ipi entry point was fixed by reinstall after prior flattening commit)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

hermes is deprecated; marathon.grain is now the canonical module.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add marathon (release/v0.2.0) as a proper git dependency instead of
requiring separate local install. Fix ToBatch.k_size to use kg.shape[0]
directly instead of count_halfspace_kvectors(kg.shape), which expects
grid dimensions (nx, ny, nz) but receives the flat k-vector array shape.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Add marathon[grain] extra to pyproject.toml
- Replace example run.sh scripts with README docs
- Add tox -e examples environment for smoke-testing examples
- Add examples CI job to tests workflow
- Remove stale marathon-dev install note from README
- Add tox commands to README development section
- Fix isort in ipi.py (drop unneeded __future__ import)
- Add uv.lock to .gitignore

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

uvloop (transitive dep via flax/orbax) does not support Windows.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Document full training workflow (data prep, config, running)
- Explain $DATASETS environment variable
- Add collapsible reference table for all training settings
- Default matmul precision to float32 instead of default

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>