* feat: add NVE energy-conservation benchmark

Port the NVE energy-conservation benchmark from the internal repo. It runs
short microcanonical (NVE, velocity-Verlet, no thermostat) MD trajectories
for four representative systems (vacuum molecule, bulk water, two solvated
peptides) and scores how well the model conserves total mechanical energy
E(t) = PE(t) + KE(t). The metric is the fitted total-energy drift over the
run divided by the kinetic-energy standard deviation, mapped through the
standard soft-threshold scorer.

- Add the benchmark module, registered and gated per-system on elements.
- Add the Streamlit UI page (per-system drift curves + linear fits) and wire
  it into the GUI.
- Mark it beta (BENCHMARKS_TO_SKIP_FOR_PUBLIC_LEADERBOARD), like the NEB
  benchmark.
- Add unit tests and checked-in test structures, plus the generic UI-page test.
- Add user-facing and API-reference docs under the General category.

The NVE velocity-Verlet integrator and SimulationState.potential_energy are
only on mlip's `develop` branch, not yet in a PyPI release, so pin mlip to git
`develop` via [tool.uv.sources] until a release ships them.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* chore: address review comments on NVE benchmark

- Drop the temporary mlip git pin now that MDIntegrator.NVE_VELOCITY_VERLET
  and SimulationState.potential_energy have shipped in mlip 0.2.2; bump the
  dependency floor to >=0.2.2 (both core and cuda extra) so resolution can't
  fall back to a release missing these features.
- Display the NVE energy-conservation benchmark on the public leaderboard.
- Document the ENERGY_DRIFT_RATIO_THRESHOLD = 1.0 rationale and why it is more
  lenient than the ~0.01 used for classical force fields.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* fix: prevent NVE Time (ps) axis title from being clipped

The total-energy-drift chart used a fixed height with container-width rendering,
which clipped the x-axis title. Size the chart to fit within its height (including
padding) so the "Time (ps)" title is fully shown.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: add CHANGELOG entry for the NVE energy-conservation benchmark

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

# Conflicts:
#	CHANGELOG.md

* fix: axis cutoff by legend

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: lwalew <l.walewski@instadeep.com>

* feat: NPT sims for water and solvent benchmarks

* feat: NPT sims for water and solvent benchmarks

* refactor: changes

* refactor: changes

* fix: make DEFAULT_CHARGE an int

Total charge is integral, and some external calculators (e.g. UMA's
FAIRChemCalculator) reject a float charge. Storing 0 instead of 0.0 fixes
those without affecting mlip models (which coerce internally).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* feat: split molecular liquids RDF and density into separate benchmarks

Split the water and solvent Molecular Liquids benchmarks into four scored
benchmarks: water/solvent x RDF/density. Each is its own Benchmark subclass,
score, leaderboard column and UI page, grouped under the "Molecular Liquids"
category.

- The RDF and density benchmark of each system group share a single NPT
  simulation via `reusable_output_id` and identical `ModelOutput` field sets,
  so the simulation is only run once when both are run together.
- Density is now scored on its own (relative deviation from the reference
  density via `compute_metric_score`), rather than only shown in the RDF UI.
- Shared simulation config, data loaders and density helpers moved to
  `utils/molecular_liquids.py`.
- New `Benchmark.data_name` lets the density benchmarks reuse the RDF input
  data without duplicating HuggingFace uploads.
- New density UI pages plot the density time series against the reference.
- Docs: added a density benchmark page and moved the RDF api-reference docs
  under `api_reference/molecular_liquids/`.

Note: the density score threshold (DENSITY_RELATIVE_DEVIATION_THRESHOLD) is a
placeholder pending sign-off from the science team.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* refactor: type Benchmark.run_mode as RunMode, drop _as_run_mode helper

`Benchmark.__init__` already coerces `run_mode` to a `RunMode`, so annotate the
stored attribute as `RunMode` and let the molecular-liquids helpers take a plain
`RunMode`. Removes the unnecessary `_as_run_mode` normalization.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* fix: use Leon's density scoring params (2% threshold, alpha=0.1)

Match the density score to Leon's NPT density analysis: relative-deviation
threshold of 0.02 and a gentle decay (DENSITY_SCORE_ALPHA=0.1), rather than the
placeholder 0.05 with the steep global scoring.ALPHA=3.0. With these values the
density scores reproduce the expected ranking (v1 models best on water, v2
models poor).

The ideal per-solvent threshold should ultimately be based on the isothermal
compressibility; still pending final sign-off.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* chore: drop verbose comment on density scoring constants

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* refactor: look up solvent structures by name in the UI, drop order comment

Address review feedback that solvent dict order isn't meaningful. The solvent
UI pages no longer hardcode ["CCl4", "methanol", "acetonitrile"] or index
`structures` positionally; they derive the system list from the results and
look structures up by name (new `ordered_structure_names` helper). Also drop
the misleading "canonical order" comment/docstring, since scoring is entirely
by-name and nothing depends on the config dict ordering.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* feat: address comments

Docs and make some functions private

* feat: remove file divider

* feat: update `data_dir` docstring

* feat: more private functions

* docs: add references

* docs: add CHANGELOG entry for molecular liquids split; simplify solvent score mean

- Add a Release 0.1.5 CHANGELOG entry describing the RDF/density split, the new
  water_density / solvent_density benchmarks, the shared-simulation reuse, and the
  new Benchmark.data_name mechanism.
- Drop the unreachable `r.score if r.score is not None else 0.0` guard in the two
  solvent benchmarks' score aggregation; the per-structure `score` field defaults to
  0.0 and is never None.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

# Conflicts:
#	CHANGELOG.md

* docs: shorten release

* docs: add references for water density

* feat: update reference solvent densities

* docs: add api reference for molecular liquids helpers and data_dir

- Add `api_reference/utils/molecular_liquids.rst` documenting `compute_densities`,
  `average_equilibrated_density`, `run_water_npt_simulation`,
  `run_solvent_npt_simulations`, and `get_solvent_system_names`, and wire it into
  the api-reference toctree (the module had no page unlike the sibling utils).
- Document the new `Benchmark.data_dir` property via `autoproperty`.
- Reword `compute_densities` `Returns:` to clear an ambiguous `densities`
  cross-reference warning in the docs build.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* chore: trigger claude-review

* feat: bump version to 0.1.5

* refactor: share density scoring, drop vestigial SOLVENT_PEAK_RANGE, clarify RDF docs

- Add a `score_density` helper in `utils/molecular_liquids.py` and use it from both
  the water and solvent density benchmarks, removing the duplicated relative-deviation
  -> compute_metric_score block.
- Drop the now-unused `SOLVENT_PEAK_RANGE` constant from the water RDF benchmark; the
  result's `range_of_interest` field now falls back to its `RADII_RANGE` default, which
  matches the range the MAE/RMSE metrics are actually computed over.
- Clarify in the radial-distribution docs that the metric differs by system: water uses
  MAE/RMSE against the experimental RDF plus a first-peak deviation, while the other
  solvents use the first-peak-position deviation only.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* refactor: type NPT sim helpers' force_field as ForceField | ASECalculator

Match `run_water_npt_simulation` / `run_solvent_npt_simulations` to the rest of the
codebase (e.g. `Benchmark.__init__`) instead of `Any`, improving type-checker coverage
on the shared simulation path.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Marco Carobene <marco.carobene+biontech@biontech.com>
Co-authored-by: lwalew <l.walewski@instadeep.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Leon Wehrhan <l.wehrhan@instadeep.com>