Add Al example for symplectic integrator#44
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Pass model=(flashmd_model, (symplectic_model, config_dict)) to use the fixed-point midpoint-rule integrator instead of plain FlashMD. The plain single-model API is completely unchanged. Works in both i-PI and ASE (VelocityVerlet, Bussi, Langevin). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Self-contained example showing data preparation, model training, and NVE dynamics with both plain FlashMD and the symplectic integrator via i-PI. Includes a test that runs the example end-to-end with EMT and tiny models. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Use metatrain from git main until experimental.flashmd_symplectic is released on PyPI (TODO: pin to a release once available) - Update ipi import: ipi.utils.scripting → ipi.scripting - Add ipi, tqdm, pyyaml to test deps - Suppress known deprecation/resource warnings in pytest config Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Save mlip.pt with upet.save_upet() instead of the private _model.save() call, which produced a raw TorchScript file that metatomic's load_atomistic_model() cannot read - Disable energy rescaling (rescale_energy=False) to avoid a NaN crash when the model is undertrained and predicts energy gains exceeding the kinetic energy - Reduce default epoch count from 100 to 25 and step counts to values that complete quickly on CPU - Update simulation-template.xml and test string replacements to match the new CPU-only, mlip.pt-based setup Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The pinned metatrain version always includes experimental.flashmd_symplectic, so the conditional dead code never ran. Drop the flag, the fallback code path, and the now-unused find_all_architectures import. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The `._nl.algorithm = "cell_list"` workaround guards against a vesin CUDA bug with triclinic cells (vesin#157), but accesses a private attribute. It was not present in the original PR#32 design, and verified to be unnecessary on CPU (the only target for now). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…per" This reverts commit 7c1aa52.
Allow passing the symplectic model directly as the second tuple element, without wrapping it in a (model, config) pair. Defaults to empty config. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
VelocityVerlet assumed the symplectic model was always passed as (model, config); passing just a plain model crashed with TypeError. Also adds pytest filterwarnings for torch.jit and metatomic 0.1.12+ deprecations (renamed output names/quantities) that now surface with newer dependency versions. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Extend get_pretrained() with symplectic=True to download and export the symplectic FlashMD checkpoint from HuggingFace. Add tests covering both the plain-model and (model, config) tuple API. Metatrain is pinned to the git HEAD for now since experimental.flashmd_symplectic is not yet in a released version. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Pin metatrain to 2026.2.1 in pyproject.toml. In get_pretrained, check the mtt export return code and give a helpful error if the experimental.flashmd_symplectic architecture is missing. Override metatrain with a pinned metatensor/metatrain commit in CI so the symplectic tests can actually run the export. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
warp-lang>=1.14.0 deprecated warp.config.quiet, which is used by nvalchemi-toolkit-ops==0.3.0. Suppress it so pytest's filterwarnings error mode doesn't turn it into a failure. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The existing filter only matched APICLaunchParamRecord; warp-lang 1.14.0 triggers the same warning for other ctypes structures (e.g. APICLaunchPtrLocation) on Python 3.14. Use .* to suppress all of them. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Validate that the symplectic correction model's timestep matches the FlashMD model's in SymplecticStepper, covering both the i-PI and ASE paths. Add a test pairing mismatched-timestep models. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
metatrain 2026.3 ships the experimental.flashmd_symplectic architecture, so the temporary measures for symplectic support are no longer needed: - Pin metatrain==2026.3 and remove the git-override step in the tests CI. - Drop the "install a compatible metatrain" fallbacks in get_pretrained; export failures now surface the real error directly. The newer ASE pulled in by the bump deprecates MaxwellBoltzmannDistribution, so migrate the README and tests to thermalize_momenta (ASE >= 3.29) and filter the NumPy 2.5 shape-setting deprecation raised inside ASE. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The 2026.3.1 release includes the symplectic requested_inputs fix (metatrain PR #1174), so test_symplectic.py now passes. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Adds a self-contained Al example demonstrating the full workflow for the symplectic integrator introduced in #43:
Also includes
tests/test_example_al.py, which runs the example end-to-end in CI using EMT and tiny models.This PR should be merged after #43.