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Add pbc_wrap_batched_and_get_lattice_shifts to handle unwrapped positions in nl #519

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Merged
CompRhys merged 9 commits into from
Mar 25, 2026
Merged

Add pbc_wrap_batched_and_get_lattice_shifts to handle unwrapped positions in nl #519

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c331db5
fea: add pbc_wrap_batched_and_get_lattice_shifts to remove wrapping i…
CompRhys Mar 21, 2026
11a3e2c
fix: tweak vesin deps
CompRhys Mar 21, 2026
ea8e786
fixes lowest?
CompRhys Mar 22, 2026
3485f92
alchemiops on cpu can raise a runtime error.
CompRhys Mar 22, 2026
6a295bf
fix: above nbr explosion in fix sym tests (breaking in CI due to alch…
CompRhys Mar 22, 2026
aff45e7
restore comments
CompRhys Mar 22, 2026
7b21307
Merge remote-tracking branch 'origin/main' into nbr-fixes
CompRhys Mar 23, 2026
a89ebe6
fea: add PBC shift test to validate function
CompRhys Mar 23, 2026
2f96923
bump the shift to 3 cells
CompRhys Mar 25, 2026
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5 changes: 3 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,15 +30,15 @@ dependencies = [
"h5py>=3.15.1",
"numpy>=1.26,<3; python_version < '3.13'",
"numpy>=2.3.2,<3; python_version >= '3.13'",
"nvalchemi-toolkit-ops>=0.2.0",
"nvalchemi-toolkit-ops>=0.3.0",
"tables>=3.11.1",
"torch>=2",
"tqdm>=4.67",
]

[project.optional-dependencies]
test = [
"torch-sim-atomistic[io,symmetry]",
"torch-sim-atomistic[io,symmetry,vesin]",
"platformdirs>=4.0.0",
"psutil>=7.0.0",
"pymatgen>=2025.6.14",
Expand All @@ -47,6 +47,7 @@ test = [
"spglib>=2.6",
"vesin[torch]>=0.5.3",
]
vesin = ["vesin[torch]>=0.5.3"]
io = ["ase>=3.26", "phonopy>=2.37.0", "pymatgen>=2025.6.14"]
symmetry = ["moyopy>=0.7.8"]
mace = ["mace-torch>=0.3.15"]
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4 changes: 2 additions & 2 deletions tests/test_fix_symmetry.py
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Expand Up @@ -34,7 +34,7 @@ def make_structure(name: str, repeats: int = REPEATS) -> Atoms:
"fcc": lambda: bulk("Cu", "fcc", a=3.6),
"hcp": lambda: bulk("Ti", "hcp", a=2.95, c=4.68),
"diamond": lambda: bulk("Si", "diamond", a=5.43),
"bcc": lambda: bulk("Al", "bcc", a=2 / np.sqrt(3), cubic=True),
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@CompRhys CompRhys Mar 22, 2026 •
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too dense lead to nbr explosion exceeding alchemiops padding heuristic

"bcc": lambda: bulk("Al", "bcc", a=4 / np.sqrt(3), cubic=True),
"p6bar": lambda: crystal(
"Si",
[(0.3, 0.1, 0.25)],
Expand Down Expand Up @@ -128,7 +128,7 @@ def forward(self, state: ts.SimState, **kwargs: object) -> dict[str, torch.Tenso
@pytest.fixture
def noisy_lj_model(model: LennardJonesModel) -> NoisyModelWrapper:
"""LJ model with noise added to forces/stress."""
return NoisyModelWrapper(model)
return NoisyModelWrapper(model, noise_scale=5e-1, concentration=1.0)


@pytest.fixture
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