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pymatgen nbh list update #762

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b14ac93
pymatgen nbh list update
jnsLs Dec 4, 2025
ef57871
cast each time
jnsLs Dec 4, 2025
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5 changes: 4 additions & 1 deletion src/schnetpack/transform/neighborlist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,7 +230,7 @@ def _build_neighbor_list(self, Z, positions, cell, pbc, cutoff):

class PymatgenNeighborList(NeighborListTransform):
"""
Calculate neighbor list using pymatgen.
Calculate neighbor list using pymatgen. Automatically casts Z and positions to np.float64.
"""

def _build_neighbor_list(self, Z, positions, cell, pbc, cutoff):
Expand All @@ -241,6 +241,9 @@ def _build_neighbor_list(self, Z, positions, cell, pbc, cutoff):
device = positions.device
dtype = positions.dtype

cell_np = cell_np.astype(np.float64, copy=False)
pos_np = pos_np.astype(np.float64, copy=False)

idx_i, idx_j, offsets, distances = find_points_in_spheres(
pos_np,
pos_np,
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19 changes: 18 additions & 1 deletion tests/data/test_transforms.py
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Expand Up @@ -22,15 +22,28 @@ def neighbor_list(request):
return neighbor_lists[request.param]


@pytest.fixture(params=[0, 1])
def precision(request):
precisions = [
torch.float64,
torch.float32,
]
return precisions[request.param]


class TestNeighborLists:
"""
Test for different neighbor lists defined in neighbor_list using the Argon environment fixtures (periodic and
non-periodic).

"""

def test_neighbor_list(self, neighbor_list, environment):
def test_neighbor_list(self, neighbor_list, environment, precision):
cutoff, props, neighbors_ref = environment

if precision == torch.float32:
_ = CastTo32()(props)

neighbor_list = neighbor_list(cutoff)
neighbors = neighbor_list(props)
R = props[structure.R]
Expand All @@ -44,6 +57,10 @@ def test_neighbor_list(self, neighbor_list, environment):
neighbors_ref = self._sort_neighbors(neighbors_ref)

for nbl, nbl_ref in zip(neighbors, neighbors_ref):

if nbl_ref.dtype == torch.float64:
nbl_ref = nbl_ref.to(dtype=precision)

torch.testing.assert_close(nbl, nbl_ref)

def _sort_neighbors(self, neighbors):
Expand Down