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chore: deprecate Atom class method #181

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Merged
sbillinge merged 3 commits into from
Mar 8, 2026
Merged

chore: deprecate Atom class method #181

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e19e628
chore: deprecate Atom class method
stevenhua0320 Mar 7, 2026
9751d1e
chore: change docstring
stevenhua0320 Mar 7, 2026
d6d8525
chore: rename variables to more explicit one, add test case descripti…
stevenhua0320 Mar 7, 2026
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chore: change docstring
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@stevenhua0320
stevenhua0320 committed Mar 7, 2026
commit 9751d1e5918457a0ee422cf063352b06516310be
6 changes: 2 additions & 4 deletions tests/test_atom.py
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Expand Up @@ -76,7 +76,7 @@ def test___init__(self):
# return

def test_msdLat(self):
"""Check Atom.msd_latt (and deprecated Atom.msdLat alias)."""
"""Check Atom.msdLat."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
atom_1 = Atom("C", [0, 0, 0], lattice=hexagonal, Uisoequiv=0.0123)
assert atom_1.msdLat([1, 2, 3]) == pytest.approx(0.0123, rel=0, abs=1e-15)
Expand All @@ -95,10 +95,9 @@ def test_msdLat(self):
vl = hexagonal.fractional(vc)

assert atom_2.msdLat(vl) == pytest.approx(atom_2.msd_cart(vc), rel=1e-13, abs=1e-13)
return

def test_msdCart(self):
"""Check Atom.msd_cart (and deprecated Atom.msdCart alias)."""
"""Check Atom.msdCart."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
atom_1 = Atom("C", [0, 0, 0], lattice=hexagonal, Uisoequiv=0.0456)
assert atom_1.msdCart([1, 0, 0]) == pytest.approx(0.0456, rel=0, abs=1e-15)
Expand All @@ -117,7 +116,6 @@ def test_msdCart(self):

vc = numpy.array([0.4, 1.1, -0.6], dtype=float)
assert atom_2.msdCart(vc) == pytest.approx(atom_2.msdCart(3.7 * vc), rel=1e-13, abs=1e-13)
return

def test_xyz_cartn(self):
"""Check Atom.xyz_cartn property."""
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