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Automatically center box when converting to GSD. #80

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Merged
mphoward merged 10 commits into from
Jun 4, 2025
Merged

Automatically center box when converting to GSD. #80

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334135c
Fix box centering in GSD conversion , add unit test, and ensure copy …
clpetix May 29, 2025
d16df5d
Update src/lammpsio/snapshot.py
clpetix May 30, 2025
d7330f3
Fix centering for triclinic box. Fix bug in from_hoomd_gsd.
clpetix May 30, 2025
3bc9262
Add triclinic unit test for autocentering.
clpetix May 30, 2025
ad54fe4
White space fix and refactor variables.
clpetix May 30, 2025
c39fa0c
Merge branch 'main' of https://github.com/mphowardlab/lammpsio into f…
clpetix Jun 3, 2025
e4ea2c6
Remove unnecessary copy when converting HOOMD box to numpy array in S…
clpetix Jun 3, 2025
907a335
Simplify centering using box_matrix and put centering of particles un…
clpetix Jun 3, 2025
115c6cb
Revert explicit copy in from_hoomd_gsd.
clpetix Jun 4, 2025
b7b78df
Simplify box_matrix code in Snapshot.py.
clpetix Jun 4, 2025
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14 changes: 7 additions & 7 deletions src/lammpsio/snapshot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,8 +68,8 @@ def from_hoomd_gsd(cls, frame):
frame.validate()

# process HOOMD box to LAMMPS box
L = frame.configuration.box[:3]
tilt = frame.configuration.box[3:]
L = frame.configuration.box.copy()[:3]
tilt = frame.configuration.box.copy()[3:]
if frame.configuration.dimensions == 3:
tilt[0] *= L[1]
tilt[1:] *= L[2]
Expand Down Expand Up @@ -225,12 +225,12 @@ def to_hoomd_gsd(self, type_map=None):
if self.step is not None:
frame.configuration.step = int(self.step)

# we could shift the box later, but for now this is an error
if not numpy.allclose(-self.box.low, self.box.high):
raise ValueError("GSD boxes must be centered around 0")
L = self.box.high - self.box.low
center = 0.5 * (self.box.high + self.box.low)
if self.box.tilt is not None:
tilt = self.box.tilt
tilt = self.box.tilt.copy()
tilt[0] /= L[1]
tilt[1:] /= L[2]
else:
tilt = [0, 0, 0]
frame.configuration.box = numpy.concatenate((L, tilt))
Expand All @@ -247,7 +247,7 @@ def to_hoomd_gsd(self, type_map=None):

frame.particles.N = self.N
if self.has_position():
frame.particles.position = self.position.copy()
frame.particles.position = self.position.copy() - center
if self.has_velocity():
frame.particles.velocity = self.velocity.copy()
if self.has_image():
Expand Down
10 changes: 7 additions & 3 deletions tests/test_snapshot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,10 +99,14 @@ def test_gsd_conversion():
snap2.to_hoomd_gsd()
assert numpy.all(snap2.id == [2, 1])

# check for error out on bad box
# check that box is set correctly when not originally centered
snap2.id = [1, 2]
snap2.position = [[0, 0, 0], [1, 1, 1]]
snap2.box.low = [-10, -10, -10]
with pytest.raises(ValueError):
snap2.to_hoomd_gsd()
center = (snap2.box.high + snap2.box.low) / 2
frame5 = snap2.to_hoomd_gsd()
assert numpy.allclose(frame5.configuration.box, [15, 15, 15, 0, 0, 0])
assert numpy.allclose(frame5.particles.position, snap2.position - center)


@pytest.mark.skipif(not has_gsd, reason="gsd not installed")
Expand Down