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Hey!
Dropping in here too. 'configuration/box' is a HOOMD GSD spec or part of the HOOMD snapshot not the state. All HOOMD simulations have a box which may or may not have walls defined in it. If you define a cylindrical wall which has the axis aligned with the z-axis, since the cylinder is infinite in the axis direction, the z direction inside the cylinder will be periodic since the box is.
Best,
Brandon
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snapshot.particles.types = ['octahedron']
snapshot.particles.typeid = [0] * 19
hoomd.wall.Cylinder(radius=1.95, axis=(0, 0, 1), origin=(0.0, 0.0, 0.0), inside=True, open=True)
snapshot.configuration.box = [40, 40, 40, 0, 0, 0]
with gsd.hoomd.open(name='p.gsd', mode='xb') as f:
f.append(snapshot)
I tried to use the idea of having a cylindrical wall inside a cubic box, but when I start randomizing it, based on the result, it didn’t include the walls and particles are all around the box.
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