Graphene on grain boundaries

mdapy.build.add_graphene(polycrystal, *, layers=1, coverage=1.0, clearance=3.0, bond=1.42, spacing=3.35, seed=None) puts graphene on the grain boundaries of a polycrystal from build_polycrystal: one or more layers on each face between two grains, or on a fraction of them.

from mdapy.build import add_graphene, build_crystal, build_polycrystal

copper = build_polycrystal(build_crystal("fcc", 3.615, elements="Cu"), 60.0, 6, seed=1)
composite = add_graphene(copper, layers=2, coverage=0.6, seed=2)
composite.table["element"].value_counts()  # Cu and C

A copper polycrystal of six grains, cut in half, with graphene (dark): one layer on every boundary, two layers, and one layer on half the area of the boundaries.

Name	Type	Default	Unit	Meaning
polycrystal	System			a polycrystal from build_polycrystal, with info["seeds"] and a grain column
layers	int32	1		the number of graphene layers on each face, AB stacked and centered on it
coverage	float64	1		the fraction of the area of the boundaries covered, from 0 to 1
clearance	float64	3.0	Å	atoms of the polycrystal closer than this to a carbon atom are removed, about the distance of graphene from copper
bond	float64	1.42	Å	the carbon–carbon bond of graphene
spacing	float64	3.35	Å	the distance between graphene layers
seed	int64 or numpy.random.Generator			seed of the faces chosen and of the orientations of the graphene

Each face between two grains, the face of their Voronoi cells, is covered once by a flat piece of graphene, rotated at random about the normal of the face, shifted at random within it, and cut to the face; where two faces meet, a layer off the middle ends where the planes halfway between them cross, so that the layers of the two faces meet there. With coverage below 1, whole faces are covered in a random order until that fraction of the boundary area is. Where faces meet, the carbon atoms of a later face closer than 0.85 bond lengths to those of an earlier one are left out: the pieces join with their edges, without bonds made across.

Results

The atoms of the polycrystal left, then the carbon atoms, whose grain is −1; the box and info of the polycrystal. With no face covered, the polycrystal itself.

Errors

add_graphene raises MissingProperty for a system without info["seeds"] or a grain column, and InvalidParameter for fewer than one layer, a coverage outside 0 to 1, and lengths that are not positive.