Unexpected Vacancy in Generating a Straight Edge Dislocation

[Weixinyi-Cindy]

Dear developers,
I am currently using the matscipy.dislocation module to generate a BCC edge dislocation for tungsten with the following properties:

• The Burgers vector is (1,0,0).
• The direction of the dislocation line is (0,0,−1).
• The direction of the excess half atomic plane is (0,−1,0).

I utilized the following code to generate the edge dislocation:

cylinder_r = 200
a0, C11, C12, C44 = get_elastic_constants("./potentials/w_eam4.fs", delta=1e-3)
dislocation = disl.BCCEdge100Dislocation(a0, C11, C12, C44)
bulk1, disloc_ini, disloc_fin = dislocation.build_glide_configurations(radius=cylinder_r)
u0 = disloc_ini.positions - bulk1.positions

The issue arises in the 2D image of disloc_ini.positions. Along the (-1,0,0) direction on the slip plane, an unexpected vacancy appears near R = 170, where R represents the distance to the dislocation core.

It seems that along the (-1,0,0) direction on the slip plane, atoms with R < 170 are moving towards the dislocation core, while atoms with R > 170 are moving away from it, which creates the appearance of a "vacancy" near R = 170.

I tried using different values of cylinder_r (greater than 170), but the same issue persists near R = 170. I would appreciate guidance on how to resolve this problem. Thank you!

[jameskermode]

@thomas-rocke could you take a look at this?

[thomas-rocke]

Hi @Weixinyi-Cindy ,

This issue arises because of the self-consistent way we treat the continuum linear elastic displacements for BCC dislocations - there's a divergent behaviour of the displacements for atoms at the same y coordinate as the dislocation core, which is what drives the sudden change in dislocation positions.

Below is a temporary work-around for building a dislocation cylinder, whilst we work on a more sustainable fix for this. I turn the self-consistency off, and then apply self-consistent displacements only for a small inner radius of atoms.

cylinder_r = 200
a0, C11, C12, C44 = get_elastic_constants("./w_eam4.fs", delta=1e-3)

dislocation = disl.BCCEdge100Dislocation(a0, C11, C12, C44)

# First, build a cylinder with SC turned off
bulk, disl = dislocation.build_cylinder(radius=cylinder_r, self_consistent=False)

sc_radius = 50

# Get a mask of all atoms within a radius of sc_radius
core_position = np.array(disl.info["core_positions"])[0, :]
sc_mask = np.linalg.norm(bulk.positions[:, :2] - core_position[:2], axis=-1) <= sc_radius

# Calculate the SC displacements for atoms in mask
sc_disps = dislocation.displacements(bulk.positions[sc_mask], core_position, self_consistent=True)

disloc_pos = disl.positions.copy()

# Apply SC positions to existing disloc positions
disloc_pos[sc_mask, :] = bulk.positions[sc_mask, :] + sc_disps

disl.set_positions(disloc_pos)

[Weixinyi-Cindy]

@jameskermode Thank you very much for your help!
@thomas-rocke Thank you very much for your detailed response. With the help of the program you provided, I was able to successfully generate the correct BCC dislocation configuration.