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WIP: Disloc kink structure generation #244

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merged 48 commits into from
Sep 13, 2024

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thomas-rocke
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@thomas-rocke thomas-rocke commented May 20, 2024

Tools for building kink structures both in cylinder configs, and in dislocation quadrupoles.

Planned Features:

  • Compression of disloc.unit_cell to use minimum number of atoms in cubic cell
  • Small utility for calculating coordination number
  • Dislocation Cylinders with arbitrary kink networks in x direction
  • Kink Quadrupoles for single kink in each direction
  • Displacement interpolation for quadrupoles
  • Docs covering glide & kink in more detail
  • Unittests covering kink generation

Possible extra features:

  • Multi-kink quadrupoles (i.e. kink out by 2 glides instantaneously)
  • Displacement interpolation for kink cylinders
  • Kink networks in quadrupoles?
  • More useful coordination function
    • Multiple radii at once, not just single radius
  • Increase efficiency of quad kink slicing algorithm
  • Networks of kinks in multiple glide planes for Screw dislocations
  • Rectangular periodic array of (non-quadrupolar) dislocations

@thomas-rocke thomas-rocke marked this pull request as draft May 20, 2024 14:39
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@@ -2607,6 +2609,8 @@ def _build_bulk_cyl(self, radius, core_positions, fix_rad, extension,
Will add a fictitious core at position
core_positions[i, :] + extension[i, :], for the
purposes of adding extra atoms
cyl_mask: array of bool
Optional ovverride for atomic mask to convert supercell into cyl
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expand docs on reference frame

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@thomas-rocke thomas-rocke marked this pull request as ready for review September 10, 2024 17:25
@jameskermode jameskermode merged commit 260ee3a into libAtoms:master Sep 13, 2024
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@pgrigorev
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Hi @thomas-rocke, really fantastic work. Tutorial on dislocation glide was for long time on my to do list, so I am very happy you did it. Visualisation of kink looks amazing. Also kink glide methods look very useful, can help me with few annoying things. Well done!

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3 participants