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Periodic microstructures and bug fixes - #114

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rimoli wants to merge 53 commits into

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Open

Periodic microstructures and bug fixes#114
rimoli wants to merge 53 commits into
masterfrom
develop

Commits on Sep 23, 2026
- Fix geometry bugs: ellipsoid axis ordering, exact limits, keywords
  
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  5189b34
- Fix seeding bugs: reproducibility, file round trips, positioning
  
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  db9a238
- Fix PolyMesh bugs: clipping to circular domains, edge_opt, I/O
  
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  ba996f4
- Fix TriMesh/RasterMesh bugs: mesh size limits, raster meshes, writers
  
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  b49bb90
- Fix CLI, input parsing and verification bugs
  
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- Add changelog entries for the bug fixes
  
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- Add periodic seed placement (per-axis)
  
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  9f4b213
- Add periodic 2D tessellation
  
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  13da404
- Add periodic 2D triangular and raster meshes
  
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  b5e169d
- Add the periodic option to the CLI and unwrap split grains in verification
  
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  d243eb7
- Add periodic 3D tessellation
  
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  d09ad03
- Add periodic 3D tetrahedral meshes
  
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  939bd01
- Label merged amorphous cells consistently in periodic meshes
  
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  a39cd17
- Take the attributes and facets of periodic meshes from the polymesh
  
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  f8a399f
- Mesh periodic domains with the quality and size settings of other meshes
  
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  24fa757
- Add examples of periodic microstructures
  
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  4070fef
- Use the published overlap-tolerance fit (CMAME 370, Eqs. 14-15)
  
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  f335141
- Size the triangles of all facets with max_edge_length in 3D
  
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  6b32d15
- Unify the vertices of the cells before cutting them at the periodic faces
  
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  f066632
- Add examples of a periodic binder-inclusion composite and of interface refinement
  
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  31517cb
- Add a margin between the seeds and the periodic faces
  
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  f8ae0a2
- Use the snapping tolerance in the periodic geometry tests
  
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  9cce19a
- Optimize the thin pieces of periodic cells with edge_opt
  
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  8fde1e0
- Cap the automatic periodic margin by the size of the smallest seed
  
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  294c129
- Open the narrow corners of the cells at the periodic faces with edge_opt
  
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  414ffa0
- Stop the passes of the 2D periodic mesher from deepening the corners
  
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  628d4e6
- Present the periodic examples like the others
  
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  5d74cd0
- Fix two cross-reference labels in the CLI documentation
  
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  df42a68
- Do not repeat 'example' after the titles of the referenced example pages
  
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  86d8dfa
- Share the small idioms of the periodic code
  
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  22fc079
- Share the helpers of the periodic tests
  
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  7b3d734
- One union-find and one point clustering for the periodic code
  
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  f99c00d
- One piece matcher and one wall lookup for 2D and 3D
  
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  387cce5
- One function pairs the points and facets of a periodic mesh
  
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  c304415
- The cell geometry helper answers which cells contain which points
  
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  e467749
- One cutting loop for the 2D and 3D periodic pieces
  
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  6bf0dcb
- Sort the facets of the meshes created from a polygonal mesh
  
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  ee870b1
Commits on Sep 24, 2026
- Sort the imports as the package's isort configuration requires
  
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  f6f2543
- Let the tests run in the continuous integration
  
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  e618e25
Commits on Sep 30, 2026
- Install pyvoro from pyvoro-rimoli, which bundles the current Voro++
  
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  2959311
- Keep the tiled reference of the 3D periodic tessellation test small
  
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  654fa27
- Build the documentation on Read the Docs with Python 3.10
  
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  5b26948
Commits on Oct 8, 2026
- Accept a number as the periodicity of a domain
  
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  df1095c
- Keep the geometry classes hashable
  
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  c428e83
- Use only the absolute tolerance when matching periodic boundary points
  
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  fe7d152
- Build no mesh after the last pass of the 2D periodic mesher
  
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  35b7478
- Compare 2D orientations modulo the symmetry of the shape
  
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  29eb126
- Keep numpy below 2 in the documentation requirements
  
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  543684e
- Write the added prose as sentences, with US spelling
  
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  f8e2e41
- Restore the overlap tolerance fit of master, which matches Fig. 10
  
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  3697c37
Commits on Oct 14, 2026
- warm start for the docs build (#115)
  
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  e4df822
- Pin pyvoro-rimoli 1.4.1 (#117)
  
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  46c3179
Commits on Oct 17, 2026
- Apply max_volume to the default phases in 2D (#118)
  
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  176d2a0

Commits

Commits on Sep 23, 2026

Commits on Sep 24, 2026

Commits on Sep 30, 2026

Commits on Oct 8, 2026

Commits on Oct 14, 2026

Commits on Oct 17, 2026