v1.6.0

Added

• Periodic microstructures, in 2D and 3D. The <periodic> field of the
  domain selects the periodic axes: True (or 1) for all of them, or
  their names, such as xz. The same option is an argument of
  cli.run, SeedList.position and PolyMesh.from_seeds.
• Periodic seed placement: seeds crossing a periodic face are placed
  without overlapping the seeds on the opposite side.
• Periodic tessellation: the Laguerre tessellation is periodic across the
  faces. Cells crossing a face are cut, and their pieces tile the domain.
• Periodic meshes: the triangular, tetrahedral and raster meshes have
  matching nodes on opposite faces. The quality and size settings
  (min_angle, max_volume, the max_volume of each phase,
  max_edge_length) act as on non-periodic meshes. In 2D, the cells next
  to the periodic faces are copied outside the faces while meshing, so that
  Triangle refines both faces the same way. In 3D, the facets are
  triangulated with the points that TetGen adds on them in a first pass,
  identically on opposite faces, and the mesh is built again with the
  facets fixed.
• gmsh is not supported for periodic meshes, which need the default mesher,
  Triangle/TetGen.
• Output of periodic meshes: the pairs of periodic points, nodes and facets
  are stored in the meshes and in their text files. The Abaqus output has a
  node set per periodic face, in matching order. The verification unwraps
  grains that are split by the faces.
• Cells of the same amorphous phase that touch across a periodic face are
  merged into one region, like cells that share a facet. Every mesher and
  writer labels the merged region with the smallest seed number among its
  cells.
• The element attributes and the facets of periodic meshes are computed
  from the geometry of the polymesh. TetGen can leave sub-faces of a facet
  unmarked when it may not modify the boundary, and its region attributes
  then leak between cells.
• Examples: periodic_2D.xml, periodic_3D.xml and
  periodic_tiling.py demonstrate periodic microstructures,
  pbx_2D.xml and pbx_3D.xml a periodic particulate composite
  (crystalline inclusions in a binder), and pbx_interface_2D.xml and
  pbx_interface_3D.xml meshes refined at the grain boundaries.
• periodic_margin (a setting, and an argument of SeedList.position
  and cli.run): the minimum distance between the surface of a seed and
  a periodic face. A seed that ends within the margin of a face, or crosses
  it by less, is placed elsewhere, since it would leave a thin piece of its
  grain on the opposite face and elements much smaller than the target size
  of the mesh there. auto uses half the target edge length of the mesh,
  or an eighth of the size of the smallest seed if that is smaller (the
  smallest seed needs about four elements across it, and cannot satisfy a
  margin larger than itself).
• PolyMesh.from_seeds(edge_opt=True, periodic_margin=...): the edge
  optimization of periodic meshes treats the thickness of each piece of a
  cell at a periodic face as a feature, like an edge. It moves the seeds of
  the pieces thinner than the margin, and of their neighbors, normal to the
  face, until the piece reaches the margin or the cell no longer crosses
  the face. The CLI passes its periodic_margin setting on.
• PolyMesh.from_seeds(edge_opt=True, min_angle=...): the corners of the
  cells at the periodic faces narrower than the minimum angle of the mesh
  are features too, since the mesher cannot reach the minimum angle there
  and fills them with shells of very small elements. The seeds on both
  sides of the facet are moved along it to open the corner. The CLI passes
  mesh_min_angle.
• Edge optimization: a trial is now kept when the shortest feature that it
  changes gets longer (for the shortest edge of the mesh, the criterion is
  unchanged). A target that does not improve in n_iter trials is left
  alone and the next one is taken, and the seeds moved across a periodic
  face are wrapped back into the domain. The CLI writes and plots the seeds
  again after the optimization, so that the seed files match the polygonal
  mesh. The periodic examples use periodic_margin auto and
  edge_opt.
• When the nodes on the periodic faces of a 2D mesh do not match after the
  first pass, the next pass starts from all the points of the mesh (those on
  a periodic face and on its image merged and put on both faces), so that
  Triangle only refines it around the merged points, instead of meshing the
  cells again with the points on the faces only, which split the narrow
  corners of the cells again at every pass, down to very small elements.
  The copies of the cells at the corners of the domain, used while meshing,
  were open on one side and partly discarded by Triangle.

Fixed

• Seed generation is reproducible: the RNG seed chain no longer depends on
  the (hash-randomized) iteration order of the phase keywords, and
  SeedList.from_info and cli.run no longer modify the rng_seeds
  and filetypes arguments (or their mutable defaults).
• <dist_type> cdf </dist_type> inputs are no longer distorted when the
  x-values in the CSV file are not evenly spaced (density=False is now
  passed to scipy.stats.rv_histogram). pdf is accepted as an alias
  of histogram.
• 3D mesh_max_volume and per-phase max_volume are now honored by
  TetGen. In 2D, a per-phase max_volume larger than the global value is
  no longer capped, and an infinite mesh_max_volume is no longer passed
  to Triangle as the (mis-parsed) switch ainf. The max_volume of a
  phase replaces the global value for that phase, an infinite one included,
  and phases without one, such as the default phases when none are given,
  use the global value.
• Ellipsoid.approximate mapped the axes incorrectly for the ordering
  c >= a >= b, so those grains were tessellated with the wrong orientation.
  The b >= c >= a ordering is now sorted explicitly as well.
• Seeds read back from seeds.txt can be repositioned. Ellipsoid seeds
  with a rotation sequence are written in a form that can be read back.
• Cells that intersect a circular or elliptical domain without having a
  vertex inside it are no longer dropped, cells cut twice by the boundary
  are clipped correctly, and the stored areas of clipped cells are correct
  (PolyMesh.volumes, verification.volume_fractions).
• _segment_cross no longer hangs for large coordinate values, and
  sample_pos_within raises instead of looping forever when the position
  distribution does not cover the domain.
• cli.plot_tri no longer hangs in 3D when a void grain touches the
  boundary of the domain.
• Relative <filename> and <directory> paths inside repeated tags
  (e.g. several <material> blocks) are resolved relative to the input
  file. A top-level <include> no longer discards materials, values such
  as true_cdf.csv no longer cause infinite recursion, and inf is
  parsed as a float.
• Verification: angle_rad inputs are no longer replaced by a uniform
  distribution, <orientation> random </orientation> and vector-valued
  parameters (side_lengths, axes) no longer crash, unknown phase
  fields are ignored, the caller's phases are not modified. The statistics
  of 2D orientations compare the angles modulo the symmetry of the shape,
  a half turn for ellipses and rectangles and a quarter turn for squares.
• RasterMesh: elements are counter-clockwise / right-handed (valid for
  Abaqus CPS4/C3D8), facets and their attributes are correct, vtk and
  abaqus output work (including with voids), 3D plotting works.
• TriMesh.write: valid .ele/.edge/.face files, Abaqus
  exterior surface unions reference only defined surfaces, full-precision
  points in text files, no dangling headers for meshes without attributes.
• PolyMesh.from_seeds(edge_opt=True) leaves the seed list in the
  accepted state (positions and breakdowns consistent) and is quiet unless
  verbose. PolyMesh.write(format='poly') writes the file, and
  PolyMesh.__eq__ is silent and no longer cubic.
• Circle and Sphere are hashable, by identity, like the other
  geometries, so they can be put in sets and used as dictionary keys.
• Ellipse(axes=...), Ellipse(matrix=...), Ellipsoid(c=.., ratio_bc=..), Square.area_expectation(side_lengths=...), the
  *_expectation methods with numpy scalars, Sphere.plot and 3D
  PolyMesh.plot/SeedList.plot_breakdown on a fresh figure,
  Rectangle.within for rotated rectangles, reflect for ellipses
  and ellipsoids, single-material color_by settings, numpy arrays as
  per-item plot keywords.

Changed

• pyvoro is installed from the pyvoro-rimoli package instead of
  pyvoro-mmalahe. Both provide the same pyvoro module.
  pyvoro-mmalahe bundles Voro++ 0.4.6, whose radical (Laguerre)
  tessellation can return a cell uncut when the compiler fuses
  multiply-adds. On macOS, pip compiles pyvoro-mmalahe from source, and
  Apple clang fuses them by default on Apple silicon. The cells then
  overlap, and Triangle and TetGen can crash on the resulting polygonal
  mesh. pyvoro-rimoli bundles the current Voro++, which gives the same
  cells either way, and has wheels for Linux, macOS and Windows. Uninstall
  pyvoro-mmalahe before upgrading (pip uninstall pyvoro-mmalahe),
  since the two packages install the same files.
• The continuous integration installs the current pytest and no longer
  installs tox from the requirements. The pinned tox 3.14 forced an old
  pluggy, with which pytest itself fails to import, so no test could run.
  The jobs of the test matrix no longer cancel each other on a failure.
• Read the Docs builds the documentation with Python 3.10 instead of 3.8,
  which pyvoro-rimoli and the current versions of other dependencies do not
  support. It installs requirements.txt like the documentation check of
  the continuous integration, and docs/requirements.txt also keeps numpy
  below 2, so that numpy is installed once.
• The facets of the triangular and tetrahedral meshes created from a
  polygonal mesh are sorted (nodes in ascending order within a facet,
  facets in lexicographic order), whatever the mesher. Triangle and TetGen
  list the edges/faces of a mesh in an order, and with an orientation, that
  vary from one run to the next, so the mesh files of otherwise identical
  runs differed in the order of their facets.
• max_edge_length (mesh_max_edge_length) acts in 3D on the triangles
  of the grain boundaries: when it is set, the facets of the polyhedral mesh
  are triangulated to that edge length (with Triangle, minimum angle 20
  degrees) before TetGen meshes the cells, for periodic and non-periodic
  meshes alike, so that the elements can be smaller at the interfaces than
  inside the grains (see the pbx_interface_3D.xml example). The
  geometric tests of a mesh against its polymesh use the non-planarity of
  the facets (from the snapping of the points to the periodic faces) as
  their tolerance, and each element is assigned to the cell in which its
  centroid is deepest.
• Ellipsoid.limits is exact for rotated ellipsoids (it was sampled).
• A Seed created with a position (or a geometry with a center) has
  its breakdown at that position. The geometry center is no longer reset
  to the origin.
• Ellipse, Ellipsoid and NBox geometries compare equal when
  their parameters are equal, and keep their identity-based hash.
• Unused sampling helpers were removed from seeding.seedlist.