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CHANGELOG.md

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Changelog

All notable changes to libcasm-xtal will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[2.0a12] - 2024-12-10

Fixed

  • Fixed xtal::Lattice::_generate_voronoi_table(). The acute angle test resulted in the FCC lattice missing a row for the normal that lies along a conventional unit cell lattice vector, so voronoi number was 4 instead of 5 for the octahedral interstitial coordinate).

Added

  • Added Lattice.voronoi_table, Lattice.voronoi_number, and Lattice.voronoi_inner_radius.

Changed

  • Build macos x86_64 wheels with macos-13 Github Actions runner

[2.0a11] - 2024-08-09

Added

  • Added Lattice.copy, Lattice.__copy__, Lattice.__deepcopy__, Lattice.__repr__, Lattice.to_dict, and Lattice.from_dict
  • Added AtomComponent.copy, AtomComponent.__copy__, AtomComponent.__deepcopy__, AtomComponent.__repr__, AtomComponent.to_dict, and AtomComponent.from_dict
  • Added Occupant.copy, Occupant.__copy__, Occupant.__deepcopy__, Occupant.__repr__, Occupant.to_dict, and Occupant.from_dict
  • Added DoFSetBasis.copy, DoFSetBasis.__copy__, DoFSetBasis.__deepcopy__, DoFSetBasis.__repr__, DoFSetBasis.to_dict, and DoFSetBasis.from_dict
  • Added Prim.copy, Prim.__copy__, Prim.__deepcopy__, and Prim.__repr__
  • Added SymOp.copy, SymOp.__copy__, SymOp.__deepcopy__, and SymOp.__repr__
  • Added Structure.copy and Structure.__repr__
  • Added IntegralSiteCoordinate.copy, IntegralSiteCoordinate.__copy__, and IntegralSiteCoordinate.__deepcopy__
  • Added IntegralSiteCoordinateRep.copy, IntegralSiteCoordinateRep.__copy__, IntegralSiteCoordinateRep.__deepcopy__, and IntegralSiteCoordinateRep.__repr__
  • Added usage documentation for Structure manipulation and input / output

Changed

  • Changed IntegralSiteCoordinate.__str__ to IntegralSiteCoordinate.__repr__ and changed the output from "b, i j k" to "[b, i, j, k]"
  • Changed xtal::make_point_group to remove the symmetrized_with_fractional step.
  • Changed construction of factor group translations to set components very close to zero (absolute value less than tol * 1e-5) to exactly zero.

Fixed

  • Make a user-defined CASM::xtal::SymInfo copy constructor so that member xtal::Coordinate have the correct "home" lattice

[2.0a10] - 2024-07-12

Changed

  • Clarified documentation for libcasm.xtal.Lattice.is_equivalent_to
  • Wheels compiled with numpy>=2.0.0
  • Run github actions on push, pull_request, and weekly
  • Use ruff NPY201

[2.0a9] - 2024-03-13

Fixed

  • Fix CASM::xtal::make_primitive, which was not copying unique_names. This also fixes the output of libcasm.xtal.make_primitive which was losing the occ_dof list as a result.
  • Fix JSON output of xtal::BasicStructure site label
  • Changed pseudoinverse calculation for basis changes to completeOrthogonalDecomposition().pseudoInverse()

Changed

  • Changed make_primitive to act on either Prim or Structure.
  • Changed default of xtal.Structure.to_dict to output in fractional coordinates
  • Added excluded_species and frac parameters to xtal.Structure.to_dict

Added

  • Add to libcasm.xtal: make_primitive_prim (equivalent to current make_primitive), make_primitive_structure, and make_canonical_structure.
  • Add options to the BCC and FCC structure factory functions in libcasm.xtal.structures to make the conventional cubic unit cells.
  • Add to libcasm.xtal: StructureAtomInfo namedtuple, and methods sort_structure_by_atom_info, sort_structure_by_atom_type, sort_structure_by_atom_coordinate_frac, and sort_structure_by_atom_coordinate_cart
  • Add to libcasm.xtal: substitute_structure_species
  • Add to libcasm.xtal.Prim: method labels, constructor parameter labels
  • Add to libcasm.xtal.Lattice: methods reciprocal, volume, lengths_and_angles, from_lengths_and_angles
  • Added unit_cell, diagonal_only, and fixed_shape parameters to libcasm.xtal.enumerate_superlattices.
  • Add to libcasm.xtal: combine_structures, filter_structure_by_atom_info, make_structure_atom_info, and make_structure_from_atom_info

[2.0a8] - 2023-11-15

Changed

  • Updated docs for PyData Sphinx Theme 0.14.3, particularly dark theme colors and logo

Fixed

  • Fixed broken docs links to xtal.SymOp
  • Fixed return type docs

Deprecated

  • The to_json and from_json methods of xtal.Prim, xtal.Structure, and xtal.SymInfo are deprecated in favor of the to_dict / from_dict methods and the builtin json module

[2.0a7] - 2023-11-14

Changed

  • Add py::is_operator() in the bindings of the __mul__ operators xtal.SymOp and xtal.IntegralSiteCoordinateRep so it possible to add __rmul__ operators to classes in other modules.

[2.0a6] - 2023-11-07

Changed

  • Allow integer array parameters to be either C or F ordered numpy arrays.
  • Added Lattice to CASM::xtal::SymInfo to avoid bad pointers in Coordinate members
  • Changed Prim.lattice and Structure.lattice docs to specify that the lattice is returned as a copy.

[2.0a5] - 2023-10-25

Added

  • Added SymOp.matrix_rep to get matrix representations for transforming CASM-supported properties in the standard basis

Changed

  • Do not allow automatic conversion from floating point arrays to integer Eigen objects.
  • Added a parameter, mode, to Structure.from_poscar and Structure.from_poscar_str to specify whether the POSCAR should be read as atoms, molecules, or both. The default was set to "atoms". Previous behavior was equivalent to using "both".

Fixed

  • Fixed the xtal::Site::dof error message thrown when the requested DoF type does not exist on the site
  • Updated documentation for the local_dofs parameters in libcasm.xtal.prims

[2.0a4] - 2023-09-29

Fixed

  • Fixed xtal::Site::has_dof to check for either occ or continuous DoF

[2.0a3] - 2023-08-11

This release separates out casm/crystallography from CASM v1, in particular removing remaining dependencies on casm/symmetry for constructing symmetry representations and getting basic symmetry operation info. It creates a Python package, libcasm.xtal, that enables using casm/crystallography and may be installed via pip install, using scikit-build, CMake, and pybind11. This release also includes usage and API documentation for using libcasm.xtal, built using Sphinx.

Added

  • Added xtal::SymOpSortKeyCompare for sorting xtal::SymOp
  • Added xtal::make_crystal_point_group to make the crystal point group from a sorted_factor_group (std::vectorxtal::SymOp)
  • Added xtal::make_internal_translations to get translations from the factor group
  • Added standalone methods xtal::fast_pbc_displacement_cart and xtal::robust_pbc_displacement_cart using Eigen::Vector3d for coordinates
  • Added xtal::Molecule::identical overload for checking for identical Molecule up to a permutation
  • Added OccupantDoFIsEquivalent::atom_position_perm to get Molecule atom position permuation
  • Added xtal::make_simple_structure from a POSCAR stream
  • Added xtal::apply and xtal::copy_apply methods for transforming xtal::SimpleStructure including properties
  • Added xtal::make_inverse for xtal::SymOp
  • Added xtal::is_equivalent for comparing xtal::SimpleStructure
  • Added Python package libcasm.xtal to use CASM crystallography methods for building lattices, structures, and parent crystal structures and allowed degrees of freedom (prim); enumerating superlattices; creating superstructures; finding primitive and reduced cells; and determining symmetry operations.
  • Added scikit-build, CMake, and pybind11 build process
  • Added GitHub Actions for unit testing
  • Added GitHub Action build_wheels.yml for Python x86_64 wheel building using cibuildwheel
  • Added Cirrus-CI .cirrus.yml for Python aarch64 and arm64 wheel building using cibuildwheel
  • Added Python documentation

Changed

  • Moved StrainConverter into crystallography, removing symmetry dependencies
  • Moved SymInfo into crystallography from symmetry, using only xtal::SymOp
  • Moved class SymBasisPermute from symmetry to struct UnitCellCoordRep

Removed

  • Removed autotools build process
  • Removed boost dependencies