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What's new

.. currentmodule:: crystals

Release 1.7.0

  • Added support for NumPy 2, in addition to NumPy 1.

Release 1.6.2

  • Fixed an issue where the crystals version was not correctly interpolated when writing CIFs (#14).
  • Added file name to some parser warnings (#15).
  • Added support for spglib 2.0.
  • Added explicit testing for Python 3.10 and Python 3.11.

Release 1.6.1

  • Fixed an issue where writing some crystal structures to CIF did not work correctly (#13).

Release 1.6.0

Release 1.5.0

  • Added some typing information.
  • Added the :attr:`Supercell.scaled_lattice_vectors` property and associated documentation (#11).
  • Protein Data Bank downloads are now done through HTTPS rather than FTP, which is recommended by the RCSB data bank.
  • Fixed some documentation formatting.

Release 1.4.1

  • Fixed an issue with the tag attribute of Atom not being propagated properly (#9).

Release 1.4.0

  • Added the ability to read and write POSCAR files from the Vienna Ab initio Simulation Package (VASP). Contributed by Chenxing Luo (#8).

Release 1.3.2

  • Releases are now automatically performed using Github Actions
  • Fixed an issue where uncertainties in atom site occupancy in CIF files would not be parsed correctly (#7).

Release 1.3.1

1.3.0

1.2.2

  • The sorting of AtomicStructure objects is now stable.
  • Fixed an issue where checking the containership of atoms did not work properly.
  • Fixed an issue where downloading structures from the Materials Project failed on macOS/Linux.
  • Code snippets in documentation are now tested for correctness.
  • Tests are now included in the package itself.

1.2.1

  • Fixed deprecations that came with Python 3.9, involving comparison of crystal structures.

1.2.0

  • Added the ability to write crystal structures to CIF/XYZ files with the Crystal.to_cif and Crystal.to_xyz methods. Also, structures can be converted to ASE's Atoms class with Crystal.to_ase. This can be used to convert crystal structures from one format to another!
  • Added the symmetry_reduction function, and associated method Crystal.asymmetric_cell(), to determine the smallest asymmetric cell that generates a unit cell.
  • The method Lattice.bounded_reflections now takes in an additional parameter, min_bound, to find reflections between a lower and upper bound.
  • Fixed an issue where in certain cases, atoms related by symmetry were not pruned appropriately (#5)
  • Official support for Python 3.9.

1.1.2

  • Atom site occupancies are now parsed from CIF files (#3).

1.1.1

  • Orbital instances are now orderable, i.e. Orbital("1s") < Orbital("2p").
  • The Element class can now be initialized from another Element, and also from full atomic names (e.g. "hydrogen"). This simplifies the normalization for input types.
  • Added the ElectronicStructure.outer_shell method to quickly get the outermost shell.

1.1.0

  • Added the ability to describe the electronic structure of atoms using the ElectronicStructure class.

1.0.0

  • Added the ability to set a Materials Project API key as environment variable MATERIALS_PROJECT_API_KEY.
  • Added the Materials Project constructor to the crystals info script.

0.6.7

  • Added the Crystal.from_mp constructor to create crystals through the Materials Project API.
  • Added the method Crystal.indexed_by, which allows to index reflections of a crystal by using another lattice.
  • Re-organized the Crystal class hierarchy to be more specific. This change should not affect anyone.

0.6.6

  • Added command-line utilities, including the crystals info script.

0.6.5

  • New algorithm to determine the lattice vectors from lattice parameters. Results should be the same except in edge cases.
  • Space-group and symmetry information has been inserted into immutable dictionaries
  • Fixed an issue where the parsing of CIF files without Hall symbol would fail because the International Table number was parsed as a string, not an integer.
  • Updated minimum dependency bound on PyCifRW to 4.4.1 because of potential issues with Python 3.7.
  • Refactoring of internal string handling to use f-strings.

0.6.4

  • Crystal.ideal and Crystal.primitive will now preserve subclasses.
  • Crystal.primitive will now always return a new Crystal, even if the Crystal already has a primitive cell.
  • Supercell is no longer a subclass of Crystal. The only recommended way of building supercells is now Crystal.supercell.
  • Lattice.scattering_vector and Lattice.miller_indices now work on single vectors of shape (3,).
  • Added the Lattice.bounded_reflections generator.

0.6.3

  • Added the constructor Crystal.from_pwscf to create crystal instances from output files generated by the Plane-Wave Self-Consistent Field (PWSCF) program.
  • Added the Crystal.ideal method to create idealized crystal structures.
  • Added the Crystal.reciprocal_symmetry_operations method to determine crystal symmetry operations in reciprocal basis.
  • Symmetry-determination via Crystal.symmetry() and related methods now raises a RuntimeError if symmetry-determination fails, rather than returning None
  • Added the Atom.tag property, which can be used to tag Atom instances with extra information. This is for internal use. So far, it is used to label the order of Atoms from a PWSCF output file.

0.6.2

  • Added the Crystal.symmetry_operations method to determine crystal symmetry operations.

0.6.1

  • Fixed an issue where cache directories on MacOS could not be used.
  • CODParser will now try to download files from three Crystallography Open Database mirrors.
  • AtomicStructure and subclasses now support "truthiness", i.e. they are considered False if empty, and True otherwise.
  • Added the AtomicStructure.satisfying method, to extract atoms satisfying a predicate from structures
  • Added the is_element function. It can be used to make AtomicStructure.satisfying more readable.