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UPDATES.rst

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Updates

Version 1.3.1

  • Atoms.prop_atype updated for new atype handling.
  • defect.GammaSurface default plotting behavior improved.

Version 1.3.0

  • Support for Python < 3.6 removed. Python 2 support removed due to its imminent end at the new year. Minimal version of 3.6 selected to take advantage of f-strings.

  • Atoms and System natype, atypes behavior changed to allow for unassigned atype values and/or symbols. Now, atype values must be > 0 and natypes = max(atype). CAUTION: this could conceivably break backwards compatibility.

  • lammps.Potential expanded.

    • allsymbols property added to support pair_styles that require all symbols to be listed in the pair_coeff lines even if they are not used.
    • status property added that indicates if the potential is known to have been superseded by a newer version or retracted for being invalid.
    • pair_info now supports an optional masses parameter for overriding default mass values.

  • load.atom_data now recognizes image flags in the Atoms tables, and reads values from the Masses tables. Parameter checking is performed allowing for more informative errors to be thrown.

  • dump.atom_data updated to allow Potential objects to be passed directly, and for pair_info to be included in the generated info LAMMPS input lines.

  • System.masses attribute added. This is used for saving mass values from load.atom_data, and for overriding default Potential.masses values in dump.atom_data.

  • defect.dislocation_array debugged, documented, and made consistent with Volterra solutions.

  • defect.IsotropicVolterraDislocation displacements fixed and adjusted to predict displacements and stresses consistent with values from defect.Stroh.

  • defect.solve_volterra_dislocation simplified to remove unnecessary pre-check of elastic constants.

  • region submodule added that allows for geometries in space to be defined and used to slice systems and per-atom properties.

  • Box is now a subclass of region.Shape allowing it to be used for region-based selection as well.

Version 1.2.8

  • defect.GammaSurface support added for setting shift vectors using Miller-Bravais 4-term vectors.
  • tools.duplicates_allclose added that identifies unique value sets based on absolute tolerances.
  • load('phonopy'), System.dump('phonopy') bug fixes.
  • System.atoms_ix compatibility checks changed and reduced from throwing an error to throwing a warning.
  • Atoms.extend and System.atoms_extend methods added for adding atoms to existing Atoms/System objects.

Version 1.2.7

  • Atoms.model and Box.model added to create/read data model representations of the objects.
  • System.composition added that returns string composition.
  • System.model, load('system_model'), System.dump('system_model') data model format improved to capture all system information.
  • tools.Miller functions for converting between Miller and Miller-Bravais crystal planes.
  • defect.GammaSurface combining of multiple plots better supported.
  • defect.StackingFault minimum r parameter added allowing all atoms to be at least a certain distance apart.
  • defect.free_surface_basis added for identifying system orientations associated with free surface configurations.

Version 1.2.6

  • lammps.NEBLog added for nudged elastic band calculation log files.
  • tools.Miller transformations now all take float values and primitive-conventional cell conversions added.
  • Box.volume bug fix to ensure returned volume is always positive.
  • defect.StackingFault stacking fault configuration generator added.
  • nlist, dvect, dmag, defect.slip_vector routines improved using Cython, alternate implementations of routines removed.

Version 1.2.5

  • Box.volume parameter added. Also, new class methods for initializing boxes based on crystal systems (cubic, hexagonal, etc.).
  • load('poscar') now supports excess per-atom lines.
  • System.atoms_ix added for indexing atoms at the system level.
  • defect.GammaSurface reworked with improved design and features.

Version 1.2.4

  • Atoms.prop_atype() added to allow properties to be assigned by prop_atype.
  • ElasticConstants.normalized_as() and ElasticConstants.is_normal() added to force/check crystallographic symmetry of elastic tensors.
  • load('atom_data') updated to support reading files containing # comments.
  • lammps.Potential now supports specifying potentials with static charges.
  • defect.IsotropicVolterraDislocation class added as defect.Stroh could not calculate isotropic solutions. Both classes are now children of defect.VolterraDislocation, and wrapper function defect.solve_volterra_dislocation() has been added.
  • defect.dislocation_array() added that transforms a bulk system into a periodic array of dislocations, where the two system boundaries in the slip plane are periodic, and the third boundary is not.
  • defect.differential_displacement() updated to provide users more options and control over the plots.
  • MANIFEST.in corrected so non-code files should be properly copied during installation.

Version 1.2.3

  • load() updated with more uniform parameters across the different styles. Style 'phonopy_Atoms' added.
  • System.wrap() made slightly more robust.

Version 1.2.2

  • System scale/unscale bug fix.
  • defect.GammaSurface.model() returned format improved for saving/loading results.
  • load('system_model') updated with symbols parameter.

Version 1.2.1

  • Corrections to setup.py for properly loading/building cython code.

Version 1.2.0

  • Overhaul for Python 2/3 compatibility.
  • Reorganization of code and renaming of some features.
  • Cython routines added for dvect and neighbor list calculations.
  • Improved documentation.