Atomman

- **atomman.lammps.Log** bug fix for properly reading performance data
for restart runs.

- **atomman.library** and **atomman.settings** modules updated to reflect
the reworked potentials package version 0.3.0.

- **atomman.load_lammps_potential** and **atomman.load** options 'prototype'
and 'crystal' updated for the new library module. load style
'dft_reference' added.

- **atomman.lammps.Potential** now is a function that returns either a
potentials.record.PotentialLAMMPS or potentials.record.PotentialLAMMPSKIM
object.

- **atomman.lammps.run** now has options for passing string input scripts
rather than reading from files, and for turning off log file output.
**atomman.lammps.checkversion** simplified due to the changes to run.

- **atomman.cluster.BondAngleMap** added for characterizing the three-body
interactions as predicted by interatomic potentials.

- **atomman.tools.atomic_info** updated for recently assigned element names
and to be more lenient for isotopes.

- **atomman.dump.atom_data** updated to support using kim commands for kim
model potentials.

- **atomman.dump.lammps_commands** added - NOT DEBUGGED FOR
NON-CUBIC/ORTHORHOMBIC SYSTEMS!

- **atomman.defect.GammaSurface** updates and fixes related to the units
parameters for the plotting methods.

- **atomman.defect.SDVPN** bug fixes related to model() generation, loading,
and the units parameters for the plotting methods.

- **atomman.Settings** is now a renaming/import of potentials.Settings.

- **atomman.defect.Dislocation** class added that handles the generation of
dislocation monopole and periodic array of dislocation atomic configurations
in a more user-friendly interface than the previous functions.

- **atomman.region.PlaneSet** class added that allows for a region/shape to be
defined using a list of planes. This allows for the construction of
multi-faceted and/or open-ended shapes.

- **atomman.Box.planes** changed so that the order of the planes returned is
consistent with the underlying indices.

- **atomman.build_lammps_potential** inherited from potentials package.

- **System.r0** added which finds the shortest interatomic spacing.

- **System.rotate** made more robust.

- **atomman.tools.miller.plane_crystal_to_cartesian** added that identifies
the Cartesian normal associated with a crystallographic plane.

- **atomman.lammps.Potential** made consistent with
potentials.LAMMPSPotential. Upcoming versions of atomman will have
potentials as a requirement eliminating the duplication: (this class will
simply be a renaming of the class from potentials).

- **atomman.lammps.LammpsError** error type added.

- **atomman.defect.dislocation_system_basis** and
**atomman.defect.dislocation_system_transform** functions added supporting
the identification of dislocation system orientations based on
material-specific parameters.

- The "n" parameter in **atomman.defect.free_surface_basis** was renamed to
maxindex consistency with the new dislocation_system functions.

- **atomman.defect.VolterraDislocation**, **atomman.defect.Stroh**,
**atomman.defect.IsotropicVolterraDislocation**, and
**atomman.defect.solve_volterra_dislocation** were updated by integrating in
the dislocation_system functions. This makes it possible to now easily define
dislocation solutions based on the slip plane, line direction and Burgers
vector alone.

- **atomman.defect.dislocation_periodic_array** was updated to add an old_id
parameter to the returned dislocation system making it easier to map the atoms
in the defect system back to the perfect crystal base system used during
construction.

- **atomman.defect.FreeSurface** class for generating free surface
configurations from a unit cell and (hkl) plane was added.

- **atomman.defect.StackingFault** class completely rebuilt as a subclass of
FreeSurface to make it easier to use, i.e. systems can be generated directly
from unit cell, (hkl) and shift values.

- **atomman.defect.DifferentialDisplacement** class created. This class offers
more plotting options than the old differential_displacement function while
dividing the calculation and plotting into separate steps to make it easier
to work with.

- **atomman.defect.SDVPN** class updated to allow for VolterraDislocation
objects to be directly used as input parameters. This makes it easier to
work with as the transformations between dislocation orientations and gamma
surface orientations can be automatically identified and handled.
Additionally, solution summary and plotting tools incorporated into the
class for convenience.