Atomman

- The structure generation methods of **atomman.defect.Dislocation** now all
have a center parameter that allows for the dislocation's position to be
shifted. This is useful for setting up NEB runs.

- **atomman.lammps.run** now supports lammps_command paths that contain spaces.

- **atomman.defect.Boundary** has been further improved and some supporting
tools developed. Not fully finalized yet.

- **neb_replica** dump style added that creates the atomic configurations used
by LAMMPS for defining the final (and intermediate) replicas.

- More tools and operations related to Miller crystal vectors and planes have
been added. These should make it possible for future revisions of the
defect generators to be simplified and made more uniform.

- Record classes have been updated to support a URL field for assigning
persistent identification (PID) values once uploaded to a CDCS database.

- Import of dump styles is now fully modular and delayed. This allows for
new styles to be introduced that have additional package requirements without
breaking all of atomman. The delayed loading also makes it possible for dump
methods to call other dump or load methods without import errors.

- **atomman.dump.primitive_cell** now works properly because of the above.

- Internal use of **atomman.tools.crystalsystem** functions changed to use the
corresponding **atomman.Box** methods introduced in 1.4.4. instead.

- XSL and XSD files added for the defined record styles to better support
integration of the reference records with potentials.nist.gov.

- **atomman.defect.FreeSurface** now has a unique_shifts() method that uses
crystal symmetry to filter out most symmetrically equivalent termination
planes.

- **atomman.dump.primitive_cell** has been added that uses spglib to take an
atomic system and return a new system corresponding to the identified
primitive unit cell.

- **atomman.dump.phonopy_Atoms** is updated for newer versions of phonopy.

- **strain** methods have been added to **atomman.defect.VolterraDislocation**
and its subclasses to provide the strain associated with the dislocation
solutions. Stress and displacement methods in **atomman.defect.Stroh** have
been adjusted to improve calculation speed.

- **atomman.defect.pn_arctan_disldensity** added and
**atomman.defect.pn_arctan_disregistry** updated for consistency and new
options. These give classic Peierls-Nabarro dislocation width models.

- **load_table** method has been added to **atomman.cluster.BondAngleMap**
allowing for the data generated by save_table to be read back in.

- New methods added to **atomman.Box**

- **reciprocal_vects** method added that computes the reciprocal lattice
vectors associated with the Box's vectors.

- **vector_crystal_to_cartesian** and **plane_crystal_to_cartesian** from
**atomman.tools.miller** have been added as Box methods.

- **position_relative_to_cartesian** replaces **atomman.System.unscale** and
**position_cartesian_to_relative** replaces **atomman.System.scale** as the
new operations are better named and only relate to Box information.

- **identifyfamily**, **iscubic**, **ishexagonal**, **istetragonal**,
**isrhombohedral**, **isorthorhombic**, **ismonoclinic** and
**ismonoclinic** methods added from **atomman.tools**.

- **atomman.region.Plane** has new methods **operate**, **__eq__** and
**isclose** for transforming and comparing Planes.

- **atomman.plot.interpolate_contour** reworked to allow
matplotlib.pyplot.axes to be passed through allowing for the color contour
plots to be added on top of existing plots. Options also added to turn off
features.

- **atomman.defect.DifferentialDisplacement** has new plot_with_nye method that
overlays Nye tensor color contours with the differential displacement plots.

- Overhaul of **atomman.library** operations reflecting that underlying
database handling is now branched off into the separate yabadaba package.

- **Dislocation**, **FreeSurface**, **PointDefect** and **StackingFault**
Record classes related to defect parameter sets have been moved from iprPy
to **atomman.library.record** This is to support future updates where these
parameter sets can be directly passed to the defect generator classes.

- Typing hints added to all of atomman's code.

- **atomman.dump.pymatgen_Structure** updated for new pymatgen versions.

- **atomman.defect.DifferentialDisplacement** bug fix related to handling
the atomcolor and atomcmap parameters.

- **atomman.tools** now imports aslist, iaslist, screen_input, uber_open_rmode,
and atomic_info from potentials to remove duplicate code.

- **atomman.library** various updates related to keeping record handling
consistent with updates in potentials version 0.3.1.