3.2.0

• Add fast chempot heatmap plotting for arbitrary dimension systems; see https://doped.readthedocs.io/en/latest/chemical_potentials_tutorial.html#analysing-and-visualising-the-chemical-potential-limits
• Modularise DefectsParser in preparation for additional code support (Quantum Espresso; #133)
• Automatically identify dimer bonds in defect supercells and inform user of potential spin polarisation
• Detect cases of matching kpoint grids but mismatching shifts
• Update defect clustering naming behaviour (https://doped.readthedocs.io/en/latest/doped.thermodynamics.html#doped.thermodynamics.name_defect_cluster)
• Updates to be fully compatible with latest pymatgen (#144)
• numpy v2 (and v1) compatibility
• Various robustness updates and improvements.

3.1.0

• Update chemical potentials code:
  • Handle recent breaking changes in pymatgen (Apr 2025).
  • Auto check compatibility of INCAR\s and POTCAR\s in competing phases calculations (as already done for supercell calculations).
  • Merge ExtrinsicCompetingPhases to CompetingPhases
• Directly parse spin magnetisation from VASP outputs, including handling for NCL spins.
• Add site-competition handling in defect concentration functions; usage in this paper <https://doi.org/10.26434/chemrxiv-2025-j44qd>, see docstring <https://doped.readthedocs.io/en/latest/doped.thermodynamics.html#doped.thermodynamics.DefectThermodynamics.get_equilibrium_concentrations>.
• Include 'adsorbate' interstitial sites for structures with significant vacuum volume.
• Avoid multiprocessing errors with python scripts that don't use if __name__ == "__main__": (#105, #108)
• Improved algorithm for defect site clustering (for plotting & concentration analyses).
• Use primitive cell for parsed Defect\s, rather than supercell.
• delta_gap updates:
  • Add delta_gap option to FermiSolver methods
  • Allow delta_gap to be given as a function for temperature-dependent methods
• Many efficiency updates.
• Miscellaneous minor bug fixes, improvements and docs updates.

3.0.0

• Major efficiency updates to most parts of the workflow, mostly implemented as helper functions in
  doped.utils.efficiency and doped.utils.configurations, including:

  • Fast and intelligent structure matching (patching various parts of pymatgen's StructureMatcher code).
  • Voronoi tessellation for interstitial generation
  • Defect generation
  • Wyckoff site detection
  • Defect site detection and matching, including very large supercells.
  • DefectThermodynamics initialisation (and defect grouping by distance between equivalent sites).

• FermiSolver and ChemicalPotentialGrid classes in #46, for
  advanced defect/carrier thermodynamics, allowing various constraints (e.g. mobile/fixed defects / charge
  states etc), with a number of convenience functions (e.g. for scanning temperature / chemical potentials
  etc, optimising output properties over many-dimensional chemical potential spaces etc). Usage
  demonstrated in https://doped.readthedocs.io/en/latest/fermisolver_tutorial.html.

• Add is_shallow DefectEntry property, and DefectThermodynamics._get_in_gap_fermi_level_stability_window
  method. Shallow defect states now automatically excluded from formation energy diagram plots for cleaner
  outputs, controllable with the unstable_entries kwarg. Large charge correction errors for
  shallow/unstable defects (typically higher and a common indication of 'false charge state' behaviour)
  now do not throw a warning during parsing.

• CompetingPhases now compatible with both legacy and new Materials Project APIs, with automatic
  handling (and appropriate warnings) for cases of unstable host materials/compositions.

• Internal overhaul of CompetingPhasesAnalyzer code, using ComputedStructureEntry objects.
  Initialisation now much faster and more convenient, JSON-serializable outputs, further visualisation and
  plotting, and queryability.

• Various robustness improvements, including:

  • Handling mixed-valence systems
  • Handling systems with very large inter-atomic distances.
  • As a robustness test, defect generation for all materials on the Materials Project proceeds
    efficiently and without issue (as performed as part of https://arxiv.org/abs/2412.19330).
  • Improved eigenvalue parsing and comparisons (for automated shallow defect detection).
  • Dynamic adjustment of symprec for edge cases.

• Miscellaneous convenience updates.

• Docs, tutorials and tests updates.

• BETA: Add doped.utils.configurations functions to quickly generate CC diagram structures / initial
  NEB paths for defect transformations, ensuring correct initial orientations (to give shortest path).

2.4.7

• Update doping/carrier concentration functions to be more accurate and robust (following logic discussed
  here: materialsproject/pymatgen#3879).
• Improve reverse-supercell-matrix determination for generate_supercell=False
• Refactor bulk_band_gap_path to bulk_band_gap_vr in DefectsParser/DefectParser,
• Update docstrings to reiterate that bulk supercell VBM is used as VBM reference point for the Fermi level
  by default, unless alternative bulk_band_gap_vr provided.

2.4.6

• Update Defect, DefectEntry and DefectThermodynamics properties/methods to be even more
  efficient with calculations of formation energies and concentrations. Gives ~10x speedup in Fermi
  solving and concentration calculations (e.g. from 2 hours to 12 minutes for 2D chempot vs temp CdTe grid
  in thermodynamics tutorial).
• Avoid unnecessary DeprecationWarnings from latest spglib release.

2.4.5

• Enforce shakenbreak>=2.3.4 requirement.

2.4.4

• Make oxidation state guessing more efficient, semi-significant speed up in generation/parsing for tough cases.
• Add bulk_site_concentration property to DefectEntry, giving the concentration of the corresponding lattice site of that defect in the pristine bulk.
• Minor updates to ensure compatibility with recent pymatgen and ASE releases.

2.4.3

• Remove spglib<=2.0.2 dependency (set to avoid unnecessary warnings), and update installation instructions accordingly.

2.4.2

• Allow cases where the calculated host material is unstable wrt competing phases (above the hull), by downshifting to the hull and warning the user about this.
• General updates to chemical potentials code; more robust (better error catches and messages, API key handling), more informative, cleaner outputs.
• Updates to match recent changes in pymatgen object types (e.g. #68)
• Minor efficiency & robustness updates

2.4.1

• Speed up eigenvalue parsing by using the faster doped site-matching functions rather than MakeDefectStructureInfo from pydefect
• Minor efficiency & robustness updates.
• Minor docs & tutorials updates
• Minor tests updates