Releases | Open Source Science

doped - 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.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] 9 months ago

doped - 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 https://github.com/SMTG-Bham/doped/pull/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).

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 1 year ago

doped - 2.4.7

Update doping/carrier concentration functions to be more accurate and robust (following logic discussed here: https://github.com/materialsproject/pymatgen/pull/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.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

doped - 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.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

doped - 2.4.5

Enforce shakenbreak>=2.3.4 requirement.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

doped - 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.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

doped - 2.4.3

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

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

doped - 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. https://github.com/SMTG-Bham/doped/issues/68)
Minor efficiency & robustness updates

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

doped - 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

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

doped - JOSS Release

Release of doped to be archived on Zenodo, for the JOSS paper.

Comprises doped version 2.4.0, along with minor updates to documentation and warnings as suggested in the JOSS review.

Scientific Software - Peer-reviewed - Python
Published by kavanase almost 2 years ago

doped - 2.4.0

Electronic structure analysis by @adair-nicolson & @kavanase:
- Adds DefectEntry.get_eigenvalue_analysis() method to plot single-particle eigenvalues and analyse orbital character and localisation; usage and examples shown on the docs Tips <https://doped.readthedocs.io/en/latest/Tips.html#eigenvalue-electronic-structure-analysis>__ page and the advanced analysis tutorial <https://doped.readthedocs.io/en/latest/advanced_analysis_tutorial.html#eigenvalue-electronic-structure-analysis>__.
- Projected eigenvalues can be parsed from vasprun.xml(.gz) files (preferred, as more accurate with 4 decimal places; c.f. 3 in PROCAR(.gz); more convenient and only ~5% slower) or PROCAR(.gz) files in calculation directories (both with significantly expedited parsing compared to pymatgen methods). Compatible with spin-polarised, unpolarised and SOC calculations. Comes with update by @kavanase to easyunfold PROCAR.gz parsing.
More efficient defect calculation parsing
Add get_magnetization_from_vasprun and get_nelect_from_vasprun functions to doped.utils.parsing, as these attributes are not available from pymatgen.io.vasp.outputs.Vasprun.
Improve testing efficiency

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

doped - 2.3.3

General robustness updates:
- Updated file parsing to avoid hidden files.
- Sanity check in DefectsGenerator if input symmetry is P1.
- Add NKRED to INCAR mismatch tests.
- Re-parse config & spin degeneracies in concentration/symmetry functions if data not already present (if user is porting DefectEntrys from older doped versions or manually).
- Avoid unnecessary DeprecationWarnings
Updated docs and linting

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

doped - 2.3.2

Update to match breaking change in pymatgen==2024.3.1 (released today), handling incar_params.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

doped - 2.3.1

Refactor (phase diagram) facet to (chemical potential) limit in doped chemical potential functions, as this is more intuitive for most users.
Tests updates.
Minor efficiency/verbosity/robustness/docs improvements.
Update default KPOINTS for convergence/production runs in chemical_potentials based on testing.
Add optional projections of site displacements upon given vectors by @ireaml

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

doped - 2.3.0

DefectsThermodynamics class has been added to replace and greatly expand the functionality of the DefectPhaseDiagram object. See tutorials for functionality and usage (plotting, Fermi level / concentration analysis, dopability, transition levels (with/out metastable etc).
Overhaul supercell generation as discussed, now optimises directly off minimum periodic image distance (thanks to efficient optimisation algorithm) with some prudent constraints. Significantly reduces supercell sizes required in most cases.
Overhaul defect grouping as discussed, to use the distance between equivalent defect sites (with this controllable via the dist_tol parameter).
Add point symmetry and orientational/spin degeneracy parsing, automatically included in thermodynamics analysis (and customisable by user).
Many efficiency improvements (particularly in defect & input file generation, and symmetry functions).
Check and warning for large defect displacements far from defect site.
Site displacement (local strain) plotting by @ireaml 🙌
Auto determination of X-poor/rich facets.
More control over site selection for eFNV correction.
Clean, grouped parsing warnings for DefectsParser (in case many warnings...)
__repr__ methods for all doped classes for informative outputs.
Tests and tutorials updates.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 2 years ago