Change Log
v.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.
v.2.4.6
Update
Defect
,DefectEntry
andDefectThermodynamics
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
DeprecationWarning``s from latest ``spglib
release.
v.2.4.5
Enforce
shakenbreak>=2.3.4
requirement.
v.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
andASE
releases.
v.2.4.3
Remove
spglib<=2.0.2
dependency (set to avoid unnecessary warnings), and update installation instructions accordingly.
v.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
v.2.4.1
Speed up eigenvalue parsing by using the faster
doped
site-matching functions rather thanMakeDefectStructureInfo
frompydefect
Minor efficiency & robustness updates.
Minor docs & tutorials updates
Minor tests updates
v.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 page and the advanced analysis tutorial.Projected eigenvalues can be parsed from
vasprun.xml(.gz)
files (preferred, as more accurate with 4 decimal places; c.f. 3 inPROCAR(.gz)
; more convenient and only ~5% slower) orPROCAR(.gz)
files in calculation directories (both with significantly expedited parsing compared topymatgen
methods). Compatible with spin-polarised, unpolarised and SOC calculations. Comes with update by @kavanase toeasyunfold
PROCAR.gz
parsing.
More efficient defect calculation parsing
Add
get_magnetization_from_vasprun
andget_nelect_from_vasprun
functions todoped.utils.parsing
, as these attributes are not available frompymatgen.io.vasp.outputs.Vasprun
.Improve testing efficiency
v.2.3.3
- General robustness updates:
Updated file parsing to avoid hidden files.
Sanity check in
DefectsGenerator
if input symmetry isP1
.Add
NKRED
toINCAR
mismatch tests.Re-parse config & spin degeneracies in concentration/symmetry functions if data not already present (if user is porting
DefectEntry``s from older ``doped
versions or manually).Avoid unnecessary ``DeprecationWarning``s
Updated docs and linting
v.2.3.2
Update to match breaking change in
pymatgen==2024.3.1
(released today), handlingincar_params
.
v.2.3.1
Refactor (phase diagram)
facet
to (chemical potential)limit
indoped
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 inchemical_potentials
based on testing.Add optional projections of site displacements upon given vectors by @ireaml
v.2.3.0
DefectsThermodynamics
class has been added to replace and greatly expand the functionality of theDefectPhaseDiagram
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.
v.2.2.0
- Added
DefectsParser
class for parsing defect calculations: Uses multiprocessing and shared bulk data to massively speed up parsing of many defect supercell calcs at once (e.g. from 17 min to < 3 mins for 54 defects in CdTe).
Automatically checks
INCAR
,KPOINTS
,POTCAR
and charge correction compatibility between all calculations, and warns the user if any are likely to affect formation energies.
- Added
Make
csv
input toCompetingPhasesAnalyzer
more flexible, along with other code and docstrings updates.Format point group symbol in formation energy plots.
Refactor
elt
/elt_refs
toel/el_refs
by @adair-nicolsonCharge states can now be automatically determined even when
POTCAR
s are not setup by the user.
Updates reflected in the doped
parsing tutorial.
v.2.1.0
- Update finite-size defect corrections implementations:
pydefect
used directly for eFNV correction (with optimisation for efficiency). Moreover, the fully relaxed defect structure (with defect site determined by doped) is used.FNV correction now uses optimised version of
pymatgen-analysis-defects
implementation.Updated corrections plotting (much nicer formats, more informative etc)
The actual energy error in the correction is now estimated, and the user is warned if this exceeds
error_tolerance
(optional parameter, 0.05 eV by default)Bandfilling corrections no longer automatically calculated as (1) almost always not recommended and (2) will show an example of calculating these if needed using our code in
pymatgen
on the docs
Efficiency improvements in obtaining defect site info (Wyckoff positions)
Additional utils and functions for defect generation and manipulation.
(Many) updated tests.
Added functionality for robustly determining the point group symmetry of _relaxed_ defects 🔥
v.2.0.5
- Update oxi-state handling to:
Use pre-assigned oxi states if present
Handle
pymatgen
oxi-state guessing failures (non-integer oxi states, inaccurate oxi states with max_sites, failures for extremely large systems etc)
Update default
probability_threshold
from 0.01 to 0.0075.Account for rare possibility of user being on a non UTF-8 system.
Italicise “V” for vacancy in plotting.
SMTG-UCL -> SMTG-Bham
Tests and formatting updates.
v.2.0.4
Add supercell re-ordering tests for parsing
Ensure final _relaxed_ defect site (for interstitials and substitutions) is used for finite-size charge corrections
Consolidate functions and input sets with
ShakeNBreak
Update defect generation tests
Use more efficient Wyckoff determination code
v.2.0.3
Sort defect entries in
DefectPhaseDiagram
for deterministic behaviour (particularly for plotting).Tests updates (archive test plots, update extrinsic generation tests etc).
Avoid long stacklevel issue which cropped up in
python3.8
tests forSnB
Update PDF figure
savefig
settings, and add_get_backend
function.
v.2.0.2
Refactor
_check_user_potcars()
toDefectDictSet
rather thanDefectRelaxSet
, and addwrite_input ()
method (which runs_check_user_potcars()
first).Update defect generation tests
Add troubleshooting docs page and update tips docs page
v.2.0.1
Update naming handling in
DefectPhaseDiagram
to be more robust/flexible, following failure case noted by @utf 🙌Ensure package data files are correctly included in the package distribution, again noted by @utf 🙌
Updates to chemical potentials code.
Refactoring of site-matching code.
Tests updates and code cleanup.
v.2.0.0
Major overhaul to rebase onto the new
pymatgen
defects code (>v2022.7.25
).Add documentation (https://doped.readthedocs.io/en/latest)
Add
DefectsGenerator
class with major upgrade in functionality.Add
DefectsSet
classes invasp.py
v.1.1.2
Cap
numpy
to1.23
to avoidpymatgen
dependency issues.Update example workbook to use recommended
CubicSupercellTransformation
Add/remove some
TODO
s
v1.1.1
doped
now installable fromconda-forge
! 🎉- Major overhaul of primary parsing workflow (in
defect_entry_from_paths()
): Automatic charge-state determination (throwing warning when user specification doesn’t match auto-determined)
Automatic charge correction determination and application
Improved error handling and more informative warning messages
- Major overhaul of primary parsing workflow (in
Add
test_defectsmaker.py
,test_corrections.py
andtest_analysis.py
-> significantly improve test coverageAdd
_convert_dielectric_to_tensor()
function to be more flexible to user inputRemove old unsupported/deprecated code.
Add check and warning if multiple output files (
vasprun.xml
/OUTCAR
/LOCPOT
) present in bulk/defect directory.Minor bug fixes, formatting, docstrings improvement, the usual
Add and remove
TODO
s
v1.0.6
Start keeping a
CHANGELOG
README
updates to give step-by-step instructions on setting up MP API key,POTCAR
s forpymatgen
and virtualconda
environments fordoped
andShakeNBreak
Major overhaul of
vasp_input
functions setup to be far more streamlined and customisable.Major overhaul of
chemical_potentials
code; now with improved algorithm for selecting potential competing phasesUpdate of example notebooks
Add tests for parsing calculations, chemical_potentials and vasp_input
Add GH Actions workflows (for tests, GH releases and pypi packaging)
Adopt recommended versioning convention based on dates
General tidy up, docstring padding, formatting and
TODO
addition/removalEnsure all inputs/outputs are
JSON
able, now recommending this for better forward/backward compatibilityRefactor
dope_stuff
toplotting
andanalysis
to be more clear and PROfessional, yoRefactor from hard-coded defaults / slightly-less-human-readable
json
files toyaml
files with default settings.Refactor
defectsmaker
output, more efficient, cleaner and informative