Atomec

Changelog:

Bugfixes (code)
* Error in calculation of Hartree potential fixed (incorrect synchronization of lower and upper integrals): means fewer grid points required for convergence (196)
* Error in the matrix solver which makes the initial guess for the eigenvalues fixed (199)

Bugfixes (other - test suite, CI, etc.)
* Rename tests so that pytest sees all tests (204)
* Make `mixfrac` explicitly re-defined in each test, as this was causing occasional failures (206)
* Update package requirements in docs to make them more up-to-date (210)

New features and improvements (code)
* Square-root grid implemented: usually requires many fewer points for converged calculations (179)
* Explicit use of diagonal matrices in numerov solver: yields massive speed-ups and reduced memory requirements (194)
* Speed-up for Hartree potential calculation (198)
* Update to a better set of defaults (201)
* Allow faster convergence after 2 SCF cycles (205)
* Add method B for virial pressure in kinetic energy calculation (180)
* Allow suppression of some warnings (208)
* Update stated temperature range of atoMEC (209)

New features and improvements (other - test suite, CI, etc.)
* Change installation of libxc: we now install from the official libxc latest stable tarball, which means atoMEC can be run on more Python versions (and we don't rely on an unofficial wheels distribution) (223)
* Update default Python version to 3.12: it was noticed during benchmarking that atoMEC runs ~20% faster with Python 3.12 compared to Python<=3.11 (212 - just the final commit)
* Introduce (optional) development tests to benchmark performance (215)
* Update out-of-date information in the README (214) and improve it (188)
* Improve manual running of test suite (i.e. running without `pytest`) (192)


**Full Changelog**: https://github.com/atomec-project/atoMEC/compare/v1.3.0...v1.4.0

Changelog:

Bugfixes (code)
* Resolved issue with entropy calculation for very high temperatures (172)
* Fixed the calculation of the type "B" kinetic energy density (173)

Bugfixes (other - test suite, CI, etc.)
* Fixed and updated broken CASUS mirror (170)

New features and improvements (code)
* Added `E_kin` and `E_en` attributes to `EnergyAlt` class (174)
* Added more options for pressure calculations in `postprocess.Pressure` module (175)
* Added `check_orbs` function to `staticKS.Orbitals` to check that the requested number of orbitals is sufficient (176)

New features and improvements (other - test suite, CI, etc.)
* Added codecov to github actions (169)
* Updated CI actions and environments to latest versions (171)

**Full Changelog**: https://github.com/atomec-project/atoMEC/compare/v1.2.0...v1.3.0

Changelog:

Bugfixes

- Automatic publishing to PyPI with new release (119)
- `CalcPressure` function does not permanently alter the `density` and `radius` properties of the `Atom` (126)
- Remove `np.matrix` references (will be deprecated) (137)
- Replace incorrect `if force_bound` call (151)

Improvements

- Test suite created (135) and added to CI (159)
- Chemical potential limits adjust dynamically (157)
- Temporary `joblib` folders have clearer names (138)
- Mean ionization state now property of `StaticKS.Density` object (129)
- Warning boxes added to Sphinx docs (127)

New features

- Band-structure model implemented (123)
- `postprocess.localization` module created, with functionality to calculate the electron localization function (130)
- `postprocess.conductivity` module created, with functionality to compute the Kubo-Greenwood conductivity (139)
- GGA xc-functionals now supported (142)
- Counting approach for mean ionization state (149)
- `postprocess.pressure` module created, with various methods to calculate pressure (150)

Changelog:

- Fixed typos in `CITATION.cff` so that orcid IDs are correctly linked
- Zenodo badge in `README.md` directs to latest version (previously went to `v1.0.0`)

Changelog:

Bug fixes
- Parallelization now works when multiple jobs run simultaneously from same folder (previously data was overwritten)
- Setting `config.numcores` to be a negative number now invokes parallelization (see `joblib` docs for now negative `njobs` are treated)
- KS orbitals are correct at the `ngrid` point (manually propagated from `ngrid -1` point)
- Limits for the integral of the Hartree potential are corrected
- Kinetic energy density at `ngrid` grid point is hardcoded to reasonable value to reduce numerical error
- `calc_v_Hxc` function in `EnergyAlt` class now correctly accounts for the constant shift in the KS potential

Improvements
- Matrix diagonalization in `numerov` module is made more robust and faster thanks to better initial estimate of eigenvalues

New features
- "quantum" is now an accepted argument for the `unbound` parameter in `models.ISModel` class (this treats unbound electrons on same footing as bound ones)
- Famous "dimensionless parameters" of warm dense matter are computed with creation of `Atom` object
- `postprocess` module is added, which contains functionality to compute the inverse participation ratio (IPR)
- New function to compute kinetic energy density with two choices for how it is computed

Changelog:
- First release of `atoMEC`