7. Changelog

7.1. v3.0.1 - Dec 18, 2024

  • New features

    • Add GDSMFB thermal functional (thanks to @theonov13)

    • Improve HDF5 extra

      • Proper dataset and group creation

      • Support compression

      • Recognize more file types

    • Weekly builds

    • Produce PyPI and Docker build attestations

  • Miscellaneous

    • Miscellaneous CI improvements

    • Migrate from pip to uv in Docker and CI

    • Update Docker image to Python 3.13

      • Use Jupyter lab instead of notebook

7.2. v3.0.0 - Oct 28, 2024

  • New features

    • eminus preprint release!

    • Full type hint support!

    • Rewritten minimizer

      • Massive speedup for more k-points

      • Fixed some convergence issues

    • Add non-iterative SCDM localization

      • Use them as the initial guess for Wannier localization

      • Use Wannier orbital COMs for FLO generations if no FODs are given

    • Add magnetization functions

    • Add POSCAR read and write functions

    • Add a simple HDF5 file extra

    • Allow setting of external functional parameters (internal and in pylibxc)

  • Coding style

    • Reformat the codebase using Ruff

    • Activate more linting rules

    • Add SPDX license identifiers

    • Modernize CI pipelines

    • Add CI release pipelines

    • Move tox.ini and setup.py contents to pyproject.toml

    • Merge all handle_k decorators into one

  • Miscellaneous

    • Fix hexagonal grid generation

    • Fix gradient convergence check, get_ip, and Efermi in extras/viewer

    • Allow plotting densities in viewer functions for all unit cell types

    • Add an option to plot both spin channels in band structure plots

    • Add DOS calculation and plot functions

    • Add an isovalue keyword to the density viewer

    • Reduce the default surfaces from 20 to 10 in the density viewer to improve performance

    • Add pass-through keyword arguments in the Cell creation

    • Add view and write class methods to Atoms, SCF, and KPoints objects

    • Set default values for uninitialized SCF attributes to None

    • Mark the log attribute as private in Atoms and SCF classes

    • Sync GTH files (this changes values for Na-q9)

    • Small tests improvements

    • Update Docker image to Python 3.12

    • Indicate Python 3.13 support

    • Use Python 3.13 as the CI base image

    • Add an eminus Discord server

    • Add citation information

  • Breaking

    • Cleanup main namespace by only including unified read and write functions

    • The rewritten minimizer will change the convergence behavior of some systems!

7.3. v2.7.1 - Feb 09, 2024

  • New features

    • Stabilize Fermi smearing!

  • Updated docs

    • Restyle many documentation pages

    • Add a citation page

    • Add an overview page with a workflow example

    • Add a smearing example

  • Miscellaneous

    • Small performance improvements

    • Temperature unit conversion functions

    • Tests for the smearing implementation

    • Update Ruff rules

    • Misc coding style updates

7.4. v2.7.0 - Jan 19, 2024

  • New features
    • Add k-points!

      • Add k-point dependent calculations

      • Add a k-points object

      • Add a band structure, k-point, and Brillouin zone viewer

      • Add minimization functions for fixed Hamiltonians

    • Add a symmetry extra to symmetrize k-points

  • Updated docs

    • Add k-point examples

    • Increase coverage precision

  • Coding style

    • Activate several Ruff rules

    • Lint check notebooks

    • Rewrite operator handling

    • Add a lot of new tests

  • Miscellaneous

    • Add a contour line viewer

    • Plot lattice vectors in the view_atoms function

    • Add a NixOS CI test

    • Add a Nix lock file

    • Use Python 3.12 as the CI base image

    • Move Matplotlib to dev extras

    • Unpin the notebook version

    • Small performance improvements, e.g, in Atoms object creation

  • Experimental

    • Smearing functionalities

7.5. v2.6.1 - Oct 04, 2023

  • New features

    • Add a Cell generation function

    • Add k-point generation functionalities

    • Add support to handle trajectory files

  • Updated docs

    • Add a FOD optimization and a reduced density gradient example

    • Add references to data

  • Miscellaneous
    • Breaking

      • Rename X to pos in Atoms

      • Merge R into a in Atoms

    • Indicate Python 3.12 support

    • Support viewing multiple files

    • Support non-cubic cells in Atoms, io, and viewer functions

    • Support viewing trajectory files

    • Fix Nix flake

7.6. v2.6.0 - Aug 07, 2023

  • New features
    • Complete rewrite of the Atoms and SCF classes

      • Easily allow systems with different charge or multiplicity

      • Document all public properties

      • Use properties when parsing input arguments

      • Allow direct setting of attributes

      • Better input handling

      • Use an Occupations object to store electronic states information in Atoms

      • Use a GTH object to store GTH data in SCF

      • Add some properties to the objects, e.g., the volume element dV in Atoms

      • Indicate non-input arguments and non-results as private or read-only

      • Breaking

        • Use unrestricted instead of Nspin

        • Use spin and charge instead of Nstate and f

        • Remove f and s as keyword arguments, can be set after initialization

        • Remove cgform as a keyword argument, use the run function to pass it to minimizers

        • Rename min keyword to opt

        • Merge symmetric with guess

    • Add DFT-D3 dispersion correction as an extra

  • Updated docs

    • Add a theory introduction page

    • Add documentation to module data/constants

    • Add a list of all packages and their respective licenses

    • Re-add documentation of operators to Atoms

    • Add a custom functional example

    • Improve the geometry optimization example

    • Add PNGs to the downloads section

    • Sort attributes groupwise

    • Fix a lot of typos

  • Coding style

    • Type check with mypy

    • Fix a lot of type warnings from mypy

    • Add type hints to scripts in docs and setup.py

    • Rename some arguments to not shadow builtins

  • Miscellaneous
    • Create the eminus-benchmarks repository

      • Move the SimpleDFT example to said repository

    • Small performance improvements, mostly for meta-GGAs

    • Add an error message when attempting to use operators of an unbuilt Atoms object

    • Add Matplotlib to the viewer setup to generate images in the examples

    • More tests, e.g, for different spin and charge states

    • Add a small demo function

7.7. v2.5.0 - Jul 10, 2023

  • New features
    • Add meta-GGA functionals!

      • Use all meta-GGAs that don’t need a Laplacian from Libxc using pylibxc or PySCF

    • Improve minimizer

      • Add new auto minimizer that functions like pccg but can fallback to sd steps

      • Add Dai-Yuan conjugate-gradient form

      • Fancier-looking output from the minimizer

      • Option to converge the gradient norm

      • Print <S^2> after an unrestricted calculation

      • Add eigenenergies to the debug output

    • Improve file viewer

      • Support PDB files

      • Allow usage outside of notebooks

  • Updated docs

    • Update the introduction page in the documentation

    • Upload the HTML coverage report

    • Add a simple geometry optimization example

  • Coding style

    • Simplify H function

    • Simplify minimizer module

    • Reduce McCabe code complexity

    • Switch linter from flake8 to Ruff

    • Comply with different linting rules, e.g., use triple-quotes in docstrings

    • More tests and more coverage

  • Miscellaneous

    • Performance fix by using precomputed values correctly

    • Improve GGA performance

    • Do an unpaired calculation automatically if the system is unpaired

    • Option to use a symmetric initial guess, i.e., the same guess for both spin channels

    • Add trajectory keyword to XYZ and PDB writer to append geometries

    • Read the field data from CUBE files

    • New functions for the

      • Electron localization function (ELF)

      • Positive-definite kinetic energy density

      • Reduced density gradient

      • Expectation value of S^2 and the multiplicity calculated from it

    • Option to set a path to directories containing GTH pseudopotential files

    • The SCF class now contains the xc_type and is_converged variables

    • Support functional parsing using pylibxc

    • Allow using custom densities when using the atoms viewer

    • Remove Gaussian initial guess

    • Remove exc_only keyword from functionals since it was basically unused

    • Fix GTH files not being installed when using the PyPI version

    • Fix mapping of field entries with the respective real-space coordinate

    • Fix GGA SIC evaluation

7.8. v2.4.0 - May 23, 2023

  • New features
    • Add GGA functionals!

      • Add internal PBE, PBEsol, and Chachiyo functionals

      • Option to use all GGAs from Libxc using pylibxc or PySCF

  • Miscellaneous

    • Add Thomas-Fermi and von Weizsaecker kinetic energy density functions

    • Rewrite functionals for better readability

    • Fix Torch operators in some edge cases

    • Merge configuration files in tox.ini

    • Update minimum versions of dependencies

7.9. v2.3.0 - May 02, 2023

  • New features
    • Add Torch powered FFT operators as an extra

      • Up to 20% faster calculations

    • Add a consolidated configuration class

      • Easier configuration and more performance infos

    • Add a complete test suite

      • Add CI/CD coverage reports

    • Nix developer shell support

  • Miscellaneous

    • Rewritten FODs guess function

    • Simplify the FOD interface in io and viewer

    • Fix a plethora of small bugs

    • Update Docker image to Python 3.11

7.10. v2.2.2 - Mar 03, 2023

  • New features

    • Improve performance, i.e, in operators, dotprod, and density calculations

    • Large and/or spin-polarized systems are much faster!

  • Coding style

    • Make Energies a dataclass

  • Miscellaneous

    • Drop Python 3.6 support

    • Raise minimum version SciPy from 1.4 to 1.6

    • Add repository statistics to the PyPI sidebar

7.11. v2.2.1 - Feb 22, 2023

  • Hotfix for the broken PyPI installation

  • Use MANIFEST.in over package_data

  • Skip tests if pylibxc is not installed

7.12. v2.2.0 - Feb 21, 2023

  • New features

    • Supercell Wannier localization

    • Rewritten xc parser

    • Modularize each functional

    • Greatly improve functional performance

    • Add modified functional variants

    • Modularize io module

    • Rewritten save and load functions to use JSON

    • Add a bunch of tests

    • Add a small ASCII logo in the info function

    • Update logo typography

  • Updated docs

    • Add a nomenclature page of commonly used variables

    • Remove the package name from the module headings

    • Document members of classes

    • Add a germanium solid example

  • Coding style

    • More secure coding practices

    • Remove the usage of eval, exec, and pickle

  • Miscellaneous

    • Rename save and load to write_json and read_json

    • Fix PW spin-polarized functional

    • Align Chachiyo functional with Libxc

    • Add a recenter method to the Atoms and SCF class

    • Use pc-1 over pc-0 in the PyCOM extra

    • Add a pyproject.toml

7.13. v2.1.2 - Dec 15, 2022

  • New features

    • Add a Dockerfile and -container

    • Rewrite the grid view function as an atoms viewer

    • Use plotly over VisPy

    • Option to plot densities from SCF objects

  • Updated docs

    • Add Docker instructions under Installation section

    • Update examples to use the new atoms viewer

  • Miscellaneous

    • Unify read, write, and view functions

    • Add an optional density threshold for functionals

    • Add covalent radii and CPK colors to data

    • Add changelog to the PyPI description

    • Fix flake8 configuration file

    • Fix Libxc functional warnings

7.14. v2.1.1 - Oct 24, 2022

  • New features

    • Use the PySCF Libxc interface if pylibxc is not installed

    • Rework the addons/extras functionality inclusion

    • Dependencies can now be installed individually

    • Rework the Atoms object initialization

  • Miscellaneous

    • Test different platforms and more Python versions in CI

    • Add kernel aliases to Atoms and SCF methods

    • Allow mixing Libxc and internal functionals

    • Add platform version in the info function

    • Improve logging in some places

    • Improve file writer formatting

    • Rename addons to extras

    • Rename filehandler to io

    • Update PyPI identifiers (e.g. to display Python 3.11 support)

7.15. v2.1.0 - Sep 19, 2022

  • New features

    • Support for spin-polarized calculations!

    • Rewritten GTH parser to use the CP2K file format

    • This adds support for the elements Ac to Lr

    • Built-in Chachiyo correlation functional

    • New pseudo-random starting guess for comparisons with SimpleDFT

  • Updated docs

    • Improve displaying of examples in the documentation

    • Convert notebooks to HTML pages

    • New overview image

    • Minify pages

  • Miscellaneous

    • Minimal versions for dependencies

    • GUI option for viewer and better examples

    • Rename Ns to Nstate to avoid confusion with Nspin

    • Adapt to newer NumPy RNG generators (use SFC64)

    • Update default numerical parameters

    • Option to set charge directly in atom when calculating single atoms

    • Adapt print precision from convergence tolerance

    • CI tests for the minimal Python version

    • Some code style improvements (e.g. using pathlib over os.path)

    • Misc performance improvements (e.g. in Ylm_real and get_Eewald)

    • Fix some bugs (e.g. the Libxc interface for spin-polarized systems)

7.16. v2.0.0 - May 20, 2022

  • Performance improved by 10-30%

  • New features

    • SCF class

    • Domains

    • Libxc interface

    • Examples

    • CG minimizer

    • Simplify and optimize operators

  • Updated docs

    • New theme with dark mode

    • Add examples, changelog, and license pages

    • Add dev information

    • Enable compression

  • Coding style

    • Improve comments and references

    • A lot of refactoring and renaming

    • Google style docstrings

    • Use loggers

    • Unify coding style

    • Remove legacy code

  • Miscellaneous

    • Improve setup.py

    • More tests

    • Improve readability

    • Fix various bugs

7.17. v1.0.1 - Nov 23, 2021

  • Add branding

  • Fix GTH files not included in PyPI build

7.18. v1.0.0 - Nov 17, 2021

  • Initial release