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ml-evs/matador: v0.9.0

Abstract

Version 0.9 PyPI release! Can now install with pip install matador-db (unfortunately matador was taken, but they are sufficiently orthogonal that the package name matador is retained here. Much improved code structure and many additional classes that wrap the raw calculation dictionaries for e.g. matador.crystal.Crystal and spectral classes. New module matador.orm containing useful models for data handling. matador.orm.orm.DataContainer as a base class that allows for easy access to underlying dictionaries. matador.orm.spectral module that contains many useful classes for manipulating and plotting e.g. bandstructures, DOS and finite temperature properties. New features in :mod:matador.hull module: Pseudo-ternary phase diagrams (building towards arbitrary n-dimensional phase diagrams). matador.hull.EnsembleHull class and submodule to support the Bayesian Error Estimate Functional (BEEF) and finite temperature phase diagrams. Refactoring of hull calculation into light-weight matador.hull.PhaseDiagram class. Finite temperature hulls based on matador.hull.EnsembleHull with matador.hull.TemperatureDependentHull. Refactored old PDF similarity module into new module :mod:matador.fingerprints. Added new fingerprint class, matador.fingerprints.PXRD, with associated plots (thanks for James Darby for some initial code). Defaults calibrated with GSAS-II. matador.fingerprints.PDF sped up by an order of magnitude using numba. matador.workflows.castep.CastepSpectralWorkflow extended to include latest projected dispersion curve developments from OptaDOS, with associated projected dispersion plots (see tutorial). Updated dispersion script to automatically perform naive Gaussian smearing if OptaDOS output not detected. Abstracted and simplified :mod:matador.compute module to allow for extension to new codes via :mod:matador.compute.calculators submodule. Should now be more robust and transferrable, with many HPC environments automatically detected. Added --scratch_prefix to run3 to allow for temporary files to e.g. be written to faster filesystem with appropriate symlinks to work folder. All CASTEP 19 keywords supported, as well as devel_code blocks. Several new tests: coverage now around 75% when CASTEP is available. New tutorials: MongoDB setup Spectral calculations with run3 Example notebooks

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