Changelog

New in release (0.10.1) [20/01/2023]

• Support for continuation and restarting of magres workflows (#306)

• Fix for CASTEP scraper to scrape both constrained and unconstrained stress tensors when both are present (#312)

New in release (0.10.0) [26/10/2022]

This release contains many accumulated changes over the course of a year. The library is now primarily in maintenance mode unless new features are contributed by others.

• Added a ray-tracing crystal visualisation module based on the Fresnel library.

• Refinements of almost all plotting types and styles, as well as making it easier to plot multiple comparative plots on the same figure (e.g., multiple phase diagrams computed with different functionals or from different sources).

• Added the matador.magres() module for referencing NMR calculations against experimental data.

• Optimised the CASTEP output reader for long concatenated geometry optimisations.

• Minimal integration with OPTIMADE by being able to download an OPTIMADE structure from a URL as a matador object.

• Support for Python 3.10

• Bug fixes for scrapers, densities of states plotting and scattering simulations.

New in release (0.9.11) [03/06/2021]

• Minor change: allow specification of arbitrary strings for CASTEP pseudopotential libraries (#156).

• Bug fix: standardize_cell script failing to use default symmetry tolerance value (#157).

• Bug fix: scraping of .cif files with single atoms and no symmetries (#173)

• Bug fix: scraping of Hubbard U values from .castep files, and associated bugs when performing relaxations with Hubbard U (#180)

• Dependency updates and Python 3.6 deprecation warning (#158, #181)

New in release (0.9.10) [23/02/2021]

• Windows compatibility changes (#149)

• Dependency updates (#146, #148, #149)

New in release (0.9.9) [16/10/2020]

• Added support for CASTEP kpoint path BREAK directive (#107)

• Improvements to magres plotting and magres workflow (#112)

• Added ability to scrape electric field gradient values and compute quadrupolar quantities from NMR calculations (#115)

• Added ability to run all several examples under Binder (#106, #130).

• JOSS paper accepted! (#129)

New in release (0.9.8) [10/08/2020]

• Improvements to PDIS functionality (#94).

  • Rasterized scatter points for more efficient exporting and fewer graphical artifacts

  • Made underlying matador.plotting.spectral_plotting.dos_plot() and matador.plotting.spectral_plotting.dispersion_plot() more API friendly, and added example notebook.

  • Fixed bug in cell scraping for old BS_* style keywords.

• Improvements to magres functionality, including scraping of units (#90)

• Example notebooks that do not need external data/databases are now run as part of CI (#91).

• New workflow for NMR calculations and refactoring of old workflows (#96).

  • New workflow performs relaxation and high-quality SCF before NMR calculation.

  • Old workflows refactored and improved to enforce certain required parameters for e.g. checkpointing.

  • Enabled phonon workflow for CASTEP PHONON+EFIELD task.

  • Made file scrapers less dependent on file type.

• Updated CASTEP parameter list to 20.1 (#97).

• Tweaked spectral plotting defaults, including --colours flag to dispersion script (#98).

New in release (0.9.7) [29/07/2020]

• Bug fixes to problems introduced in 0.9.6.

• Cosmetic fixes to logging and misleading status reports in workflows.

New in release (0.9.6) [28/07/2020]

• Improvements to ASE and pymatgen interoperability (#80)

• Fixed bug in matador.hull.TemperatureDependentHull which would crash when not provided a list of temperatures (#82).

• Added plotting functions for magres data, and improved its handling inside matador.crystal.Crystal (#79).

New in release (0.9.5) [25/06/2020]

• This release is mostly to trigger Zenodo archiving.

• Updated README and tests for recent Python versions.

New in release (0.9.4) [08/06/2020]

• Fixed flag help strings for pxrd_calculator (#65)

• Changed default PDF broadening for 3x speedup (#65)

• Reverted cpu_count to use version that works correctly in most cases, by chance (#66).

New in release (0.9.3) [07/06/2020]

• Fixes for the CIF reader: now works with awkward linebreaks and alternative symmetry operation specifications (#61).

• Added several new flags to pxrd_calculator script (#60 and 61).

• Usability fixes for spectral_plotting in the case of projected dispersion curves (#59).

New in release (0.9.2) [01/06/2020]

• Optimised CIF reader considerably (#50)

• Updated PXRD calculator to allow for partial occupancy, monochromated beam angles and text export, and added pxrd_calculator script for convenience when handling CIF files.

• Added ability to choose which projectors are plotted with dispersion (#47)

• Various minor fixes and updates:

  • Updates to docs for CLI and configuration.

  • Allow nan-values to be reset inside matador.crystal.Crystal.

  • Fixed display ordering of fingerprint-filtered cursors.

New in release (0.9.1) [20/05/2020]

• Fixed issue with local pip installs after 0.9 release

• Fixed issue with multi-node MPI tasks by switching to proc.communicate() after an initial polling stage (#37)

• Fixed issue where bands would be reordered multiple times in spectral plots (#40)

• Tweaked spectral plot defaults (#40)

• Replaced multiprocessing.cpu_count() calls with psutil.cpu_count(logical=False) to avoid double-counting hyperthreaded cores

New in release (0.9) [15/05/2020]

• 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 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 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 matador.compute module to allow for extension to new codes via 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

New in release (0.8b) [03/08/2018]

• Wholesale changes, complete refactoring of most of the code.

• Released open source under the MIT license!

• Documentation now hosted on readthedocs,

• Workflows: chaining up job steps with run3:

  • spectral and phonons (combined DOS, dispersion calculations) with automated kpoint paths.

  • bulk modulus calculations and EOS fitting.

• New tutorials:

  • Geometry optimisations with run3

• Temperature-dependent convex hulls (thanks to Angela Harper).

• New per-used configuration that allows changing of plotting styles, colourschemes, database names etc.

• Improvements to compute module:

  • automatically handle walltime constraints for Slurm and PBS.

  • estimate memory usage with CASTEP and skip if exceeds machine capacity,

• All CASTEP 18 keywords supported.

• Better support for electronic structure data, OptaDOS, NMR calculations, CIF files, partial occupancy.

New in version (0.7b) [13/04/2017]

• Ternary voltage curves.

• Similarity/uniqueness filtering with element-projected PDFs.

• Updated compute engine for remote calculations (see compute.py and new script oddjob).

• Improved test suite and full pip compatiblity.

• Many bugfixes and usability changes.

New in version (0.6b) [01/06/2017]

• Intercalation voltage curves, e.g. matador voltage -c Li:SnS2.

• Ternary phase diagrams with heatmaps for structure prediction sampling, gravimetric capacity and formation enthalpy matador hull -c ABC --sampmap --efmap --capmap.

• Substructural similarity interface with Can Kocer’s code, as proposed by Yang et al., PRB (2014).