1.6.2

What's Changed

• fix the error in the jumps calculation with minimal_residence by @v1kko in #369

Maintenance

• Update citation listing by @stefsmeets in #367
• Add pdf for workshop to readme by @stefsmeets in #365

Full Changelog: 1.6.1...1.6.2

1.6.1

This release contains bug fixes for 1.6.0

What's Changed

• Add color option to plot_points by @stefsmeets in #357
• Add cmap option to plotly shape function by @stefsmeets in #359
• Add warning if there are no species in range of site by @stefsmeets in #361
• Raise error when disordered structure is passed to Transitions by @stefsmeets in #364

Full Changelog: 1.6.0...1.6.1

1.6.0

What's Changed

• Correct label in radial_distribution_between_species by @AstyLavrinenko in #350
• Bug fixes by @stefsmeets in #355
• Work-around for atoms without label when reading lammps data by @stefsmeets in #356
• Add option to change the colormap for shape analysis by @AstyLavrinenko in #347
• Add polar plot of orientation vectors by @tfamprikis in #358

Full Changelog: 1.5.1...1.6.0

1.5.1

What's Changed

• Refactor radial_distribution_between_species() by @stefsmeets in #340
• Fix all mypy issues by @stefsmeets in #341
• Fix crash in Transitions.occupancy if input sites are disordered by @stefsmeets in #342

Full Changelog: 1.5.0...1.5.1

1.5.0

This is a small update that adds a new plotting method to gemdat.Trajectory.

What's Changed

• Add RDFs calculation based on species by @AstyLavrinenko in #338
• Fix vibration amplitudes plot by @stefsmeets in #336

Maintenance

• Update README.md by @stefsmeets in #334
• Fix coverage badge by @stefsmeets in #332

Full Changelog: 1.4.0...1.5.0

1.4.0

This is a small update that adds GROMACS support and fixes a bug in the rendering of plots with a shaded region.

What's Changed

• Add GROMACS support by @AstyLavrinenko in #330
• Fix shaded rendering for msd plot by @stefsmeets in #331

Full Changelog: 1.3.0...1.4.0

1.3.0

The highlights for this release are:

• All plots have been updated for better clarity and are now available as both matplotlib and plotly varieties. You can choose the backend by passing backend='matplotlib' or backend='plotly' to the plot methods.
• A trajectory reader for LAMMPS data through Trajectory.from_lammps(...)
• A new method to calculate a jump graph from the Jumps class: G = jumps.to_graph(). The edges are tagged with the activation energies.

What's Changed

• Update Orientations api by @stefsmeets in #303
• Update captions for plots by @stefsmeets in #308
• Add option to show shaded area for std by @stefsmeets in #309
• Add plotly plots by @stefsmeets in #313
• Add shortcut for calculating and plotting RDFs by @stefsmeets in #318
• Add option to switch between plotting backends by @stefsmeets in #326
• Add LAMMPS trajectory reader by @stefsmeets in #327
• Add plotly plot for shape by @SCiarella in #324
• Add method to create a graph from jumps by @stefsmeets in #325

Under the hood

• Refactor Pathway class by @stefsmeets in #305

Bug fixes

• Add warning for multiple paths by @SCiarella in #323
• Tweak method names and update default dimensions by @stefsmeets in #301
• Fix rdf plotly test by @stefsmeets in #320
• Fix ruff config by @stefsmeets in #321

Maintanance

• Add zenodo link and how to cite by @stefsmeets in #304
• Minor housekeeping changes by @stefsmeets in #310
• Move legacy.py out of main library by @stefsmeets in #316
• Move to ruff for autoformatting by @stefsmeets in #317

Full Changelog: 1.2.1...1.3.0

1.2.1

What's Changed

• Fix broken publish action by @stefsmeets in #295

Full Changelog: 1.2.0...1.2.1

1.2.0

The highlights for this release are:

• Orientation tracker, with this version of GEMDAT you can track the orientation of a group of atoms (e.g. tetrahedra) in your trajectory and plot them
• Haven ratio calculator

What's Changed

• Added some plotly plots by @v1kko in #278
• Rename all displacement_per_site to displacement_per_atom by @v1kko in #280
• Add orientations tracker by @tfamprikis in #220
• Implement Haven ratio by @stefsmeets in #283
• Add option to select MSD algorithm by @SCiarella in #291
• Improve Orientations API by @SCiarella in #293

Under the hood

• Refactor 3d plots module by @stefsmeets in #284
• Refactor Volume class to support multiple data types by @stefsmeets in #282

Bug fixes

• Fix periodic jumps of matplotlib jumps_3d plot by @v1kko in #279

Maintanance

• Update actions versions by @stefsmeets in #294

New Contributors

• @tfamprikis made their first contribution in #220

Full Changelog: 1.1.0...1.2.0

1.1.0

The highlights for this release are:

• The SitesData class has been refactored into Transitions and Jumps, including improved algorithm for jumps calculations. This will make the code more maintainable and easier to extend for the long term.
• Many small api changes to make the code more intuitive and earier to use, for example, many plots are now accessible through class methods
• New methods for calculating and plotting multiple energy paths

What's Changed

• Make orthographic projection for density plot by @AstyLavrinenko in #233
• Return structure with occupancy set as Composition by @stefsmeets in #246
• Improve MSD calculation by @SCiarella in #248
• Turn Jumps.rates and Jumps.activation energies into dataframes by @stefsmeets in #250
• Add peak labels to free energy plots by @SCiarella in #213
• Add option to calculate multiple paths by @SCiarella in #258
• Make user api more intuitive by @stefsmeets in #259
• Make user api more accessible by @stefsmeets in #264
• Calculate transitions with custom radii per site type by @stefsmeets in #265

Under the hood

• Improve jump specification criteria by @v1kko in #228
• jumps calculation: switched joined prerequisites to independent prerequisites by @v1kko in #247
• Add method to extend trajectory by @stefsmeets in #242
• Refactor sites methods/attrs into other classes by @stefsmeets in #251
• Small tweaks to Transitions by @stefsmeets in #256

Bug fixes

• Fix number of sites by type by @AstyLavrinenko in #238
• Fix wrong n_floating bug by @stefsmeets in #253
• Fix RDF test by @stefsmeets in #255

Maintanance

• Fix documentation build by @stefsmeets in #257
• Fix docs build by @stefsmeets in #261

Full Changelog: 1.0.0...1.1.0