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

1.0.0

The highlights for this release are:

• A new logo 🤩
• Tools for site shape analysis
• The dashboard was split off to its own repo

What's Changed

• Add functions to perform site shape analysis by @AstyLavrinenko in #166
• Add mean squared displacement plot by @AstyLavrinenko in #195
• Add optional argument to gemdash, to specify trajectory location by @v1kko in #214
• Logo by @SCiarella in #219
• Allow custom lattice for density plot and ShapeAnalyzer by @stefsmeets in #225
• Add methods to calculate and apply offsets for shape analysis by @stefsmeets in #224
• Add function to display sites on shape plot by @stefsmeets in #232

Under the hood

• Speed up percolation test by @stefsmeets in #188
• Hide warning when loading a cif file through pymatgen by @stefsmeets in #223

Bug fixes

• Fix squared radius in shape_analysis by @AstyLavrinenko in #190
• Remove double mention by @AstyLavrinenko in #209
• Use kBoltzmann from scipy by @SCiarella in #207
• Fix mismatch with i variable in activation_energies by @AstyLavrinenko in #194
• Make sure filtering matching happens against a collection, not a string by @v1kko in #217
• Fix issues and tweak api for ShapeAnalyzer by @stefsmeets in #230

Maintanance

• Update CITATION.cff by @AstyLavrinenko in #210
• Add Simone to CITATION.cff by @SCiarella in #211
• Move dashboard to its own repo by @stefsmeets in #222
• Switch to bump-my-version by @stefsmeets in #229
• Use svg covbadge by @stefsmeets in #231

Full Changelog: 0.9.4...1.0.0

0.9.4

This release introduces some new features and improvements:

• minimal energy pathways are introduced
• errors can be calculated (and shown on the dashbord)
• some plots have been converted to plotly and are now interactive

What's Changed

• Tweak density plotting function by @AstyLavrinenko in #175
• Make sure the aspect ratio of the density plot is similar to the volume by @v1kko in #176
• Improving plots by @v1kko in #177
• Metrics with standard deviation by @v1kko in #182
• Fix number of colors for plot_points by @AstyLavrinenko in #184
• Implement energy landscapes and pathways from simulation by @SCiarella in #178

Full Changelog: 0.9.3...0.9.4

0.9.3

What's Changed

• add the data of the package to the manifest by @v1kko in #152
• Enable testing of dashboard inside github action by @v1kko in #155
• Allow uneven splits with np.array_split by @v1kko in #162
• Fix known material MnO2 by @stefsmeets in #169
• Update volume.py by @AstyLavrinenko in #160
• Add support for loading NPT data with varying lattice by @stefsmeets in #171
• Fix hash function by @stefsmeets in #172
• Add density plot to dashboard by @stefsmeets in #174

New Contributors

• @SCiarella made their first contribution in #168
• @AstyLavrinenko made their first contribution in #160

Full Changelog: 0.9.2...0.9.3

0.9.2

This is a test

What's Changed

• Add repr to Trajectory by @stefsmeets in #139
• Update workflow to generate requirements.txt by @stefsmeets in #142
• Add PyPI badges to readme by @stefsmeets in #143
• Refactor Volume.to_structure and revert to padded watershed for pbc by @stefsmeets in #141

Full Changelog: 0.9.1...0.9.2

0.9.1

Added notebooks to the documentation

What's Changed

• Added submodule for notebooks by @v1kko in #137

Full Changelog: 0.9.0...0.9.1