v0.10.2

Full Changelog: v0.10.1...v0.10.2

v0.10.1

What's Changed

• fix np.generic type issue by @PythonFZ in #379
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #381
• use .parameter by @PythonFZ in #385
• bump to v0.9.2 by @PythonFZ in #386
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #388
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #392
• Uvtest by @M-R-Schaefer in #393
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #394
• update install docs by @Tetracarbonylnickel in #395
• update flax and ipsuite tests by @M-R-Schaefer in #391
• uv sync by @M-R-Schaefer in #397
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #398

Full Changelog: v0.9.1...v0.10.1

v0.9.1

Full Changelog: v0.9.0...v0.9.1

v0.9.0

What's Changed

• Update README.md by @PythonFZ in #372
• PBP dataset performance enhancements by @M-R-Schaefer in #361
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #374
• Py 3.12 compatibility, rm chex and jaxtyping by @M-R-Schaefer in #375
• prepare for ZnTrack v0.8.0 release by @PythonFZ in #356
• fixed md function transformations by @M-R-Schaefer in #378
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #377
• Flexible property prediction heads by @M-R-Schaefer in #362

Full Changelog: v0.8.0...v0.9.0

v0.8.0

Contains important bug fix for JaxMD

What's Changed

• cleaned up gm implementation by @M-R-Schaefer in #338
• Adaptive BAL by @M-R-Schaefer in #330
• AdEMAmix, Gradient clipping by @M-R-Schaefer in #342
• new empirical correction interface, added exponential correction by @M-R-Schaefer in #343
• ensemble batch eval fix, repulsion fix by @M-R-Schaefer in #348
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #345
• removed black badge by @M-R-Schaefer in #349
• fixed usage of multiple callbacks by @M-R-Schaefer in #350
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #351
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #354
• Use tensorflow by @PythonFZ in #355
• implemented fix atom constraint and constraint API by @M-R-Schaefer in #352
• updated piecewise linear T schedule by @M-R-Schaefer in #353
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #357
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #359
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #363
• Update pytest.yaml by @PythonFZ in #368
• Fix Grammar in Docs by @MrJulEnergy in #366
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #365
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #369
• New config by @Tetracarbonylnickel in #371

New Contributors

• @MrJulEnergy made their first contribution in #366

Full Changelog: v0.7.0...v0.8.0

v0.7.0

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #323
• MD perf stats by @M-R-Schaefer in #325
• added uncertainty checks to jax md by @M-R-Schaefer in #328
• Update README.md by @PythonFZ in #329
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #331
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #336
• full ensemble fix, feature model fix by @M-R-Schaefer in #332
• fix calibration factors not available in calculator by @M-R-Schaefer in #337
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #339
• added w_init to template, updated default by @M-R-Schaefer in #334
• cleaned up validation error messages by @M-R-Schaefer in #333

Full Changelog: v0.6.0...v0.7.0

v0.6.0

Notable Changes

• Uncertainties in jaxmd
• Interface for adding new models (currently an equivariant MP model is
• Added Post hoc calibration for ASE calculator as function
• Added temperature schedules for
• Various bug fixes and doc updates

Breaking Changes
All functionality of previous versions was preserved. However you might need to adapt your input files.
For training, the model section now requires the field name: gmnn (or other model).
For MD, the temperature field was replaced with the temperature_schedule field.
Check the config template to see an example of a constant temperature simulation.

What's Changed

• use store="time" by @PythonFZ in #303
• save energy as scalar by @PythonFZ in #304
• fix batch_eval by @PythonFZ in #306
• [MDAnalysis fix]: Do not save units by @PythonFZ in #307
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #310
• updated jax CUDA installation instructions by @M-R-Schaefer in #301
• Uncertainty Calibration by @M-R-Schaefer in #302
• Calibration Nodes docs update by @M-R-Schaefer in #311
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #313
• moved BAL selection node from ips to apax by @M-R-Schaefer in #315
• added temperature schedules by @M-R-Schaefer in #318
• Improved schema command by @M-R-Schaefer in #316
• switch ase batch predict to CachedDataset by @M-R-Schaefer in #314
• added uncertainty estimation on dump interval for jaxmd by @M-R-Schaefer in #312
• Model extension by @M-R-Schaefer in #317
• automatically publish on PyPi by @PythonFZ in #321
• zbl no longer Nan by @M-R-Schaefer in #320
• added missing so3krates scaling parameter by @M-R-Schaefer in #322

Full Changelog: v.0.5.0...v0.6.0

v0.5.0

v0.5.0 Release

notable changes:

• New learning rate schedules
• New batch-evaluationb method for the ase calculator
• h5md dataset loading
• new dataset optimized for differently sized structures
• new Bessel-like basis functions
• shallow ensembles for uncertainty estimation and NLL, CRPS loss functions
• added feature model
• switched linting to ruff
• force features for BAL

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #266
• add repository link by @PythonFZ in #267
• EMA, SAM update, cyclic LR schedule by @M-R-Schaefer in #269
• train_config.py fix default no. contractions by @Tetracarbonylnickel in #272
• NVE bug fix by @Tetracarbonylnickel in #276
• Add MD restart support and fix config loading by @PythonFZ in #271
• bump znh5md by @PythonFZ in #278
• implemented apax batch evaluation node by @M-R-Schaefer in #280
• H5MD data loading by @M-R-Schaefer in #282
• Per Batch Padded Dataset by @M-R-Schaefer in #281
• allow for non NTK linear layers in model by @M-R-Schaefer in #283
• New Basis function interface by @M-R-Schaefer in #284
• Mlflow fix by @M-R-Schaefer in #286
• Node fix by @M-R-Schaefer in #289
• fixed memory leak in pbp ds by @M-R-Schaefer in #290
• Shallow ensembles by @M-R-Schaefer in #275
• refactored distance computation, added feature model by @M-R-Schaefer in #285
• use znh5md v0.3 by @PythonFZ in #292
• replace isort, flake8 and black with ruff by @PythonFZ in #294
• Collective changes from my absence by @M-R-Schaefer in #293
• bump project version, pin orbax and flax versions by @M-R-Schaefer in #296
• v0.5.0 by @M-R-Schaefer in #297

Full Changelog: v0.4.0...v.0.5.0

v0.4.0

What's Changed

• MD end checkpoint & ensemble NPT fix by @M-R-Schaefer in #225
• merge main by @PythonFZ in #226
• remove linting CI in favor of pre-commit.ci by @PythonFZ in #227
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #228
• update dev branch with new CI by @M-R-Schaefer in #230
• fixed jax nl always allocating in cartesian coords by @M-R-Schaefer in #229
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #231
• fixed bug where positions where not initialized for gas phase systems by @M-R-Schaefer in #232
• Batch evaluation by @M-R-Schaefer in #233
• Remove JaxMD dependency by @M-R-Schaefer in #234
• Moredocs nico by @Tetracarbonylnickel in #235
• Moredocs nico by @Tetracarbonylnickel in #236
• Moredocs nico by @Tetracarbonylnickel in #237
• Moredocs nico by @Tetracarbonylnickel in #238
• Moredocs nico by @Tetracarbonylnickel in #240
• Fix eval by @Tetracarbonylnickel in #241
• Update io.py by @Tetracarbonylnickel in #243
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #244
• Moredocs nico by @Tetracarbonylnickel in #242
• Input Pipeline rework by @M-R-Schaefer in #245
• Huber Loss by @M-R-Schaefer in #249
• Input Autocomplete by @M-R-Schaefer in #250
• Cache dataset by @M-R-Schaefer in #248
• unit fix by @Tetracarbonylnickel in #258
• Batch Pbar by @M-R-Schaefer in #256
• Mlflow by @M-R-Schaefer in #255
• ZnTrack Nodes by @PythonFZ in #254
• FIX Neighborlist for periodic structures by @M-R-Schaefer in #259
• Dataparallel Training by @M-R-Schaefer in #257
• Moredocs nico by @Tetracarbonylnickel in #261
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #260
• removed disfunctional docs action by @M-R-Schaefer in #262
• Docs Examples by @M-R-Schaefer in #217
• update version to 0.4.0 by @M-R-Schaefer in #263
• spell check by @Tetracarbonylnickel in #265
• Cummulative 0.4.0 Changes by @M-R-Schaefer in #264

New Contributors

• @pre-commit-ci made their first contribution in #228

Full Changelog: v0.3.0...v0.4.0

v0.3.0

What's Changed

• Update pyproject.toml by @PythonFZ in #214
• added model loading edge case for experiment="" by @M-R-Schaefer in #216
• Poetry Update and Orbax fix by @M-R-Schaefer in #218
• added stress triL loss function by @M-R-Schaefer in #221
• JIT multiple train steps by @M-R-Schaefer in #220
• Version 0.3.0 changes by @M-R-Schaefer in #223

Full Changelog: v0.2.0...v0.3.0