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Recent Releases of https://github.com/apax-hub/apax

https://github.com/apax-hub/apax - v0.12.2

What's Changed

  • Update README.md by @PythonFZ in https://github.com/apax-hub/apax/pull/457
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/458
  • fix apax calibrate metrics by @PythonFZ in https://github.com/apax-hub/apax/pull/459
  • fix an issue with using the calibrated model by @PythonFZ in https://github.com/apax-hub/apax/pull/463
  • Update .pre-commit-config.yaml by @PythonFZ in https://github.com/apax-hub/apax/pull/468
  • add .paramter to ApaxCalibrate node by @PythonFZ in https://github.com/apax-hub/apax/pull/467
  • add get_descriptors to the ASECalculator by @PythonFZ in https://github.com/apax-hub/apax/pull/464
  • bump version to 0.12.2 by @PythonFZ in https://github.com/apax-hub/apax/pull/469
  • Fix batchpred stress, orbax absolute path, ASE calc LL interface by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/466

Full Changelog: https://github.com/apax-hub/apax/compare/v0.12.1...v0.12.2

- Python
Published by PythonFZ 8 months ago

https://github.com/apax-hub/apax - v0.12.1

What's Changed

  • fix config keywords by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/454
  • patience Min delta and small bug fixes by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/456

Full Changelog: https://github.com/apax-hub/apax/compare/v0.12.0...v0.12.1

- Python
Published by M-R-Schaefer 8 months ago

https://github.com/apax-hub/apax - v0.12.0

What's Changed

  • fixed equiv mp training as shallow ensemble by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/441
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/440
  • Transfer Learning Freeze layers by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/443
  • removed buggy n jit steps option by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/446
  • orbax checkpoint saving / loading by @PythonFZ in https://github.com/apax-hub/apax/pull/445
  • test selection on atoms without calc by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/447
  • add ApaxApplyTransformation by @PythonFZ in https://github.com/apax-hub/apax/pull/433
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/452
  • bump version to 0.12.0 by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/453

Full Changelog: https://github.com/apax-hub/apax/compare/v0.11.0...v0.12.0

- Python
Published by M-R-Schaefer 9 months ago

https://github.com/apax-hub/apax - v0.11.0

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/400
  • add project.urls by @PythonFZ in https://github.com/apax-hub/apax/pull/403
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/402
  • Update pyproject.toml by @PythonFZ in https://github.com/apax-hub/apax/pull/405
  • fix time per step on check triggered by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/401
  • fix InvalidEscapeSequence by @PythonFZ in https://github.com/apax-hub/apax/pull/406
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/407
  • Correct elapsed sim time in performance summary by @Chronum94 in https://github.com/apax-hub/apax/pull/412
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/411
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/413
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/414
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/415
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/416
  • Update checkpoints.py by @PythonFZ in https://github.com/apax-hub/apax/pull/418
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/417
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/420
  • Triclinic cell fix by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/422
  • ApaxImport node fix by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/423
  • inconsistent label fix by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/425
  • Md check fix and extention by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/424
  • Updated deprecated jax.tree_util imports by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/427
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/426
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/428
  • added FixLayerConstrain by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/430
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/431
  • added wrapped param to md_config by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/429
  • added option to rebuild model up to specific readout layer by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/396
  • fix BAL models type hints by @PythonFZ in https://github.com/apax-hub/apax/pull/434
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/432
  • optimize znh5md setup by @PythonFZ in https://github.com/apax-hub/apax/pull/437
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/apax-hub/apax/pull/438
  • bump version by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/439

New Contributors

  • @Chronum94 made their first contribution in https://github.com/apax-hub/apax/pull/412

Full Changelog: https://github.com/apax-hub/apax/compare/v0.10.2...v0.11.0

- Python
Published by M-R-Schaefer 9 months ago

https://github.com/apax-hub/apax - v0.10.2

Full Changelog: https://github.com/apax-hub/apax/compare/v0.10.1...v0.10.2

- Python
Published by M-R-Schaefer about 1 year ago

https://github.com/apax-hub/apax - v0.10.1

What's Changed

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

Full Changelog: https://github.com/apax-hub/apax/compare/v0.9.1...v0.10.1

- Python
Published by M-R-Schaefer about 1 year ago

https://github.com/apax-hub/apax - v0.9.1

Full Changelog: https://github.com/apax-hub/apax/compare/v0.9.0...v0.9.1

- Python
Published by M-R-Schaefer about 1 year ago

https://github.com/apax-hub/apax - v0.9.0

What's Changed

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

Full Changelog: https://github.com/apax-hub/apax/compare/v0.8.0...v0.9.0

- Python
Published by M-R-Schaefer about 1 year ago

https://github.com/apax-hub/apax - v0.8.0

Contains important bug fix for JaxMD

What's Changed

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

New Contributors

  • @MrJulEnergy made their first contribution in https://github.com/apax-hub/apax/pull/366

Full Changelog: https://github.com/apax-hub/apax/compare/v0.7.0...v0.8.0

- Python
Published by M-R-Schaefer about 1 year ago

https://github.com/apax-hub/apax - v0.7.0

What's Changed

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

Full Changelog: https://github.com/apax-hub/apax/compare/v0.6.0...v0.7.0

- Python
Published by M-R-Schaefer over 1 year ago

https://github.com/apax-hub/apax - v0.7.0

What's Changed

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

Full Changelog: https://github.com/apax-hub/apax/compare/v0.6.0...v0.7.0

- Python
Published by M-R-Schaefer over 1 year ago

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

Full Changelog: https://github.com/apax-hub/apax/compare/v.0.5.0...v0.6.0

- Python
Published by M-R-Schaefer over 1 year ago

https://github.com/apax-hub/apax - v0.6.0

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

Full Changelog: https://github.com/apax-hub/apax/compare/v.0.5.0...v0.6.0

- Python
Published by M-R-Schaefer over 1 year ago

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

Full Changelog: https://github.com/apax-hub/apax/compare/v0.4.0...v.0.5.0

- Python
Published by M-R-Schaefer over 1 year ago

https://github.com/apax-hub/apax - v0.4.0

What's Changed

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

New Contributors

  • @pre-commit-ci made their first contribution in https://github.com/apax-hub/apax/pull/228

Full Changelog: https://github.com/apax-hub/apax/compare/v0.3.0...v0.4.0

- Python
Published by M-R-Schaefer almost 2 years ago

https://github.com/apax-hub/apax - v0.3.0

What's Changed

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

Full Changelog: https://github.com/apax-hub/apax/compare/v0.2.0...v0.3.0

- Python
Published by M-R-Schaefer about 2 years ago

https://github.com/apax-hub/apax - v0.2.0

What's Changed

  • Val bs fix and distance computation refactor by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/188
  • Vmap ensemble training and jaxmd inference by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/187
  • BAL integration test by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/195
  • Added DOI by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/202
  • Absl logging fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/197
  • unpinned cuda jax version for Flax compatibility by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/201
  • CLI test by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/206
  • Docs update by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/204
  • Fix neighbour calc by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/207
  • Transfer Learning fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/200
  • Typo in README.md by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/210
  • NPT validation and MD checkpoints by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/208
  • implemented model loading from arbitray locations by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/212
  • 0.2.0 Release by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/213

Full Changelog: https://github.com/apax-hub/apax/compare/v0.1.0...v0.2.0

- Python
Published by M-R-Schaefer about 2 years ago

https://github.com/apax-hub/apax - v0.1.0 First Public Release

This first release of apax includes the following features

  • training GMNN models on energies force and virials.
  • an ASE calculator that can handle ensembles and uncertainties
  • performant MD simulations with via JAX MD
  • batch active learning

What's Changed

  • Auto linting by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/2
  • Dataset statistics by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/3
  • Checkpoints, per-parameter group optimizer by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/6
  • Metrics and Loss Functions by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/7
  • Dataset by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/8
  • Added MD utility by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/9
  • Trainer by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/13
  • Best model checkpoint by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/16
  • Cpu fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/14
  • train and val data can noe be read in from seperate files by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/17
  • Clean up by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/18
  • Parameter Initialization fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/26
  • Progress bars for NL precomputing, Training and JaxMD by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/31
  • Non default model loading by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/30
  • Installtion fix, intialization fix, progress bars, ASECalc fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/33
  • Non ase labels by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/32
  • Cummulative PR for the past Month by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/34
  • First fully functional version of the GMNN Model + training by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/35
  • removed old LinReg testing class and example by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/36
  • fixed ase calc not accounting for cell and particle number changes by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/37
  • CLI by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/38
  • Fixed ase recompilation bug by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/43
  • removed old MD example by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/40
  • poetry update by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/44
  • Update pyproject.toml by @PythonFZ in https://github.com/apax-hub/apax/pull/47
  • removed old examples and weight transfer by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/49
  • md without pbc by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/55
  • Added saving of initial struc to md traj by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/58
  • InputPipeline now checks if the number of data points is < batch_size by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/57
  • MD temp fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/60
  • Ckpt interval & moving logging out of CLI by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/54
  • pbc fix in ase calculator by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/61
  • Validate config command by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/63
  • Config docs by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/62
  • Allowing for variable number of NN layers in GMNN. by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/70
  • Switched MD from running for n_steps to a duration in fs by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/71
  • Visualize by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/72
  • Project structure cleanup by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/74
  • Splitting idx by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/75
  • Fp64 by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/67
  • Templates by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/76
  • Test eval by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/77
  • eval refactoring by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/79
  • removed comment by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/81
  • Variable sizes by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/78
  • Allow 0 weights in los config for grid searches by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/82
  • Update pyproject.toml by @PythonFZ in https://github.com/apax-hub/apax/pull/85
  • Cummulative Update by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/88
  • Variable cell sizes, Flax Model, Transfer learning by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/90
  • gmnn-jax to apax by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/98
  • Improved Config Validation by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/101
  • Logging additions by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/100
  • changes dependencies of the new organisation name by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/102
  • updated README by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/103
  • Efficient Temperature and calculation of energy in JaxMD loop by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/105
  • Option to disable embedding and limit number of contractions by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/106
  • Bug fixes #111 #108 #104 by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/112
  • Remove Haiku by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/113
  • bumped np version, updated email, added keywords by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/110
  • Accumulated changes from dev since Jan. 25. by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/114
  • Jax update by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/115
  • Improved pipeline performance by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/120
  • Empirical Corrections, SAM, stress sketch by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/117
  • Neighborlist fix by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/121
  • loss is now averaged over batch by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/122
  • added offsets to visualize command by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/123
  • fix n_secies bug issue #119 by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/124
  • dependencies adapted to IPSuite by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/126
  • poetry bug fix by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/127
  • Different scaling and shifting schemes by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/128
  • Cli performance by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/133
  • Merge pull request #133 from apax-hub/cli_perf by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/141
  • Eval fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/134
  • NL fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/136
  • H5md by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/139
  • Early stopping by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/140
  • Add stress by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/142
  • Update train_config.py by @PythonFZ in https://github.com/apax-hub/apax/pull/148
  • Triclinic cell fix by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/144
  • ASE NPT by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/147
  • Ensemble & stress fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/150
  • ase stress fix by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/152
  • fix h5md not writing pbc info by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/153
  • Fix jax-md = "0.2.5" by @PythonFZ in https://github.com/apax-hub/apax/pull/154
  • Ase calc properties fix by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/155
  • Max batchsize adjustment by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/156
  • Tensorboard refactor by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/157
  • Pydantic V2 migration by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/167
  • fixed NL overflow using wrong neighbors by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/162
  • Corrections refactor by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/159
  • Unifying abstractions for train and eval by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/158
  • Uncertainty driven dynamics by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/166
  • Bump jax and Python 3.11 compatibility by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/169
  • Remove deprecated features by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/170
  • implemented GAMD refactored into separate module by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/171
  • Load momenta & NPT implementation by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/172
  • ASE MD neighbour fix by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/173
  • 130 unit conversion is broken by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/176
  • batch active learning by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/175
  • Remove pytest ini by @PythonFZ in https://github.com/apax-hub/apax/pull/183
  • Matscipy neighbours preprocessing by @Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/184
  • Accumulated Changes since March 23 by @M-R-Schaefer in https://github.com/apax-hub/apax/pull/185

New Contributors

  • @M-R-Schaefer made their first contribution in https://github.com/apax-hub/apax/pull/3
  • @PythonFZ made their first contribution in https://github.com/apax-hub/apax/pull/47

Full Changelog: https://github.com/apax-hub/apax/commits/v0.1.0

- Python
Published by M-R-Schaefer over 2 years ago