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