Chgnet

CHGNet is much faster now :rocket: :rocket: :rocket:

Main updates in this release:

1. Implement fast Cython graph converter in https://github.com/CederGroupHub/chgnet/pull/40 by AegisIK, yielding a 2 - 3x speed up in graph conversion depending on system size. Molecular dynamics now runs 1.5 - 2 x faster as well!

2. CHGNet API docs went live at https://chgnet.lbl.gov :tada: in https://github.com/CederGroupHub/chgnet/pull/39 by janosh

4. Better tests and docstrings by BowenD-UCB

All PRs since previous release
* API Docs by janosh in https://github.com/CederGroupHub/chgnet/pull/39
* Fix `ValueError: ndarray is not C-contiguous` CI errors by janosh in https://github.com/CederGroupHub/chgnet/pull/41
* 2.4x avg speedup on PMG struct to CHGNET graph conversion by AegisIK in https://github.com/CederGroupHub/chgnet/pull/40
* More descriptive names for single-letter variables by janosh in https://github.com/CederGroupHub/chgnet/pull/42
* Fix `ruff` `PERF203` + `PERF401` violations by janosh in https://github.com/CederGroupHub/chgnet/pull/43
* FIXED MEMORY LEAK in fast graph converter. Also cleaned up unneeded code. by AegisIK in https://github.com/CederGroupHub/chgnet/pull/44
* Add `CHGNet.todict` method needed for ASE JSON serialization by janosh in https://github.com/CederGroupHub/chgnet/pull/49
* Added garbage collection cyclic references turnoff for fast graph converter by AegisIK in https://github.com/CederGroupHub/chgnet/pull/50
* Solved final memory leak in fast converter by AegisIK in https://github.com/CederGroupHub/chgnet/pull/51
* Use `MaterialsProject2020Compatibility` to correct final energy in `fine_tuning.ipynb` by janosh in https://github.com/CederGroupHub/chgnet/pull/46

New Contributors
* AegisIK made their first contribution in https://github.com/CederGroupHub/chgnet/pull/40

**Full Changelog**: https://github.com/CederGroupHub/chgnet/compare/v0.1.04...v0.2.0

This release mainly cleans up the code (e.g. Graph creation) and adds docstrings. It also introduces a function to parse VASP outputs for training CHGNet.

Minor bug fixes:
1. CHGNet detault initialization now matches pretrained model
2. energy_loss_ratio now functions correctly
3. GraphData now functions correctly

What's Changed
* More `ruff` by janosh in https://github.com/CederGroupHub/chgnet/pull/31
* Fix arg-type annotations missing `None` by janosh in https://github.com/CederGroupHub/chgnet/pull/33
* Use PyPI trusted publishing in CI `release` job by janosh in https://github.com/CederGroupHub/chgnet/pull/36
* Drop `jupyter-dash` and update CTK relax viewer by janosh in https://github.com/CederGroupHub/chgnet/pull/37


**Full Changelog**: https://github.com/CederGroupHub/chgnet/compare/v0.1.03...v0.1.04

**The first published PyPI version.** 🚀 📦

What's Changed
* Fix markdown in `examples/fine_tuning.ipynb` by janosh in https://github.com/CederGroupHub/chgnet/pull/26
* Notebook tweaks by janosh in https://github.com/CederGroupHub/chgnet/pull/27
* coverage reporting by lbluque in https://github.com/CederGroupHub/chgnet/pull/28
* Publish to PyPI by janosh in https://github.com/CederGroupHub/chgnet/pull/29


**Full Changelog**: https://github.com/CederGroupHub/chgnet/compare/v0.1.01...v0.1.02

What's Changed
* Add kwarg on_isolated_atoms: ignore | warn | error = error to CrystalGraphConverter.forward() by janosh in https://github.com/CederGroupHub/chgnet/pull/1
* ruff + pre-commit by janosh in https://github.com/CederGroupHub/chgnet/pull/2
* Report CHGNet device by janosh in https://github.com/CederGroupHub/chgnet/pull/3
* Tests by janosh in https://github.com/CederGroupHub/chgnet/pull/4
* Style, docstring and minor edits by lbluque in https://github.com/CederGroupHub/chgnet/pull/5
* Refactor package setup by janosh in https://github.com/CederGroupHub/chgnet/pull/6
* Use future type annotations by janosh in https://github.com/CederGroupHub/chgnet/pull/7
* Packaging with pyproject.toml only by lbluque in https://github.com/CederGroupHub/chgnet/pull/8
* Test CHGNet keyword combinations by janosh in https://github.com/CederGroupHub/chgnet/pull/9
* Add test for `predict_structure()` by janosh in https://github.com/CederGroupHub/chgnet/pull/11
* cleanup graph classes by lbluque in https://github.com/CederGroupHub/chgnet/pull/12
* Add `test_graph.py` by janosh in https://github.com/CederGroupHub/chgnet/pull/13
* Crystaltoolkit Relaxation Viewer by janosh in https://github.com/CederGroupHub/chgnet/pull/14
* Relax viewer show dft energy by janosh in https://github.com/CederGroupHub/chgnet/pull/15
* Plot force in Crystal Toolkit relaxation viewer by janosh in https://github.com/CederGroupHub/chgnet/pull/16
* StructureData types and docs by janosh in https://github.com/CederGroupHub/chgnet/pull/17
* Fix `use_device` not set correctly by janosh in https://github.com/CederGroupHub/chgnet/pull/18
* Add readme table with "Open in Colab" badges for example notebooks by janosh in https://github.com/CederGroupHub/chgnet/pull/19
* Add cell that installs CHGNet on Colab to example notebooks by janosh in https://github.com/CederGroupHub/chgnet/pull/20
* Fix typo in filename `tests/test_(crytalgraph -> crystal_graph).py` by janosh in https://github.com/CederGroupHub/chgnet/pull/21
* Use `urllib` to read example structure from GitHub raw URL if local file not found by janosh in https://github.com/CederGroupHub/chgnet/pull/22
* Add `tests/test_encoders.py` by janosh in https://github.com/CederGroupHub/chgnet/pull/23
* Add `tests/test_converter.py` by janosh in https://github.com/CederGroupHub/chgnet/pull/24


**Full Changelog**: https://github.com/CederGroupHub/chgnet/compare/v0.0.01...v0.1.01

Initial release of CHGNet with the pre-trained weights.

**Full Changelog**: https://github.com/CederGroupHub/chgnet/commits/v0.0.01-beta