Change Log

v1.0.1 (2025/04/11))

Other Changes

  • Update installation docs by @mjwen in https://github.com/openkim/kliff/pull/211

Full Changelog: https://github.com/openkim/kliff/compare/v1.0.0…v1.0.1

v1.0.0 (2025/04/11)

This is a backward incompatible version update from v0.x.x to v1.x.x. The functionality of v.0.x.x is completely kept in the legacy branch. In addition, most of the functionality are kept in kliff.legacy of v1.x.x.

New Features 🎉

  • Dataset object for v1 by @ipcamit in https://github.com/openkim/kliff/pull/135

  • Fundamental changes to KIM models, transforms, and parameter classes by @ipcamit in https://github.com/openkim/kliff/pull/140

  • Added complete transform module for graph generation and by @ipcamit in https://github.com/openkim/kliff/pull/153

  • KIM Trainer and tests by @ipcamit in https://github.com/openkim/kliff/pull/183

  • Kliff DNN torch trainer by @ipcamit in https://github.com/openkim/kliff/pull/185

Bug Fixes 🐛

  • Fix tests due to function name changes by @mjwen in https://github.com/openkim/kliff/pull/156

  • Order of arguments path and ase_atoms_list was switched in Dataset by @marcoscaa in https://github.com/openkim/kliff/pull/161

  • Colabfit enhancments by Eric by @ipcamit in https://github.com/openkim/kliff/pull/162

  • Added tests for newer modules by @ipcamit in https://github.com/openkim/kliff/pull/164

Enhancements 🛠

  • Format using black 24.1.0 by @mjwen in https://github.com/openkim/kliff/pull/157

  • ColabFit Changes by @EFuem in https://github.com/openkim/kliff/pull/174

Other Changes

  • GitHub cache by @mjwen in https://github.com/openkim/kliff/pull/136

  • Add Py3.10 by @mjwen in https://github.com/openkim/kliff/pull/138

  • Kliff master v1 lightning by @ipcamit in https://github.com/openkim/kliff/pull/182

  • Moved older descriptor, calculator, loss to legacy + tests fixed by @ipcamit in https://github.com/openkim/kliff/pull/186

  • Documentation and minor usability fixes by @ipcamit in https://github.com/openkim/kliff/pull/204

  • Kliff master v1 by @ipcamit in https://github.com/openkim/kliff/pull/206

  • Merged main and v1 by @ipcamit in https://github.com/openkim/kliff/pull/207

New Contributors

  • @marcoscaa made their first contribution in https://github.com/openkim/kliff/pull/161

Full Changelog: https://github.com/openkim/kliff/compare/v0.4.4…v1.0.0

v0.4.4 (2024/04/12)

Bug Fixes 🐛

  • Fix reading/writing xyz using T/F as PBC by @mjwen in https://github.com/openkim/kliff/pull/170

Enhancements 🛠

  • Deprecate travis build by @mjwen in https://github.com/openkim/kliff/pull/146

  • Add codecov check for test coverage by @mjwen in https://github.com/openkim/kliff/pull/165

  • Install kimpy from conda in GH actions by @mjwen in https://github.com/openkim/kliff/pull/167

Documentation 📖

  • Update installation docs for dependencies by @mjwen in https://github.com/openkim/kliff/pull/148

  • Simplify installation docs by @mjwen in https://github.com/openkim/kliff/pull/149

Other Changes

  • Fix GH test with ptemcee by @mjwen in https://github.com/openkim/kliff/pull/145

  • Update conda installation guide by @mjwen in https://github.com/openkim/kliff/pull/147

  • Fix readthedoc docs build by @mjwen in https://github.com/openkim/kliff/pull/150

  • Remove installing kimpy from conda in CI, it causes problem on macOS by @mjwen in https://github.com/openkim/kliff/pull/171

  • Add ptemcee from yonatank93’s repo as dependency by @mjwen in https://github.com/openkim/kliff/pull/193

  • Refactor UQ tests by @yonatank93 in https://github.com/openkim/kliff/pull/192

  • Update kim_SW_Si.ipynb by @ProfessorMiller in https://github.com/openkim/kliff/pull/202

  • Debug cutoff radius update in KIM model by @dengtq in https://github.com/openkim/kliff/pull/205

New Contributors

  • @ProfessorMiller made their first contribution in https://github.com/openkim/kliff/pull/202

  • @dengtq made their first contribution in https://github.com/openkim/kliff/pull/205

Full Changelog: https://github.com/openkim/kliff/compare/v0.4.3…v0.4.4

v0.4.3 (2023/12/17)

  • Fix installing ptemcee

v0.4.2 (2023/12/16)

Enhancements 🛠

  • Refactor test by @mjwen in https://github.com/openkim/kliff/pull/125

  • Update the ptemcee dependency by @yonatank93 in https://github.com/openkim/kliff/pull/137

  • Update GH actions to use latest conda-forge kim-api and test on macOS by @mjwen in https://github.com/openkim/kliff/pull/143

Documentation 📖

  • Recreate docs building codes by @mjwen in https://github.com/openkim/kliff/pull/129

Other Changes

  • Fix neighbor list bug by @mjwen in https://github.com/openkim/kliff/pull/90

  • Fix _WrapperCalculator by @mjwen in https://github.com/openkim/kliff/pull/95

  • Remove requirements.txt, add info in setup.py by @mjwen in https://github.com/openkim/kliff/pull/108

  • Add multiple species support of LJ by @mjwen in https://github.com/openkim/kliff/pull/112

  • Update CI to fix cmake version by @mjwen in https://github.com/openkim/kliff/pull/117

  • WIP: Implement bootstrap by @yonatank93 in https://github.com/openkim/kliff/pull/107

v0.4.1 (2022/10/06)

Added

  • Uncertainty quantification via MCMC (@yonatank93). New tutorial and explanation of the functionality provided in the doc.

  • Issue and PR template

Fixed

  • Linear regression model parameter shape

  • NN multispecies calculator to use parameters of all models

Updated

  • Documentation on installing KLIFF and dependencies

v0.4.0 (2022/04/27)

Added

  • Add ParameterTransform class to transform parameters into a different space (e.g. log space) @yonatank93

  • Add Weight class to set weight for energy/forces/stress. This is not backward compatible, which changes the signature of the residual function. Previously, in a residual function, the weights are passed in via the data argument, but now, its passed in via an instance of the Weight class. @yonatank93

Fixed

  • Fix checking cutoff entry @adityakavalur

  • Fix energy_residual_fn and forces_residual_fn to weigh different component

Updated

  • Change to use precommit GH action to check code format

v0.3.3 (2022/03/25)

Fixed

  • Fix neighlist (even after v0.3.2, the problem can still happen). Now neighlist is the same as kimpy

v0.3.2 (2022/03/01)

Added

  • Enable params_relation_callback() for KIM model

Fixed

  • Fix neighbor list segfault due to numerical error for 1D and 2D cases

v0.3.1 (2021/11/20)

  • add gpu training for NN model; set the gpu parameter of a calculator (e.g. CalculatorTorch(model, gpu=True)) to use it

  • add pyproject.toml, requirements.txt, dependabot.yml to config repo

  • switch to furo doc theme

  • changed: compute grad of energy wrt desc in batch mode (NN calculator)

  • fix: set fingerprints_filename and load descriptor state dict when reuse fingerprints (NN calculator)

v0.3.0 (2021/08/03)

  • change license to LGPL

  • set default optimizer

  • put kimpy code in try except block

  • add state_dict for descriptors and save it together with model

  • change to use loguru for logging and allows user to set log level

v0.2.2 (2021/05/24)

  • update to be compatible with kimpy v2.0.0

v0.2.1 (2021/05/24)

  • update to be compatible with kimpy v2.0.0

  • use entry entry_points to handle command line tool

  • rename utils to devtool

v0.2.0 (2021/01/19)

  • add type hint for all codes

  • reorganize model and parameters to make it more robust

  • add more docstring for many undocumented class and functions

v0.1.7 (2020/12/20)

  • add GitHub actions to automatically deploy to PyPI

  • add a simple example to README

v0.1.5 (2020/2/13)

  • add neighborlist utility, making NN model independent on kimpy

  • add calculator to deal with multiple species for NN model

  • update dropout layer to be compatible with the pytorch 1.3

v0.1.4 (2019/8/24)

  • add support for the geodesic Levenberg-Marquardt minimization algorithm

  • add command line tool model to inquire available parameters of KIM model

v0.1.3 (2019/8/19)

  • add RMSE and Fisher information analyzers

  • allow configuration weight for ML models

  • add write optimizer state dictionary for ML models

  • combine functions generate_training_fingerprints() and generate_test_fingerprints() of descriptor to generate_fingerprints() (supporting passing mean and stdev file)

  • rewrite symmetry descriptors to share with KIM driver

v0.1.2 (2019/6/27)

  • MPI parallelization for physics-based models

  • reorganize machine learning related files

  • various bug fixes

  • API changes * class DataSet renamed to Dataset * class Calculator moved to module calculators from module calculator

v0.1.1 (2019/5/13)

  • KLIFF available from PyPI now. Using $pip install kliff to install.

  • Use SW model from the KIM website in tutorial.

  • Format code with black.

v0.1.0 (2019/3/29)

First official release, but API is not guaranteed to be stable.

v0.0.1 (2019/1/1)

Pre-release.