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Change Log

v1.0.1 (2025/04/11))

Other Changes

  • Update installation docs by @mjwen in #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 #135
  • Fundamental changes to KIM models, transforms, and parameter classes by @ipcamit in #140
  • Added complete transform module for graph generation and by @ipcamit in #153
  • KIM Trainer and tests by @ipcamit in #183
  • Kliff DNN torch trainer by @ipcamit in #185

Bug Fixes 🐛

  • Fix tests due to function name changes by @mjwen in #156
  • Order of arguments path and ase_atoms_list was switched in Dataset by @marcoscaa in #161
  • Colabfit enhancments by Eric by @ipcamit in #162
  • Added tests for newer modules by @ipcamit in #164

Enhancements 🛠

  • Format using black 24.1.0 by @mjwen in #157
  • ColabFit Changes by @EFuem in #174

Other Changes

  • GitHub cache by @mjwen in #136
  • Add Py3.10 by @mjwen in #138
  • Kliff master v1 lightning by @ipcamit in #182
  • Moved older descriptor, calculator, loss to legacy + tests fixed by @ipcamit in #186
  • Documentation and minor usability fixes by @ipcamit in #204
  • Kliff master v1 by @ipcamit in #206
  • Merged main and v1 by @ipcamit in #207

New Contributors

  • @marcoscaa made their first contribution in #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 #170

Enhancements 🛠

  • Deprecate travis build by @mjwen in #146
  • Add codecov check for test coverage by @mjwen in #165
  • Install kimpy from conda in GH actions by @mjwen in #167

Documentation 📖

  • Update installation docs for dependencies by @mjwen in #148
  • Simplify installation docs by @mjwen in #149

Other Changes

  • Fix GH test with ptemcee by @mjwen in #145
  • Update conda installation guide by @mjwen in #147
  • Fix readthedoc docs build by @mjwen in #150
  • Remove installing kimpy from conda in CI, it causes problem on macOS by @mjwen in #171
  • Add ptemcee from yonatank93's repo as dependency by @mjwen in #193
  • Refactor UQ tests by @yonatank93 in #192
  • Update kim_SW_Si.ipynb by @ProfessorMiller in #202
  • Debug cutoff radius update in KIM model by @dengtq in #205

New Contributors

  • @ProfessorMiller made their first contribution in #202
  • @dengtq made their first contribution in #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 #125
  • Update the ptemcee dependency by @yonatank93 in #137
  • Update GH actions to use latest conda-forge kim-api and test on macOS by @mjwen in #143

Documentation 📖

  • Recreate docs building codes by @mjwen in #129

Other Changes

  • Fix neighbor list bug by @mjwen in #90
  • Fix _WrapperCalculator by @mjwen in #95
  • Remove requirements.txt, add info in setup.py by @mjwen in #108
  • Add multiple species support of LJ by @mjwen in #112
  • Update CI to fix cmake version by @mjwen in #117
  • WIP: Implement bootstrap by @yonatank93 in #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.

  • Add more docs to {ref}reference.

v0.0.1 (2019/1/1)

Pre-release.