LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
docs/Makefile
docs/generate_api_docs.py
docs/make.bat
docs/requirements-docs.txt
docs/source/changelog.md
docs/source/command_line.rst
docs/source/conf.py
docs/source/contributing_guide.md
docs/source/faq.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/introduction.rst
docs/source/legacy.rst
docs/source/theory.rst
docs/source/tutorials.rst
docs/source/advanced/lammps.rst
docs/source/apidoc/kliff.analyzers.rst
docs/source/apidoc/kliff.atomic_data.rst
docs/source/apidoc/kliff.calculators.rst
docs/source/apidoc/kliff.dataset.rst
docs/source/apidoc/kliff.descriptors.rst
docs/source/apidoc/kliff.error.rst
docs/source/apidoc/kliff.log.rst
docs/source/apidoc/kliff.loss.rst
docs/source/apidoc/kliff.models.rst
docs/source/apidoc/kliff.neighbor.rst
docs/source/apidoc/kliff.nn.rst
docs/source/apidoc/kliff.parallel.rst
docs/source/apidoc/kliff.rst
docs/source/apidoc/kliff.uq.rst
docs/source/apidoc/kliff.utils.rst
docs/source/howto/howto.rst
docs/source/howto/install_kim_model.rst
docs/source/howto/new_model.rst
docs/source/howto/parallelize.rst
docs/source/howto/save_load_model.rst
docs/source/img/bootstrap.png
docs/source/img/logo.jpg
docs/source/img/uq_cartoon.png
docs/source/introduction/ConfigurationTransforms.ipynb
docs/source/introduction/Dataset.ipynb
docs/source/introduction/Trainer_and_kim.ipynb
docs/source/introduction/Trainer_dnn.ipynb
docs/source/introduction/Trainer_gnn.ipynb
docs/source/modules/calculators.rst
docs/source/modules/dataset.rst
docs/source/modules/descriptors.rst
docs/source/modules/loss.rst
docs/source/modules/models.rst
docs/source/modules/modules.rst
docs/source/modules/uq.rst
docs/source/tutorials/kim_SW_Si.ipynb
docs/source/tutorials/lennard_jones.ipynb
docs/source/tutorials/linear_regression.ipynb
docs/source/tutorials/nn_Si.ipynb
docs/source/tutorials/nn_SiC.ipynb
docs/source/tutorials/parameter_transform.ipynb
docs/source/tutorials/uq_bootstrap.ipynb
docs/source/tutorials/uq_mcmc.ipynb
examples/README.txt
examples/Si_training_set.tar.gz
examples/example_kim_SW_Si.py
examples/example_lennard_jones.py
examples/example_linear_regression.py
examples/example_nn_Si.py
examples/example_nn_SiC.py
examples/example_parameter_transform.py
examples/example_uq_bootstrap.py
examples/example_uq_mcmc.py
examples/legacy/eg_Fisher_info_kim_SW.py
examples/legacy/eg_RMSE_analysis_kim_SW.py
examples/legacy/eg_RMSE_analysis_nn.py
examples/legacy/eg_continue_nn_Si.py
examples/legacy/multiple_calculators.py
kliff/__init__.py
kliff/atomic_data.py
kliff/error.py
kliff/log.py
kliff/parallel.py
kliff/utils.py
kliff.egg-info/PKG-INFO
kliff.egg-info/SOURCES.txt
kliff.egg-info/dependency_links.txt
kliff.egg-info/entry_points.txt
kliff.egg-info/not-zip-safe
kliff.egg-info/requires.txt
kliff.egg-info/top_level.txt
kliff/analyzers/__init__.py
kliff/analyzers/fisher.py
kliff/analyzers/rmse.py
kliff/cmdline/__init__.py
kliff/cmdline/cli.py
kliff/cmdline/dataset.py
kliff/cmdline/model.py
kliff/dataset/__init__.py
kliff/dataset/dataset.py
kliff/dataset/dataset_torch.py
kliff/dataset/extxyz.py
kliff/dataset/weight.py
kliff/legacy/__init__.py
kliff/legacy/loss.py
kliff/legacy/nn.py
kliff/legacy/calculators/__init__.py
kliff/legacy/calculators/calculator.py
kliff/legacy/calculators/calculator_torch.py
kliff/legacy/descriptors/__init__.py
kliff/legacy/descriptors/descriptor.py
kliff/legacy/descriptors/bispectrum/__init__.py
kliff/legacy/descriptors/bispectrum/bispectrum.cpp
kliff/legacy/descriptors/bispectrum/bispectrum.hpp
kliff/legacy/descriptors/bispectrum/bispectrum.py
kliff/legacy/descriptors/bispectrum/bispectrum_bind.cpp
kliff/legacy/descriptors/bispectrum/helper.cpp
kliff/legacy/descriptors/bispectrum/helper.hpp
kliff/legacy/descriptors/symmetry_function/__init__.py
kliff/legacy/descriptors/symmetry_function/helper.cpp
kliff/legacy/descriptors/symmetry_function/helper.hpp
kliff/legacy/descriptors/symmetry_function/sym_fn.cpp
kliff/legacy/descriptors/symmetry_function/sym_fn.hpp
kliff/legacy/descriptors/symmetry_function/sym_fn.py
kliff/legacy/descriptors/symmetry_function/sym_fn_bind.cpp
kliff/models/__init__.py
kliff/models/kim.py
kliff/models/lennard_jones.py
kliff/models/linear_regression.py
kliff/models/model.py
kliff/models/model_torch.py
kliff/models/neural_network.py
kliff/models/parameter.py
kliff/neighbor/__init__.py
kliff/neighbor/helper.hpp
kliff/neighbor/neighbor.py
kliff/neighbor/neighbor_list.cpp
kliff/neighbor/neighbor_list.h
kliff/neighbor/neighbor_list_bind.cpp
kliff/trainer/__init__.py
kliff/trainer/base_trainer.py
kliff/trainer/kim_trainer.py
kliff/trainer/lightning_trainer.py
kliff/trainer/torch_trainer.py
kliff/trainer/utils/__init__.py
kliff/trainer/utils/dataloaders.py
kliff/trainer/utils/lightning_utils.py
kliff/trainer/utils/losses.py
kliff/transforms/__init__.py
kliff/transforms/parameter_transforms.py
kliff/transforms/property_transforms.py
kliff/transforms/configuration_transforms/__init__.py
kliff/transforms/configuration_transforms/configuration_transform.py
kliff/transforms/configuration_transforms/default_hyperparams.py
kliff/transforms/configuration_transforms/descriptor_initializers.py
kliff/transforms/configuration_transforms/descriptors.py
kliff/transforms/configuration_transforms/utils.py
kliff/transforms/configuration_transforms/graphs/__init__.py
kliff/transforms/configuration_transforms/graphs/generate_graph.py
kliff/transforms/configuration_transforms/graphs/periodic_table.hpp
kliff/transforms/configuration_transforms/graphs/radial_graph.cpp
kliff/uq/__init__.py
kliff/uq/bootstrap.py
kliff/uq/mcmc.py
kliff/uq/mcmc_utils.py
tests/conftest.py
tests/test_neighbor.py
tests/test_parallel.py
tests/test_scipy_optimize.py
tests/calculators/test_calculator.py
tests/calculators/test_calculator_torch.py
tests/dataset/test_ase_parser.py
tests/dataset/test_configurations.py
tests/dataset/test_extxyz.py
tests/dataset/test_weight.py
tests/descriptors/test_bispectrum.py
tests/descriptors/test_descriptor.py
tests/descriptors/test_symmetry_function.py
tests/misc/test_utils.py
tests/models/test_kim.py
tests/models/test_lennard_jones.py
tests/models/test_parameter.py
tests/models/test_parameter_transform.py
tests/test_data/configs/Si.xyz
tests/test_data/configs/Si_4.xyz
tests/test_data/configs/MoS2/MoS2_energy.xyz
tests/test_data/configs/MoS2/MoS2_energy_forces.xyz
tests/test_data/configs/MoS2/MoS2_energy_forces_stress.xyz
tests/test_data/configs/SiC_4/T300_step5000.xyz
tests/test_data/configs/SiC_4/T300_step5100.xyz
tests/test_data/configs/SiC_4/T300_step5200.xyz
tests/test_data/configs/SiC_4/T300_step5300.xyz
tests/test_data/configs/Si_4/Si_T300_step_0.xyz
tests/test_data/configs/Si_4/Si_T300_step_1.xyz
tests/test_data/configs/Si_4/Si_T300_step_2.xyz
tests/test_data/configs/Si_4/Si_T300_step_3.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i0_j0.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i0_j1.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i0_j2.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i0_j3.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i0_j4.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i0_j5.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i1_j1.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i1_j2.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i1_j3.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i1_j4.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i1_j5.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i2_j2.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i2_j3.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i2_j4.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i2_j5.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i3_j3.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i3_j4.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i3_j5.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i4_j4.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i4_j5.xyz
tests/test_data/configs/bilayer_graphene/bilayer_sep3.36_i5_j5.xyz
tests/trainer/test_descriptor_trainer.py
tests/trainer/test_kim_trainer.py
tests/trainer/test_lightning_trainer.py
tests/transformations/test_configuration_transform.py
tests/transformations/test_descriptors.py
tests/transformations/test_graphs.py
tests/transformations/test_property_transforms.py
tests/uq/conftest.py
tests/uq/test_bootstrap_empirical.py
tests/uq/test_bootstrap_nn.py
tests/uq/test_bootstrap_nn_separate_species.py
tests/uq/test_mcmc.py