├── .clang-format ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml ├── release.yml └── workflows │ ├── publish.yml │ ├── testing.yml │ └── update-precommit.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── devtool ├── README.md ├── format_sources.py └── update_version.py ├── docs ├── Makefile ├── generate_api_docs.py ├── make.bat ├── requirements-docs.txt └── source │ ├── advanced │ └── lammps.rst │ ├── apidoc │ ├── kliff.analyzers.rst │ ├── kliff.atomic_data.rst │ ├── kliff.dataset.rst │ ├── kliff.error.rst │ ├── kliff.log.rst │ ├── kliff.models.rst │ ├── kliff.neighbor.rst │ ├── kliff.parallel.rst │ ├── kliff.rst │ ├── kliff.uq.rst │ └── kliff.utils.rst │ ├── changelog.md │ ├── command_line.rst │ ├── conf.py │ ├── contributing_guide.md │ ├── faq.rst │ ├── howto │ ├── howto.rst │ ├── install_kim_model.rst │ ├── new_model.rst │ ├── parallelize.rst │ └── save_load_model.rst │ ├── img │ ├── bootstrap.png │ ├── conv.png │ ├── infl_dist_graph.png │ ├── logo.jpg │ └── uq_cartoon.png │ ├── index.rst │ ├── installation.rst │ ├── introduction.rst │ ├── introduction │ ├── ConfigurationTransforms.rst │ ├── Dataset.rst │ ├── Trainer_and_kim.rst │ ├── Trainer_dnn.rst │ └── Trainer_gnn.rst │ ├── legacy.rst │ ├── modules │ ├── calculators.rst │ ├── dataset.rst │ ├── descriptors.rst │ ├── loss.rst │ ├── models.rst │ ├── modules.rst │ └── uq.rst │ ├── theory.rst │ ├── theory │ ├── staged_graphs.rst │ └── theory.rst │ ├── tutorials.rst │ └── tutorials │ ├── kim_SW_Si.rst │ ├── lennard_jones.rst │ ├── linear_regression.rst │ ├── nn_Si.rst │ ├── nn_SiC.rst │ ├── parameter_transform.ipynb │ ├── uq_bootstrap.ipynb │ └── uq_mcmc.ipynb ├── examples ├── README.txt ├── SiC_training_set.tar.gz ├── Si_training_set.tar.gz ├── Si_training_set_4_configs.tar.gz ├── example_kim_SW_Si.py ├── example_lennard_jones.py ├── example_linear_regression.py ├── example_nn_Si.py ├── example_nn_SiC.py ├── example_parameter_transform.py ├── example_uq_bootstrap.py ├── example_uq_mcmc.py └── legacy │ ├── eg_Fisher_info_kim_SW.py │ ├── eg_RMSE_analysis_kim_SW.py │ ├── eg_RMSE_analysis_nn.py │ ├── eg_continue_nn_Si.py │ └── multiple_calculators.py ├── kliff ├── __init__.py ├── analyzers │ ├── __init__.py │ ├── fisher.py │ └── rmse.py ├── atomic_data.py ├── cmdline │ ├── __init__.py │ ├── cli.py │ ├── dataset.py │ └── model.py ├── dataset │ ├── __init__.py │ ├── configuration.py │ ├── dataset.py │ ├── dataset_torch.py │ ├── extxyz.py │ └── weight.py ├── error.py ├── legacy │ ├── __init__.py │ ├── calculators │ │ ├── __init__.py │ │ ├── calculator.py │ │ └── calculator_torch.py │ ├── descriptors │ │ ├── __init__.py │ │ ├── bispectrum │ │ │ ├── __init__.py │ │ │ ├── bispectrum.cpp │ │ │ ├── bispectrum.hpp │ │ │ ├── bispectrum.py │ │ │ ├── bispectrum_bind.cpp │ │ │ ├── helper.cpp │ │ │ └── helper.hpp │ │ ├── descriptor.py │ │ └── symmetry_function │ │ │ ├── __init__.py │ │ │ ├── helper.cpp │ │ │ ├── helper.hpp │ │ │ ├── sym_fn.cpp │ │ │ ├── sym_fn.hpp │ │ │ ├── sym_fn.py │ │ │ └── sym_fn_bind.cpp │ ├── loss.py │ └── nn.py ├── log.py ├── models │ ├── __init__.py │ ├── kim.py │ ├── lennard_jones.py │ ├── linear_regression.py │ ├── model.py │ ├── model_torch.py │ ├── neural_network.py │ └── parameter.py ├── neighbor │ ├── __init__.py │ ├── helper.hpp │ ├── neighbor.py │ ├── neighbor_list.cpp │ ├── neighbor_list.h │ └── neighbor_list_bind.cpp ├── parallel.py ├── trainer │ ├── __init__.py │ ├── base_trainer.py │ ├── kim_trainer.py │ ├── lightning_trainer.py │ ├── torch_trainer.py │ └── utils │ │ ├── __init__.py │ │ ├── dataloaders.py │ │ ├── lightning_utils.py │ │ └── losses.py ├── transforms │ ├── __init__.py │ ├── configuration_transforms │ │ ├── __init__.py │ │ ├── configuration_transform.py │ │ ├── default_hyperparams.py │ │ ├── descriptor_initializers.py │ │ ├── descriptors.py │ │ ├── graphs │ │ │ ├── __init__.py │ │ │ ├── generate_graph.py │ │ │ ├── periodic_table.hpp │ │ │ └── radial_graph.cpp │ │ └── utils.py │ ├── parameter_transforms.py │ └── property_transforms.py ├── uq │ ├── __init__.py │ ├── bootstrap.py │ ├── mcmc.py │ └── mcmc_utils.py └── utils.py ├── pyproject.toml ├── setup.py └── tests ├── calculators ├── test_calculator.py └── test_calculator_torch.py ├── conftest.py ├── dataset ├── test_ase_parser.py ├── test_configurations.py ├── test_dataset_import_export.py ├── test_extxyz.py └── test_weight.py ├── descriptors ├── test_bispectrum.py ├── test_descriptor.py └── test_symmetry_function.py ├── misc └── test_utils.py ├── models ├── test_kim.py ├── test_lennard_jones.py ├── test_parameter.py └── test_parameter_transform.py ├── test_data ├── configs │ ├── MoS2 │ │ ├── MoS2_energy.xyz │ │ ├── MoS2_energy_forces.xyz │ │ └── MoS2_energy_forces_stress.xyz │ ├── Si.xyz │ ├── SiC_4 │ │ ├── T300_step5000.xyz │ │ ├── T300_step5100.xyz │ │ ├── T300_step5200.xyz │ │ └── T300_step5300.xyz │ ├── Si_4.xyz │ ├── Si_4 │ │ ├── Si_T300_step_0.xyz │ │ ├── Si_T300_step_1.xyz │ │ ├── Si_T300_step_2.xyz │ │ └── Si_T300_step_3.xyz │ └── bilayer_graphene │ │ ├── bilayer_sep3.36_i0_j0.xyz │ │ ├── bilayer_sep3.36_i0_j1.xyz │ │ ├── bilayer_sep3.36_i0_j2.xyz │ │ ├── bilayer_sep3.36_i0_j3.xyz │ │ ├── bilayer_sep3.36_i0_j4.xyz │ │ ├── bilayer_sep3.36_i0_j5.xyz │ │ ├── bilayer_sep3.36_i1_j1.xyz │ │ ├── bilayer_sep3.36_i1_j2.xyz │ │ ├── bilayer_sep3.36_i1_j3.xyz │ │ ├── bilayer_sep3.36_i1_j4.xyz │ │ ├── bilayer_sep3.36_i1_j5.xyz │ │ ├── bilayer_sep3.36_i2_j2.xyz │ │ ├── bilayer_sep3.36_i2_j3.xyz │ │ ├── bilayer_sep3.36_i2_j4.xyz │ │ ├── bilayer_sep3.36_i2_j5.xyz │ │ ├── bilayer_sep3.36_i3_j3.xyz │ │ ├── bilayer_sep3.36_i3_j4.xyz │ │ ├── bilayer_sep3.36_i3_j5.xyz │ │ ├── bilayer_sep3.36_i4_j4.xyz │ │ ├── bilayer_sep3.36_i4_j5.xyz │ │ └── bilayer_sep3.36_i5_j5.xyz ├── precomputed_numpy_arrays │ └── cm_si.npy ├── trainer_data │ ├── dummy_model.pt │ ├── model_dnn.pt │ ├── training_manifest_ase_dnn.yaml.tpl │ ├── training_manifest_ase_kim.yaml.tpl │ └── training_manifest_ase_lightning_gnn.yaml.tpl └── weights │ ├── weights_1.dat │ ├── weights_4.dat │ ├── weights_4_incomplete.dat │ └── weights_4_partial.dat ├── test_dunn_optimize.py ├── test_neighbor.py ├── test_parallel.py ├── test_scipy_optimize.py ├── trainer ├── test_descriptor_trainer.py ├── test_kim_trainer.py └── test_lightning_trainer.py ├── transformations ├── test_configuration_transform.py ├── test_descriptors.py ├── test_graphs.py └── test_property_transforms.py └── uq ├── conftest.py ├── test_bootstrap_empirical.py ├── test_bootstrap_nn.py ├── test_bootstrap_nn_separate_species.py └── test_mcmc.py /.clang-format: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openkim/kliff/HEAD/.clang-format -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: 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