├── .bumpversion.cfg ├── .codecov.yml ├── .coveragerc ├── .editorconfig ├── .git-blame-ignore-revs ├── .gitattributes ├── .github └── workflows │ ├── codecov.yml │ ├── deploy-docs.yml │ ├── linter.yml │ ├── python-package.yml │ ├── python-publish-test.yml │ └── python-publish.yml ├── .gitignore ├── .pylintrc ├── CHANGELOG.md ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── NOTICE ├── README.md ├── docs ├── branch-build-docs.sh ├── build-docs.sh └── source │ ├── _templates │ └── versions.html │ ├── api │ ├── DataSet.rst │ ├── PredictSet.rst │ ├── alchemy │ │ ├── alchemy_module.rst │ │ └── mbeAlchemyScale.rst │ ├── analysis │ │ ├── ProblematicStructures.rst │ │ ├── analysis_module.rst │ │ ├── gdml_mat52.rst │ │ ├── gdml_mat52_wrk.rst │ │ └── rdf.rst │ ├── descriptors │ │ ├── com_distance_sum.rst │ │ ├── criteria.rst │ │ ├── descriptors_module.rst │ │ └── max_atom_pair_dist.rst │ ├── gdml │ │ ├── descriptor │ │ │ ├── Desc.rst │ │ │ ├── _from_r.rst │ │ │ ├── _pbc_diff.rst │ │ │ ├── _pdist.rst │ │ │ ├── _r_to_d_desc.rst │ │ │ ├── _r_to_desc.rst │ │ │ └── descriptor_module.rst │ │ ├── gdml.rst │ │ ├── predict │ │ │ ├── GDMLPredict.rst │ │ │ ├── _predict_wkr.rst │ │ │ └── predict_module.rst │ │ ├── sample │ │ │ ├── draw_strat_sample.rst │ │ │ └── sample.rst │ │ ├── symmetries │ │ │ ├── _bipartite_match_wkr.rst │ │ │ ├── bipartite_match.rst │ │ │ ├── complete_sym_group.rst │ │ │ ├── find_perms.rst │ │ │ ├── inv_perm.rst │ │ │ ├── salvage_subgroup.rst │ │ │ ├── symmetries.rst │ │ │ ├── sync_perm_mat.rst │ │ │ └── to_cycles.rst │ │ └── training │ │ │ ├── Analytic.rst │ │ │ ├── GDMLTrain.rst │ │ │ ├── Iterative.rst │ │ │ ├── _assemble_kernel_mat_wkr.rst │ │ │ ├── add_valid_errors.rst │ │ │ ├── get_test_idxs.rst │ │ │ ├── model_errors.rst │ │ │ └── training.rst │ ├── interfaces │ │ ├── ase-mbeCalculator.rst │ │ └── interfaces_module.rst │ ├── logger │ │ ├── GDMLLogger.rst │ │ ├── logger_module.rst │ │ └── set_log_level.rst │ ├── losses │ │ ├── loss_f_e_weighted_mse.rst │ │ ├── loss_f_mse.rst │ │ ├── loss_f_rmse.rst │ │ ├── losses_module.rst │ │ ├── mae.rst │ │ ├── mse.rst │ │ ├── rmse.rst │ │ └── sse.rst │ ├── mbe │ │ ├── decomp_to_total.rst │ │ ├── gen_r_entity_combs.rst │ │ ├── gen_r_idxs_worker.rst │ │ ├── mbePredict.rst │ │ ├── mbe_contrib.rst │ │ ├── mbe_module.rst │ │ └── mbe_worker.rst │ ├── models │ │ ├── gapModel.rst │ │ ├── gdmlModel.rst │ │ ├── model.rst │ │ ├── models_module.rst │ │ └── schnetModel.rst │ ├── modules.rst │ ├── periodic │ │ ├── cell.rst │ │ └── periodic_module.rst │ ├── predictors │ │ ├── _predict_gdml_wkr.rst │ │ ├── predict_gap.rst │ │ ├── predict_gap_decomp.rst │ │ ├── predict_gdml.rst │ │ ├── predict_gdml_decomp.rst │ │ ├── predict_schnet.rst │ │ ├── predict_schnet_decomp.rst │ │ └── predictors_module.rst │ ├── stress │ │ ├── stress_module.rst │ │ ├── to_voigt.rst │ │ ├── virial_atom_loop.rst │ │ └── virial_finite_diff.rst │ ├── structure_gen │ │ ├── packmol_gen │ │ │ ├── get_packmol_input.rst │ │ │ ├── packmol_gen.rst │ │ │ └── run_packmol.rst │ │ ├── structure_gen.rst │ │ └── utils │ │ │ ├── get_mixture_density.rst │ │ │ ├── get_num_mols.rst │ │ │ ├── get_shape_volume.rst │ │ │ ├── mol_to_mass_fractions.rst │ │ │ └── utils.rst │ ├── switching │ │ ├── linear_switching.rst │ │ └── switching_module.rst │ ├── training │ │ ├── mbGDMLTrain.rst │ │ └── training.rst │ └── utils │ │ ├── atoms_by_element.rst │ │ ├── atoms_by_number.rst │ │ ├── center_structures.rst │ │ ├── chunk_array.rst │ │ ├── chunk_iterable.rst │ │ ├── convert_forces.rst │ │ ├── gen_combs.rst │ │ ├── get_R_slice.rst │ │ ├── get_comp_ids.rst │ │ ├── get_entity_ids.rst │ │ ├── get_filename.rst │ │ ├── get_files.rst │ │ ├── md5_data.rst │ │ ├── parse_xyz.rst │ │ ├── save_json.rst │ │ ├── string_xyz_arrays.rst │ │ ├── utils.rst │ │ └── write_xyz.rst │ ├── conf.py │ ├── contributing.rst │ ├── files │ ├── dsets │ │ ├── 1h2o.npz │ │ ├── 2h2o-nbody.npz │ │ └── 3h2o-nbody.npz │ ├── models │ │ └── 2023-digital-discovery │ │ │ ├── 1h2o-model-gdml.npz │ │ │ ├── 2h2o-model-gdml-nbody.npz │ │ │ └── 3h2o-model-gdml-nbody.npz │ └── structures │ │ └── 2h2o-psi4-opt.xyz │ ├── images │ ├── 1,2,3-body-figure.svg │ ├── descriptors │ │ ├── global-vs-local-descriptor.png │ │ └── global-vs-local-descriptor.svg │ ├── distance-screening-3h2o.svg │ ├── energies-forces-ml-potentials.png │ ├── explicit-water-methanol-mbe-allorders.svg │ ├── free-lunches │ │ ├── curse-of-dimensionality.png │ │ └── figure-isomer-ranking-mbgdml.py │ ├── gdml-concept-e-vs-f-train.png │ ├── gdml-concept.png │ ├── mbe-explained │ │ ├── 2-body-comp-ids.png │ │ ├── 2-body-entity-ids.png │ │ ├── 2-body-example.png │ │ ├── 2-body-r.png │ │ ├── 2-body-z.png │ │ ├── 3h2o-energy-1bodies.png │ │ ├── 3h2o-energy-1bodies.svg │ │ ├── 3h2o-energy-2body-0,1.png │ │ ├── 3h2o-energy-2body-0,1.svg │ │ ├── 3h2o-energy-2body-0,2.png │ │ ├── 3h2o-energy-2body-0,2.svg │ │ ├── 3h2o-energy-2body-1,2.png │ │ ├── 3h2o-energy-2body-1,2.svg │ │ ├── 3h2o-energy.png │ │ ├── 3h2o-energy.svg │ │ ├── 3h2o.svg │ │ └── mbe-predictions.png │ ├── ml-force-field.svg │ └── training │ │ ├── 1h2o-cl-losses-1000-iter.png │ │ ├── 1h2o-cl-losses-1000-rand.png │ │ ├── 1h2o-sigma-loss-increasing.png │ │ └── 2h2o-sigma-dual-min.png │ ├── index.rst │ ├── interfaces.rst │ ├── mbe.rst │ ├── predicting.rst │ ├── roboto-font │ ├── Roboto-Black.ttf │ ├── Roboto-BlackItalic.ttf │ ├── Roboto-Bold.ttf │ ├── Roboto-BoldItalic.ttf │ ├── Roboto-Italic.ttf │ ├── Roboto-Light.ttf │ ├── Roboto-LightItalic.ttf │ ├── Roboto-Medium.ttf │ ├── Roboto-MediumItalic.ttf │ ├── Roboto-Regular.ttf │ ├── Roboto-Thin.ttf │ └── Roboto-ThinItalic.ttf │ └── training.rst ├── mbgdml ├── __init__.py ├── _gdml │ ├── __init__.py │ ├── desc.py │ ├── perm.py │ ├── predict.py │ ├── sample.py │ ├── solvers │ │ ├── __init__.py │ │ ├── analytic.py │ │ └── iterative.py │ ├── torchtools.py │ └── train.py ├── _version.py ├── active_learning │ ├── __init__.py │ ├── drive_md.py │ └── sample_md.py ├── alchemy.py ├── analysis │ ├── __init__.py │ ├── clustering.py │ ├── models.py │ ├── problematic.py │ └── rdf.py ├── data │ ├── __init__.py │ ├── basedata.py │ ├── dataset.py │ └── predictset.py ├── descriptors.py ├── interfaces │ ├── __init__.py │ └── ase.py ├── logger.py ├── losses.py ├── mbe.py ├── models │ ├── __init__.py │ ├── base.py │ ├── gap_model.py │ ├── gdml_model.py │ └── schnet_model.py ├── periodic.py ├── predictors │ ├── __init__.py │ ├── gap_predict.py │ ├── gdml_predict.py │ └── schnet_predict.py ├── stress.py ├── structure_gen │ ├── __init__.py │ ├── packmol_gen.py │ └── utils.py ├── switching.py ├── train.py └── utils.py ├── pytest.ini ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── data │ ├── datasets │ │ ├── 16h2o │ │ │ └── 16h2o.yoo.etal.boat.b-dset-mp2.def2tzvp.npz │ │ ├── 1h2o │ │ │ └── 140h2o.sphere.gfn2.md.500k.prod1.3h2o.dset.1h2o-dset.npz │ │ ├── 2h2o │ │ │ └── 16h2o.yoo.etal.boat.b.2h2o-dset.mb.npz │ │ └── 6h2o │ │ │ ├── 6h2o.temelso.etal-dset-no.data.npz │ │ │ └── 6h2o.temelso.etal-dset.npz │ ├── mbe │ │ ├── 4h2o-1body.npz │ │ ├── 4h2o-2body.npz │ │ ├── 4h2o-3body.npz │ │ └── 4h2o.npz │ ├── models │ │ ├── 140h2o.sphere.gfn2.md.500k.prod1.3h2o-model.mb-train500.npz │ │ ├── 140h2o.sphere.gfn2.md.500k.prod1.3h2o.dset.1h2o-model-train500.npz │ │ ├── 140h2o.sphere.gfn2.md.500k.prod1.3h2o.dset.2h2o.cm.6-model.mb-train500.npz │ │ └── 1h2o-model.npz │ ├── other │ │ ├── meoh-rdf │ │ │ ├── 61meoh-R.npy │ │ │ ├── 61meoh-Z.npy │ │ │ ├── 61meoh-comp_ids.npy │ │ │ └── 61meoh-entity_ids.npy │ │ └── r-for-centering │ │ │ ├── R.npy │ │ │ ├── R_center.npy │ │ │ └── Z.npy │ ├── structures │ │ └── h2o.xyz │ └── train │ │ └── 1h2o │ │ ├── K.npy │ │ ├── R_desc.npy │ │ ├── alphas_F.npy │ │ ├── train_idxs.npy │ │ ├── tril_perms_lin.npy │ │ └── valid_idxs.npy ├── test_datasets.py ├── test_descriptors.py ├── test_mbe.py ├── test_packmol_gen.py ├── test_predict.py ├── test_predictsets.py ├── test_rdf.py ├── test_structure_gen_utils.py ├── test_train.py └── test_utils.py 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