agox 3.8.0__tar.gz → 3.10.0rc1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {agox-3.8.0/agox.egg-info → agox-3.10.0rc1}/PKG-INFO +14 -8
- agox-3.10.0rc1/agox/__init__.py +24 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/models/GPR/priors/repulsive.c +144 -162
- {agox-3.8.0 → agox-3.10.0rc1}/agox/models/descriptors/fingerprint_cython/angular_fingerprintFeature_cy.c +144 -162
- agox-3.10.0rc1/agox/module.py +113 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/acquisitor_test/test_lcb.py +14 -15
- agox-3.10.0rc1/agox/test/analysis_tests/conftest.py +45 -0
- agox-3.10.0rc1/agox/test/analysis_tests/test_criterion.py +41 -0
- agox-3.10.0rc1/agox/test/analysis_tests/test_descriptor_property.py +64 -0
- agox-3.10.0rc1/agox/test/analysis_tests/test_energy_property.py +50 -0
- agox-3.10.0rc1/agox/test/analysis_tests/test_property_plot.py +19 -0
- agox-3.10.0rc1/agox/test/analysis_tests/test_restart_data.py +22 -0
- agox-3.10.0rc1/agox/test/analysis_tests/test_search_collection.py +26 -0
- agox-3.10.0rc1/agox/test/analysis_tests/test_search_data.py +69 -0
- agox-3.10.0rc1/agox/test/analysis_tests/test_succces_plot.py +21 -0
- agox-3.10.0rc1/agox/test/cli_tests/conftest.py +47 -0
- agox-3.10.0rc1/agox/test/cli_tests/test_analysis_cli.py +117 -0
- agox-3.10.0rc1/agox/test/cli_tests/test_convert_cli.py +19 -0
- agox-3.10.0rc1/agox/test/cli_tests/test_graph_sort_cli.py +26 -0
- agox-3.10.0rc1/agox/test/cli_tests/test_main_cli.py +9 -0
- agox-3.10.0rc1/agox/test/cli_tests/test_plot_cli.py +37 -0
- agox-3.10.0rc1/agox/test/conftest.py +113 -0
- agox-3.10.0rc1/agox/test/database_tests/conftest.py +65 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/database_tests/database_test.py +24 -18
- agox-3.10.0rc1/agox/test/database_tests/database_test_memory.py +56 -0
- agox-3.10.0rc1/agox/test/database_tests/database_test_written.py +54 -0
- agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db1.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db2.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db3.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db4.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db5.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/experiment.pckl +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/db1.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/db2.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/db3.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/db4.db +0 -0
- agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/experiment.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/soap_test.py +19 -15
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/spectral_graph_test.py +7 -24
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/empty_cache.py +6 -10
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/environment_tests/environment_test.py +13 -18
- agox-3.10.0rc1/agox/test/evaluator_tests/check_callback_test.py +52 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/conftest.py +33 -31
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/for_docs/nonseeded_script.py +5 -6
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/for_docs/seeded_script.py +6 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/for_docs/test_doc_scripts.py +6 -1
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/generator_test.py +22 -12
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/generator_utils.py +41 -26
- agox-3.10.0rc1/agox/test/generator_tests/test_cog.py +54 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_generators.py +26 -17
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_permutation.py +28 -17
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_random.py +22 -12
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_rattle.py +19 -13
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_replace.py +19 -13
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_sampling.py +21 -10
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_steepest_descent.py +19 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_symmetry.py +24 -13
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_symmetry_2.py +19 -15
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_symmetry_3.py +20 -13
- agox-3.10.0rc1/agox/test/model_tests/descriptors_api.py +20 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/gpr_api.py +1 -2
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/model_utils.py +16 -15
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_api.py +6 -8
- agox-3.10.0rc1/agox/test/model_tests/test_calculator_model.py +69 -0
- agox-3.10.0rc1/agox/test/model_tests/test_composition_model.py +45 -0
- agox-3.10.0rc1/agox/test/model_tests/test_global_gpr.py +80 -0
- agox-3.10.0rc1/agox/test/model_tests/test_global_gpr_jax.py +83 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_global_sparse_gpr.py +11 -5
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_global_sparse_gpr_force_training.py +11 -5
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_load.py +19 -16
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_local_gpr.py +14 -11
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_local_gpr_force_training.py +14 -11
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_ray_gpr.py +31 -29
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_ray_sgpr_ensemble_local.py +36 -31
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_ray_sgpr_global.py +39 -32
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_ray_sgpr_local.py +29 -29
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_sgpr_sparse_schedule.py +16 -13
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/modifying_examples/confinement_examples.py +32 -23
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/postprocessor_tests/disjoint_filtering_test.py +2 -3
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/postprocessor_tests/model_results_test.py +4 -9
- agox-3.10.0rc1/agox/test/postprocessor_tests/postprocessor_test.py +41 -0
- agox-3.10.0rc1/agox/test/postprocessor_tests/ray_relax.py +72 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/postprocessor_tests/surface_centering_test.py +4 -5
- agox-3.10.0rc1/agox/test/postprocessor_tests/test_survive_empty.py +34 -0
- agox-3.10.0rc1/agox/test/replica_exchange/conftest.py +66 -0
- agox-3.10.0rc1/agox/test/replica_exchange/test_sample.py +76 -0
- agox-3.10.0rc1/agox/test/replica_exchange/test_sampler.py +33 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/run_utils.py +27 -26
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_chgnet.py +6 -7
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_emt.py +6 -7
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_gpaw.py +8 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_vasp.py +38 -16
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_chgnet.py +3 -4
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_emt.py +3 -4
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_gpaw.py +5 -6
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_orca.py +9 -10
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_vasp.py +35 -13
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_chgnet.py +7 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_emt.py +7 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_gpaw.py +9 -11
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_vasp.py +39 -18
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test/automagic_analysis.ipynb +12 -7
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test_bh.py +4 -2
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/script_block_bh.py +0 -1
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/script_block_rss.py +1 -1
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/test_block_bh.py +2 -1
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/test_block_rss.py +2 -1
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/script_ce_default_gofee.py +12 -22
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/script_ce_gofee.py +17 -19
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/test_ce_default_gofee.py +5 -3
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/test_ce_gofee.py +5 -3
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ct/script_ct.py +6 -10
- agox-3.10.0rc1/agox/test/run_tests/tests_ct/test_ct.py +6 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ea/script_ea.py +7 -9
- agox-3.10.0rc1/agox/test/run_tests/tests_ea/test_ea.py +6 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_chgnet.py +13 -14
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_emt.py +13 -14
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_gpaw.py +15 -16
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_vasp.py +44 -23
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_chgnet.py +10 -11
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_emt.py +10 -11
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_gpaw.py +12 -13
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_orca.py +16 -17
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_vasp.py +41 -20
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_chgnet.py +14 -16
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_emt.py +14 -16
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_gpaw.py +16 -18
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_vasp.py +45 -24
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/test_gofee.py +3 -1
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_graph_filt/script_graph_filtering_gofee.py +18 -13
- agox-3.10.0rc1/agox/test/run_tests/tests_graph_filt/test_graph_filtering_gofee.py +10 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_lgpr_bh/script_lgpr_bh.py +10 -15
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_lgpr_bh/test_lgpr_bh.py +4 -3
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_md/script_md_bh.py +5 -7
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_md/test_md_bh.py +3 -1
- {agox-3.8.0/agox/test/run_tests/tests_pt/expected_outputs/pt_test → agox-3.10.0rc1/agox/test/run_tests/tests_pt/expected_outputs/rex_test}/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0/agox/test/run_tests/tests_pt/expected_outputs/pt_test → agox-3.10.0rc1/agox/test/run_tests/tests_pt/expected_outputs/rex_test}/confinement_plot_RattleGenerator.png +0 -0
- agox-3.10.0rc1/agox/test/run_tests/tests_pt/expected_outputs/rex_test/db0.db +0 -0
- agox-3.8.0/agox/test/run_tests/tests_pt/script_pt.py → agox-3.10.0rc1/agox/test/run_tests/tests_pt/script_rex.py +41 -16
- agox-3.10.0rc1/agox/test/run_tests/tests_pt/test_rex.py +10 -0
- agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/confinement_plot_RandomGenerator.png +0 -0
- agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/confinement_plot_RattleGenerator.png +0 -0
- agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/db0.db +0 -0
- agox-3.10.0rc1/agox/test/run_tests/tests_rex/script_rex_dft.py +149 -0
- agox-3.10.0rc1/agox/test/run_tests/tests_rex/script_rex_emt.py +143 -0
- agox-3.10.0rc1/agox/test/run_tests/tests_rex/test_replica.py +9 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_2d.py +6 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_chgnet.py +8 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_emt.py +8 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_gpaw.py +10 -11
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_vasp.py +40 -17
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_chgnet.py +5 -6
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_emt.py +5 -6
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_gpaw.py +9 -6
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_orca.py +13 -10
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_vasp.py +35 -11
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_chgnet.py +11 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_emt.py +11 -9
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_gpaw.py +13 -11
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_vasp.py +43 -17
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/test_rss.py +3 -2
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_schnet/script_schnet_bh.py +7 -13
- agox-3.10.0rc1/agox/test/run_tests/tests_schnet/test_schnet_bh.py +10 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/script_gofee_cluster_symmetry.py +12 -15
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/script_gofee_slab_symmetry.py +16 -20
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/script_rss_cluster_symmetry.py +7 -6
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/test_gofee_cluster_symmetry.py +5 -3
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/test_gofee_slab_symmetry.py +4 -2
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/test_rss_cluster_symmetry.py +4 -3
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/sampler_tests/sampler_test.py +14 -15
- agox-3.10.0rc1/agox/test/test_fixtures.py +15 -0
- agox-3.10.0rc1/agox/test/test_utils.py +132 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/cache_test.py +2 -6
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/plot_tests/colors_test.py +22 -12
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/plot_tests/plot_atoms_test.py +10 -18
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/plot_tests/plot_cell_test.py +2 -3
- agox-3.10.0rc1/agox/test/utils_tests/plot_tests/utils_test.py +26 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/test_feature_dist_filter.py +9 -7
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/test_filters.py +3 -4
- agox-3.10.0rc1/agox/test/utils_tests/test_sparsifiers.py +34 -0
- {agox-3.8.0 → agox-3.10.0rc1/agox.egg-info}/PKG-INFO +14 -8
- {agox-3.8.0 → agox-3.10.0rc1}/agox.egg-info/SOURCES.txt +49 -186
- {agox-3.8.0 → agox-3.10.0rc1}/agox.egg-info/requires.txt +9 -3
- {agox-3.8.0 → agox-3.10.0rc1}/pyproject.toml +46 -20
- agox-3.10.0rc1/setup.py +21 -0
- agox-3.8.0/agox/__init__.py +0 -25
- agox-3.8.0/agox/acquisitors/ABC_acquisitor.py +0 -211
- agox-3.8.0/agox/acquisitors/EI.py +0 -53
- agox-3.8.0/agox/acquisitors/LCB.py +0 -100
- agox-3.8.0/agox/acquisitors/LCB_penalty.py +0 -135
- agox-3.8.0/agox/acquisitors/LCB_power.py +0 -17
- agox-3.8.0/agox/acquisitors/__init__.py +0 -31
- agox-3.8.0/agox/acquisitors/meta_acquisitor.py +0 -28
- agox-3.8.0/agox/candidates/ABC_candidate.py +0 -376
- agox-3.8.0/agox/candidates/__init__.py +0 -12
- agox-3.8.0/agox/candidates/standard.py +0 -21
- agox-3.8.0/agox/cli/__init__.py +0 -6
- agox-3.8.0/agox/cli/cli_analysis.py +0 -152
- agox-3.8.0/agox/cli/cli_convert.py +0 -82
- agox-3.8.0/agox/cli/cli_example.py +0 -16
- agox-3.8.0/agox/cli/cli_graph_sorting.py +0 -134
- agox-3.8.0/agox/cli/cli_notebook.py +0 -116
- agox-3.8.0/agox/cli/main.py +0 -15
- agox-3.8.0/agox/collectors/ABC_collector.py +0 -152
- agox-3.8.0/agox/collectors/__init__.py +0 -10
- agox-3.8.0/agox/collectors/parallel_tempering.py +0 -165
- agox-3.8.0/agox/collectors/ray_collector.py +0 -97
- agox-3.8.0/agox/collectors/standard.py +0 -77
- agox-3.8.0/agox/databases/ABC_database.py +0 -103
- agox-3.8.0/agox/databases/__init__.py +0 -14
- agox-3.8.0/agox/databases/concurrent_ordered.py +0 -34
- agox-3.8.0/agox/databases/database.py +0 -458
- agox-3.8.0/agox/databases/database_concurrent.py +0 -216
- agox-3.8.0/agox/databases/database_utilities.py +0 -115
- agox-3.8.0/agox/environments/ABC_environment.py +0 -139
- agox-3.8.0/agox/environments/__init__.py +0 -16
- agox-3.8.0/agox/environments/environment.py +0 -138
- agox-3.8.0/agox/evaluators/ABC_evaluator.py +0 -119
- agox-3.8.0/agox/evaluators/__init__.py +0 -16
- agox-3.8.0/agox/evaluators/local_optimization.py +0 -127
- agox-3.8.0/agox/evaluators/rattle.py +0 -26
- agox-3.8.0/agox/evaluators/single_point.py +0 -19
- agox-3.8.0/agox/generators/ABC_generator.py +0 -219
- agox-3.8.0/agox/generators/MD.py +0 -154
- agox-3.8.0/agox/generators/__init__.py +0 -49
- agox-3.8.0/agox/generators/block_generators/ABC_block.py +0 -185
- agox-3.8.0/agox/generators/block_generators/__init__.py +0 -2
- agox-3.8.0/agox/generators/block_generators/random.py +0 -63
- agox-3.8.0/agox/generators/block_generators/rattle.py +0 -104
- agox-3.8.0/agox/generators/ce_generator.py +0 -132
- agox-3.8.0/agox/generators/cog.py +0 -57
- agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ABC_attractors.py +0 -32
- agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_another_structure.py +0 -57
- agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_current_structure.py +0 -53
- agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_interpolation.py +0 -61
- agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_kmeans.py +0 -68
- agox-3.8.0/agox/generators/complementary_energy/ce_calculators.py +0 -234
- agox-3.8.0/agox/generators/permutation.py +0 -151
- agox-3.8.0/agox/generators/random.py +0 -77
- agox-3.8.0/agox/generators/rattle.py +0 -69
- agox-3.8.0/agox/generators/replace.py +0 -74
- agox-3.8.0/agox/generators/reuse.py +0 -60
- agox-3.8.0/agox/generators/sampling.py +0 -27
- agox-3.8.0/agox/generators/steepest_descent.py +0 -55
- agox-3.8.0/agox/generators/symmetry.py +0 -340
- agox-3.8.0/agox/generators/symmetry_permutation.py +0 -233
- agox-3.8.0/agox/generators/symmetry_rattle.py +0 -475
- agox-3.8.0/agox/generators/symmetry_utils/symmetry_enforcer.py +0 -1758
- agox-3.8.0/agox/generators/symmetry_utils/symmetry_groups.py +0 -933
- agox-3.8.0/agox/helpers/__init__.py +0 -5
- agox-3.8.0/agox/helpers/confinement.py +0 -79
- agox-3.8.0/agox/helpers/gpaw_io.py +0 -169
- agox-3.8.0/agox/helpers/gpaw_subprocess.py +0 -58
- agox-3.8.0/agox/main.py +0 -305
- agox-3.8.0/agox/models/ABC_model.py +0 -618
- agox-3.8.0/agox/models/GPR/GPR.py +0 -895
- agox-3.8.0/agox/models/GPR/__init__.py +0 -5
- agox-3.8.0/agox/models/GPR/kernels/__init__.py +0 -1
- agox-3.8.0/agox/models/GPR/kernels/kernels.py +0 -149
- agox-3.8.0/agox/models/GPR/local_mean.py +0 -44
- agox-3.8.0/agox/models/GPR/priors/__init__.py +0 -1
- agox-3.8.0/agox/models/GPR/priors/setup.py +0 -5
- agox-3.8.0/agox/models/GPR/sGPR.py +0 -873
- agox-3.8.0/agox/models/GPR/sGPR_ensemble.py +0 -114
- agox-3.8.0/agox/models/__init__.py +0 -9
- agox-3.8.0/agox/models/datasets/__init__.py +0 -1
- agox-3.8.0/agox/models/datasets/loader.py +0 -10
- agox-3.8.0/agox/models/descriptors/ABC_descriptor.py +0 -155
- agox-3.8.0/agox/models/descriptors/__init__.py +0 -10
- agox-3.8.0/agox/models/descriptors/acsf.py +0 -176
- agox-3.8.0/agox/models/descriptors/exponential_density.py +0 -147
- agox-3.8.0/agox/models/descriptors/fingerprint.py +0 -130
- agox-3.8.0/agox/models/descriptors/fingerprint_cython/__init__.py +0 -0
- agox-3.8.0/agox/models/descriptors/fingerprint_cython/setup.py +0 -5
- agox-3.8.0/agox/models/descriptors/fingerprint_jax/__init__.py +0 -0
- agox-3.8.0/agox/models/descriptors/fingerprint_jax/compare_fingerprint.py +0 -114
- agox-3.8.0/agox/models/descriptors/fingerprint_jax/fingerprint_jax.py +0 -357
- agox-3.8.0/agox/models/descriptors/fingerprint_jax/utils.py +0 -355
- agox-3.8.0/agox/models/descriptors/scale_select_descriptor.py +0 -79
- agox-3.8.0/agox/models/descriptors/simple_fingerprint.py +0 -64
- agox-3.8.0/agox/models/descriptors/soap.py +0 -166
- agox-3.8.0/agox/models/descriptors/spectral_graph_descriptor.py +0 -78
- agox-3.8.0/agox/models/descriptors/type_descriptor.py +0 -47
- agox-3.8.0/agox/models/descriptors/voronoi.py +0 -264
- agox-3.8.0/agox/models/descriptors/voronoi_site.py +0 -124
- agox-3.8.0/agox/models/priors/constant.py +0 -12
- agox-3.8.0/agox/models/schnetpack/__init__.py +0 -0
- agox-3.8.0/agox/models/schnetpack/schnetpack.py +0 -432
- agox-3.8.0/agox/module.py +0 -130
- agox-3.8.0/agox/observer.py +0 -603
- agox-3.8.0/agox/postprocessors/ABC_postprocess.py +0 -127
- agox-3.8.0/agox/postprocessors/__init__.py +0 -29
- agox-3.8.0/agox/postprocessors/centering.py +0 -36
- agox-3.8.0/agox/postprocessors/disjoint_filtering.py +0 -87
- agox-3.8.0/agox/postprocessors/immunizer.py +0 -24
- agox-3.8.0/agox/postprocessors/minimum_dist.py +0 -88
- agox-3.8.0/agox/postprocessors/optimizers/__init__.py +0 -1
- agox-3.8.0/agox/postprocessors/optimizers/safe_bfgs.py +0 -31
- agox-3.8.0/agox/postprocessors/ray_relax.py +0 -154
- agox-3.8.0/agox/postprocessors/relax.py +0 -91
- agox-3.8.0/agox/postprocessors/surface_centering.py +0 -90
- agox-3.8.0/agox/postprocessors/wrap.py +0 -19
- agox-3.8.0/agox/samplers/ABC_sampler.py +0 -214
- agox-3.8.0/agox/samplers/__init__.py +0 -29
- agox-3.8.0/agox/samplers/concurrent_tempering.py +0 -143
- agox-3.8.0/agox/samplers/fixed_sampler.py +0 -39
- agox-3.8.0/agox/samplers/genetic.py +0 -208
- agox-3.8.0/agox/samplers/kernel_similarity.py +0 -144
- agox-3.8.0/agox/samplers/kmeans.py +0 -214
- agox-3.8.0/agox/samplers/metropolis.py +0 -93
- agox-3.8.0/agox/samplers/parallel_tempering.py +0 -316
- agox-3.8.0/agox/samplers/spectral_graph.py +0 -151
- agox-3.8.0/agox/test/__init__.py +0 -0
- agox-3.8.0/agox/test/conftest.py +0 -24
- agox-3.8.0/agox/test/generator_tests/test_cog.py +0 -42
- agox-3.8.0/agox/test/model_tests/__init__.py +0 -0
- agox-3.8.0/agox/test/model_tests/descriptors_api.py +0 -23
- agox-3.8.0/agox/test/model_tests/test_global_gpr.py +0 -73
- agox-3.8.0/agox/test/model_tests/test_global_gpr_jax.py +0 -74
- agox-3.8.0/agox/test/postprocessor_tests/postprocessor_test.py +0 -38
- agox-3.8.0/agox/test/postprocessor_tests/test_survive_empty.py +0 -34
- agox-3.8.0/agox/test/run_tests/tests_ct/test_ct.py +0 -5
- agox-3.8.0/agox/test/run_tests/tests_ea/test_ea.py +0 -5
- agox-3.8.0/agox/test/run_tests/tests_graph_filt/test_graph_filtering_gofee.py +0 -7
- agox-3.8.0/agox/test/run_tests/tests_pt/expected_outputs/pt_test/db0.db +0 -0
- agox-3.8.0/agox/test/run_tests/tests_pt/expected_outputs/pt_test/db0_tracker.npz +0 -0
- agox-3.8.0/agox/test/run_tests/tests_pt/test_pt.py +0 -7
- agox-3.8.0/agox/test/run_tests/tests_rss/test.py +0 -1
- agox-3.8.0/agox/test/run_tests/tests_schnet/test_schnet_bh.py +0 -9
- agox-3.8.0/agox/test/test_utils.py +0 -144
- agox-3.8.0/agox/test/utils_tests/analysis_test.py +0 -39
- agox-3.8.0/agox/test/utils_tests/plot_tests/utils_test.py +0 -23
- agox-3.8.0/agox/test/utils_tests/test_sparsifiers.py +0 -38
- agox-3.8.0/agox/test/utils_tests/tracker_test.py +0 -94
- agox-3.8.0/agox/tracker.py +0 -377
- agox-3.8.0/agox/utils/__init__.py +0 -1
- agox-3.8.0/agox/utils/batch_analysis.py +0 -843
- agox-3.8.0/agox/utils/cache.py +0 -74
- agox-3.8.0/agox/utils/constraints/__init__.py +0 -1
- agox-3.8.0/agox/utils/constraints/box_constraint.py +0 -173
- agox-3.8.0/agox/utils/convert_database.py +0 -100
- agox-3.8.0/agox/utils/data_selection.py +0 -110
- agox-3.8.0/agox/utils/decorators.py +0 -20
- agox-3.8.0/agox/utils/filters/ABC_filter.py +0 -102
- agox-3.8.0/agox/utils/filters/__init__.py +0 -26
- agox-3.8.0/agox/utils/filters/all.py +0 -25
- agox-3.8.0/agox/utils/filters/energy.py +0 -34
- agox-3.8.0/agox/utils/filters/feature_distance.py +0 -93
- agox-3.8.0/agox/utils/filters/filter.py +0 -57
- agox-3.8.0/agox/utils/filters/kmeans_energy.py +0 -57
- agox-3.8.0/agox/utils/filters/none.py +0 -25
- agox-3.8.0/agox/utils/filters/random.py +0 -29
- agox-3.8.0/agox/utils/filters/sparse_filter.py +0 -73
- agox-3.8.0/agox/utils/filters/voronoi.py +0 -119
- agox-3.8.0/agox/utils/graph_sorting.py +0 -136
- agox-3.8.0/agox/utils/jupyter_interactive.py +0 -310
- agox-3.8.0/agox/utils/matplotlib_utils.py +0 -14
- agox-3.8.0/agox/utils/metrics/__init__.py +0 -17
- agox-3.8.0/agox/utils/metrics/calibration.py +0 -285
- agox-3.8.0/agox/utils/metrics/metrics.py +0 -22
- agox-3.8.0/agox/utils/numerical_derivative.py +0 -25
- agox-3.8.0/agox/utils/plot/__init__.py +0 -4
- agox-3.8.0/agox/utils/plot/colors.py +0 -267
- agox-3.8.0/agox/utils/plot/plot_atoms.py +0 -150
- agox-3.8.0/agox/utils/plot/plot_cell.py +0 -82
- agox-3.8.0/agox/utils/plot/plot_parity.py +0 -188
- agox-3.8.0/agox/utils/plot/utils.py +0 -60
- agox-3.8.0/agox/utils/ray/__init__.py +0 -4
- agox-3.8.0/agox/utils/ray/actor.py +0 -68
- agox-3.8.0/agox/utils/ray/pool.py +0 -567
- agox-3.8.0/agox/utils/ray/pool_startup.py +0 -83
- agox-3.8.0/agox/utils/ray/pool_user.py +0 -191
- agox-3.8.0/agox/utils/ray/startup.py +0 -160
- agox-3.8.0/agox/utils/ray/testing/__init__.py +0 -2
- agox-3.8.0/agox/utils/ray/testing/log_reader.py +0 -103
- agox-3.8.0/agox/utils/ray/testing/slurm_test_functions.py +0 -81
- agox-3.8.0/agox/utils/sparsifiers/ABC_sparsifier.py +0 -125
- agox-3.8.0/agox/utils/sparsifiers/CUR.py +0 -23
- agox-3.8.0/agox/utils/sparsifiers/CUR_old.py +0 -24
- agox-3.8.0/agox/utils/sparsifiers/MBkmeans.py +0 -69
- agox-3.8.0/agox/utils/sparsifiers/__init__.py +0 -10
- agox-3.8.0/agox/utils/sparsifiers/random.py +0 -18
- agox-3.8.0/agox/writer.py +0 -153
- agox-3.8.0/setup.py +0 -19
- {agox-3.8.0 → agox-3.10.0rc1}/LICENSE.txt +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/MANIFEST.in +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/README.md +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/models/GPR/priors/repulsive.pyx +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/models/datasets/Ag5O3-dataset.traj +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/models/descriptors/fingerprint_cython/angular_fingerprintFeature_cy.pyx +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/.coveragerc +0 -0
- {agox-3.8.0/agox/generators/complementary_energy → agox-3.10.0rc1/agox/test}/__init__.py +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/AgO-dataset.traj +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/B12-dataset.traj +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/C30-dataset.traj +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/databases/mos2_databases/db1.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/databases/mos2_databases/db2.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_AgO.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_B12.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_C30.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/PermutationGenerator_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/PermutationGenerator_dataAgO_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/PermutationGenerator_dataAgO_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataAgO_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataAgO_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataB12_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataB12_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataC30_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataC30_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataAgO_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataAgO_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataB12_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataB12_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataC30_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataC30_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataAgO_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataAgO_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataB12_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataB12_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataC30_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/ReplaceGenerator_dataC30_parameter2.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SamplingGenerator_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SamplingGenerator_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SamplingGenerator_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SteepestDescentGenerator_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SteepestDescentGenerator_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SteepestDescentGenerator_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SymmetryGenerator_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SymmetryGenerator_dataAgO_parameter1.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SymmetryGenerator_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/SymmetryGenerator_dataB12_parameter1.pckl +0 -0
- {agox-3.8.0/agox/generators/complementary_energy/attractor_methods → agox-3.10.0rc1/agox/test/model_tests}/__init__.py +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/GlobalGPRJax_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/GlobalGPRJax_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/GlobalGPRJax_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/GlobalGPR_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/GlobalGPR_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/GlobalGPR_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/LocalSparseGPRForces_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/LocalSparseGPRForces_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/LocalSparseGPRForces_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/LocalSparseGPR_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/LocalSparseGPR_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/LocalSparseGPR_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/globalSparseGPRForces_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/globalSparseGPRForces_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/globalSparseGPRForces_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/globalSparseGPR_dataAgO_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/globalSparseGPR_dataB12_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/expected_outputs/globalSparseGPR_dataC30_parameter0.pckl +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/load_api.py +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/sgpr_api.py +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/sgpr_api_forces.py +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/modifying_examples/plots/cluster_confinement.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/modifying_examples/plots/surface_cluster_confinement.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/modifying_examples/plots/surface_film_confinement.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/modifying_examples/plots/surface_toplayer_unc.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/modifying_examples/plots/two_d_environment.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/expected_outputs/bh_bulk_emt_test/confinement_plot_RattleGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/expected_outputs/bh_bulk_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/expected_outputs/bh_bulk_emt_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/expected_outputs/bh_cluster_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/expected_outputs/bh_surface_emt_test/confinement_plot_RattleGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/expected_outputs/bh_surface_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/expected_outputs/bh_surface_emt_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test/confinement_plot_RattleGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test/dbs/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test/dbs/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/expected_outputs/block_bh_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/expected_outputs/block_bh_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/expected_outputs/block_rss_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/expected_outputs/block_rss_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/expected_outputs/ce_default_gofee_test/confinement_plot_ComplementaryEnergyGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/expected_outputs/ce_default_gofee_test/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/expected_outputs/ce_default_gofee_test/confinement_plot_RattleGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/expected_outputs/ce_default_gofee_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/expected_outputs/ce_gofee_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ct/expected_outputs/ct_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ea/expected_outputs/ea_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ea/expected_outputs/ea_test/population_5.traj +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_bulk_emt_test/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_bulk_emt_test/confinement_plot_RattleGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_bulk_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_bulk_emt_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_cluster_emt_test/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_cluster_emt_test/confinement_plot_RattleGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_cluster_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_surface_emt_test/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_surface_emt_test/confinement_plot_RattleGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_surface_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/expected_outputs/gofee_surface_emt_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_graph_filt/expected_outputs/graph_filtering_gofee_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_graph_filt/expected_outputs/graph_filtering_gofee_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_lgpr_bh/expected_outputs/lgpr_bh_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_md/expected_outputs/md_bh_test/confinement_plot_MDgenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_md/expected_outputs/md_bh_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_md/expected_outputs/md_bh_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_2d_test/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_2d_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_bulk_emt_test/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_bulk_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_bulk_emt_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_cluster_emt_test/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_cluster_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_cluster_emt_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_surface_emt_test/confinement_plot_RandomGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_surface_emt_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/expected_outputs/rss_surface_emt_test/db0_tracker.npz +0 -0
- /agox-3.8.0/agox/generators/symmetry_utils/__init__.py → /agox-3.10.0rc1/agox/test/run_tests/tests_rss/test.py +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/gofee_cluster_symmetry_test/confinement_plot_RattleGeneratorSym.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/gofee_cluster_symmetry_test/confinement_plot_SymmetryGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/gofee_cluster_symmetry_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/gofee_cluster_symmetry_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/gofee_slab_symmetry_test/confinement_plot_RattleGeneratorSym.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/gofee_slab_symmetry_test/confinement_plot_SymmetryGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/gofee_slab_symmetry_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/gofee_slab_symmetry_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/rss_cluster_symmetry_test/confinement_plot_SymmetryGenerator.png +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/rss_cluster_symmetry_test/db0.db +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/expected_outputs/rss_cluster_symmetry_test/db0_tracker.npz +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox.egg-info/dependency_links.txt +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox.egg-info/entry_points.txt +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/agox.egg-info/top_level.txt +0 -0
- {agox-3.8.0 → agox-3.10.0rc1}/setup.cfg +0 -0
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
Metadata-Version: 2.
|
|
1
|
+
Metadata-Version: 2.4
|
|
2
2
|
Name: agox
|
|
3
|
-
Version: 3.
|
|
3
|
+
Version: 3.10.0rc1
|
|
4
4
|
Summary: Atomistic Global Optimziation X is a framework for structure optimization in materials science.
|
|
5
5
|
Author: AGOX Developers
|
|
6
6
|
Author-email: "Mads-Peter V. Christiansen" <machri@phys.au.dk>, Nikolaj Rønne <nronne@phys.au.dk>, Bjørk Hammer <hammer@phys.au.dk>
|
|
@@ -11,14 +11,15 @@ Classifier: Development Status :: 5 - Production/Stable
|
|
|
11
11
|
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
|
|
12
12
|
Classifier: Intended Audience :: Science/Research
|
|
13
13
|
Classifier: Operating System :: OS Independent
|
|
14
|
-
Classifier: Programming Language :: Python :: 3.8
|
|
15
|
-
Classifier: Programming Language :: Python :: 3.9
|
|
16
14
|
Classifier: Programming Language :: Python :: 3.10
|
|
17
15
|
Classifier: Programming Language :: Python :: 3.11
|
|
18
|
-
|
|
16
|
+
Classifier: Programming Language :: Python :: 3.12
|
|
17
|
+
Classifier: Programming Language :: Python :: 3.13
|
|
18
|
+
Requires-Python: >=3.10
|
|
19
19
|
Description-Content-Type: text/markdown
|
|
20
20
|
License-File: LICENSE.txt
|
|
21
|
-
Requires-Dist: numpy
|
|
21
|
+
Requires-Dist: numpy<2
|
|
22
|
+
Requires-Dist: scipy
|
|
22
23
|
Requires-Dist: ase
|
|
23
24
|
Requires-Dist: matplotlib
|
|
24
25
|
Requires-Dist: cymem
|
|
@@ -29,19 +30,24 @@ Requires-Dist: importlib-resources>1.3; python_version < "3.9"
|
|
|
29
30
|
Requires-Dist: dscribe>=2.0.0
|
|
30
31
|
Requires-Dist: nbformat
|
|
31
32
|
Requires-Dist: typing_extensions
|
|
32
|
-
Requires-Dist: jax
|
|
33
|
-
Requires-Dist: jaxlib
|
|
34
33
|
Requires-Dist: ray
|
|
34
|
+
Requires-Dist: rich-click>=1.8.3
|
|
35
35
|
Provides-Extra: test
|
|
36
36
|
Requires-Dist: pytest; extra == "test"
|
|
37
|
+
Requires-Dist: pytest-mock; extra == "test"
|
|
37
38
|
Provides-Extra: docs
|
|
38
39
|
Requires-Dist: sphinx; extra == "docs"
|
|
39
40
|
Requires-Dist: furo; extra == "docs"
|
|
40
41
|
Requires-Dist: sphinx-autoapi; extra == "docs"
|
|
41
42
|
Requires-Dist: sphinx-copybutton; extra == "docs"
|
|
42
43
|
Requires-Dist: sphinx-tabs; extra == "docs"
|
|
44
|
+
Provides-Extra: torchjax
|
|
45
|
+
Requires-Dist: torch; extra == "torchjax"
|
|
46
|
+
Requires-Dist: jax; extra == "torchjax"
|
|
47
|
+
Requires-Dist: jaxlib; extra == "torchjax"
|
|
43
48
|
Provides-Extra: all
|
|
44
49
|
Requires-Dist: agox[docs,test]; extra == "all"
|
|
50
|
+
Dynamic: license-file
|
|
45
51
|
|
|
46
52
|
# Atomistic Global Optimization X (AGOX)
|
|
47
53
|
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
import os
|
|
2
|
+
|
|
3
|
+
# Versioning
|
|
4
|
+
__version_info__ = (3, 10, 0)
|
|
5
|
+
__version__ = "{}.{}.{}".format(*__version_info__)
|
|
6
|
+
|
|
7
|
+
# Extra versioning - Mainly for managing Pypi releases.
|
|
8
|
+
version_extra = os.environ.get("AGOX_VERSION_EXTRA", None)
|
|
9
|
+
if version_extra:
|
|
10
|
+
__version__ = "{}{}".format(__version__, version_extra)
|
|
11
|
+
|
|
12
|
+
try: # When installing the package we don't need to actually import.
|
|
13
|
+
from agox.module import Module # noqa
|
|
14
|
+
from agox.observer import Observer
|
|
15
|
+
from agox.writer import Writer
|
|
16
|
+
from agox.cli.main import main
|
|
17
|
+
from agox.main.state import State
|
|
18
|
+
from agox.main.agox import AGOX
|
|
19
|
+
|
|
20
|
+
__all__ = ["Module", "Observer", "Writer", "State", "AGOX", "__version__", "main"]
|
|
21
|
+
|
|
22
|
+
except ImportError as e:
|
|
23
|
+
print(e)
|
|
24
|
+
pass
|