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.
Files changed (544) hide show
  1. {agox-3.8.0/agox.egg-info → agox-3.10.0rc1}/PKG-INFO +14 -8
  2. agox-3.10.0rc1/agox/__init__.py +24 -0
  3. {agox-3.8.0 → agox-3.10.0rc1}/agox/models/GPR/priors/repulsive.c +144 -162
  4. {agox-3.8.0 → agox-3.10.0rc1}/agox/models/descriptors/fingerprint_cython/angular_fingerprintFeature_cy.c +144 -162
  5. agox-3.10.0rc1/agox/module.py +113 -0
  6. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/acquisitor_test/test_lcb.py +14 -15
  7. agox-3.10.0rc1/agox/test/analysis_tests/conftest.py +45 -0
  8. agox-3.10.0rc1/agox/test/analysis_tests/test_criterion.py +41 -0
  9. agox-3.10.0rc1/agox/test/analysis_tests/test_descriptor_property.py +64 -0
  10. agox-3.10.0rc1/agox/test/analysis_tests/test_energy_property.py +50 -0
  11. agox-3.10.0rc1/agox/test/analysis_tests/test_property_plot.py +19 -0
  12. agox-3.10.0rc1/agox/test/analysis_tests/test_restart_data.py +22 -0
  13. agox-3.10.0rc1/agox/test/analysis_tests/test_search_collection.py +26 -0
  14. agox-3.10.0rc1/agox/test/analysis_tests/test_search_data.py +69 -0
  15. agox-3.10.0rc1/agox/test/analysis_tests/test_succces_plot.py +21 -0
  16. agox-3.10.0rc1/agox/test/cli_tests/conftest.py +47 -0
  17. agox-3.10.0rc1/agox/test/cli_tests/test_analysis_cli.py +117 -0
  18. agox-3.10.0rc1/agox/test/cli_tests/test_convert_cli.py +19 -0
  19. agox-3.10.0rc1/agox/test/cli_tests/test_graph_sort_cli.py +26 -0
  20. agox-3.10.0rc1/agox/test/cli_tests/test_main_cli.py +9 -0
  21. agox-3.10.0rc1/agox/test/cli_tests/test_plot_cli.py +37 -0
  22. agox-3.10.0rc1/agox/test/conftest.py +113 -0
  23. agox-3.10.0rc1/agox/test/database_tests/conftest.py +65 -0
  24. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/database_tests/database_test.py +24 -18
  25. agox-3.10.0rc1/agox/test/database_tests/database_test_memory.py +56 -0
  26. agox-3.10.0rc1/agox/test/database_tests/database_test_written.py +54 -0
  27. agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db1.db +0 -0
  28. agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db2.db +0 -0
  29. agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db3.db +0 -0
  30. agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db4.db +0 -0
  31. agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/db5.db +0 -0
  32. agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/experiment.pckl +0 -0
  33. agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/db1.db +0 -0
  34. agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/db2.db +0 -0
  35. agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/db3.db +0 -0
  36. agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/db4.db +0 -0
  37. agox-3.10.0rc1/agox/test/datasets/databases/rss_test_databases/experiment.pckl +0 -0
  38. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/soap_test.py +19 -15
  39. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/spectral_graph_test.py +7 -24
  40. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/empty_cache.py +6 -10
  41. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/environment_tests/environment_test.py +13 -18
  42. agox-3.10.0rc1/agox/test/evaluator_tests/check_callback_test.py +52 -0
  43. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/conftest.py +33 -31
  44. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/for_docs/nonseeded_script.py +5 -6
  45. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/for_docs/seeded_script.py +6 -9
  46. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/for_docs/test_doc_scripts.py +6 -1
  47. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/generator_test.py +22 -12
  48. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/generator_utils.py +41 -26
  49. agox-3.10.0rc1/agox/test/generator_tests/test_cog.py +54 -0
  50. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_generators.py +26 -17
  51. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_permutation.py +28 -17
  52. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_random.py +22 -12
  53. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_rattle.py +19 -13
  54. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_replace.py +19 -13
  55. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_sampling.py +21 -10
  56. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_steepest_descent.py +19 -9
  57. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_symmetry.py +24 -13
  58. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_symmetry_2.py +19 -15
  59. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_symmetry_3.py +20 -13
  60. agox-3.10.0rc1/agox/test/model_tests/descriptors_api.py +20 -0
  61. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/gpr_api.py +1 -2
  62. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/model_utils.py +16 -15
  63. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_api.py +6 -8
  64. agox-3.10.0rc1/agox/test/model_tests/test_calculator_model.py +69 -0
  65. agox-3.10.0rc1/agox/test/model_tests/test_composition_model.py +45 -0
  66. agox-3.10.0rc1/agox/test/model_tests/test_global_gpr.py +80 -0
  67. agox-3.10.0rc1/agox/test/model_tests/test_global_gpr_jax.py +83 -0
  68. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_global_sparse_gpr.py +11 -5
  69. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_global_sparse_gpr_force_training.py +11 -5
  70. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_load.py +19 -16
  71. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_local_gpr.py +14 -11
  72. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_local_gpr_force_training.py +14 -11
  73. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_ray_gpr.py +31 -29
  74. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_ray_sgpr_ensemble_local.py +36 -31
  75. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_ray_sgpr_global.py +39 -32
  76. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_ray_sgpr_local.py +29 -29
  77. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/model_tests/test_sgpr_sparse_schedule.py +16 -13
  78. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/modifying_examples/confinement_examples.py +32 -23
  79. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/postprocessor_tests/disjoint_filtering_test.py +2 -3
  80. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/postprocessor_tests/model_results_test.py +4 -9
  81. agox-3.10.0rc1/agox/test/postprocessor_tests/postprocessor_test.py +41 -0
  82. agox-3.10.0rc1/agox/test/postprocessor_tests/ray_relax.py +72 -0
  83. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/postprocessor_tests/surface_centering_test.py +4 -5
  84. agox-3.10.0rc1/agox/test/postprocessor_tests/test_survive_empty.py +34 -0
  85. agox-3.10.0rc1/agox/test/replica_exchange/conftest.py +66 -0
  86. agox-3.10.0rc1/agox/test/replica_exchange/test_sample.py +76 -0
  87. agox-3.10.0rc1/agox/test/replica_exchange/test_sampler.py +33 -0
  88. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/run_utils.py +27 -26
  89. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_chgnet.py +6 -7
  90. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_emt.py +6 -7
  91. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_gpaw.py +8 -9
  92. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_vasp.py +38 -16
  93. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_chgnet.py +3 -4
  94. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_emt.py +3 -4
  95. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_gpaw.py +5 -6
  96. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_orca.py +9 -10
  97. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_vasp.py +35 -13
  98. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_chgnet.py +7 -9
  99. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_emt.py +7 -9
  100. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_gpaw.py +9 -11
  101. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_vasp.py +39 -18
  102. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test/automagic_analysis.ipynb +12 -7
  103. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/test_bh.py +4 -2
  104. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/script_block_bh.py +0 -1
  105. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/script_block_rss.py +1 -1
  106. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/test_block_bh.py +2 -1
  107. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_block/test_block_rss.py +2 -1
  108. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/script_ce_default_gofee.py +12 -22
  109. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/script_ce_gofee.py +17 -19
  110. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/test_ce_default_gofee.py +5 -3
  111. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ce/test_ce_gofee.py +5 -3
  112. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ct/script_ct.py +6 -10
  113. agox-3.10.0rc1/agox/test/run_tests/tests_ct/test_ct.py +6 -0
  114. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_ea/script_ea.py +7 -9
  115. agox-3.10.0rc1/agox/test/run_tests/tests_ea/test_ea.py +6 -0
  116. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_chgnet.py +13 -14
  117. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_emt.py +13 -14
  118. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_gpaw.py +15 -16
  119. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_vasp.py +44 -23
  120. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_chgnet.py +10 -11
  121. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_emt.py +10 -11
  122. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_gpaw.py +12 -13
  123. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_orca.py +16 -17
  124. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_vasp.py +41 -20
  125. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_chgnet.py +14 -16
  126. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_emt.py +14 -16
  127. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_gpaw.py +16 -18
  128. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_vasp.py +45 -24
  129. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/test_gofee.py +3 -1
  130. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_graph_filt/script_graph_filtering_gofee.py +18 -13
  131. agox-3.10.0rc1/agox/test/run_tests/tests_graph_filt/test_graph_filtering_gofee.py +10 -0
  132. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_lgpr_bh/script_lgpr_bh.py +10 -15
  133. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_lgpr_bh/test_lgpr_bh.py +4 -3
  134. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_md/script_md_bh.py +5 -7
  135. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_md/test_md_bh.py +3 -1
  136. {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
  137. {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
  138. agox-3.10.0rc1/agox/test/run_tests/tests_pt/expected_outputs/rex_test/db0.db +0 -0
  139. 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
  140. agox-3.10.0rc1/agox/test/run_tests/tests_pt/test_rex.py +10 -0
  141. agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/confinement_plot_RandomGenerator.png +0 -0
  142. agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/confinement_plot_RattleGenerator.png +0 -0
  143. agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/db0.db +0 -0
  144. agox-3.10.0rc1/agox/test/run_tests/tests_rex/script_rex_dft.py +149 -0
  145. agox-3.10.0rc1/agox/test/run_tests/tests_rex/script_rex_emt.py +143 -0
  146. agox-3.10.0rc1/agox/test/run_tests/tests_rex/test_replica.py +9 -0
  147. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_2d.py +6 -9
  148. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_chgnet.py +8 -9
  149. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_emt.py +8 -9
  150. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_gpaw.py +10 -11
  151. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_vasp.py +40 -17
  152. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_chgnet.py +5 -6
  153. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_emt.py +5 -6
  154. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_gpaw.py +9 -6
  155. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_orca.py +13 -10
  156. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_vasp.py +35 -11
  157. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_chgnet.py +11 -9
  158. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_emt.py +11 -9
  159. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_gpaw.py +13 -11
  160. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_vasp.py +43 -17
  161. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/test_rss.py +3 -2
  162. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_schnet/script_schnet_bh.py +7 -13
  163. agox-3.10.0rc1/agox/test/run_tests/tests_schnet/test_schnet_bh.py +10 -0
  164. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/script_gofee_cluster_symmetry.py +12 -15
  165. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/script_gofee_slab_symmetry.py +16 -20
  166. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/script_rss_cluster_symmetry.py +7 -6
  167. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/test_gofee_cluster_symmetry.py +5 -3
  168. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/test_gofee_slab_symmetry.py +4 -2
  169. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_symmetry/test_rss_cluster_symmetry.py +4 -3
  170. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/sampler_tests/sampler_test.py +14 -15
  171. agox-3.10.0rc1/agox/test/test_fixtures.py +15 -0
  172. agox-3.10.0rc1/agox/test/test_utils.py +132 -0
  173. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/cache_test.py +2 -6
  174. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/plot_tests/colors_test.py +22 -12
  175. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/plot_tests/plot_atoms_test.py +10 -18
  176. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/plot_tests/plot_cell_test.py +2 -3
  177. agox-3.10.0rc1/agox/test/utils_tests/plot_tests/utils_test.py +26 -0
  178. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/test_feature_dist_filter.py +9 -7
  179. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/utils_tests/test_filters.py +3 -4
  180. agox-3.10.0rc1/agox/test/utils_tests/test_sparsifiers.py +34 -0
  181. {agox-3.8.0 → agox-3.10.0rc1/agox.egg-info}/PKG-INFO +14 -8
  182. {agox-3.8.0 → agox-3.10.0rc1}/agox.egg-info/SOURCES.txt +49 -186
  183. {agox-3.8.0 → agox-3.10.0rc1}/agox.egg-info/requires.txt +9 -3
  184. {agox-3.8.0 → agox-3.10.0rc1}/pyproject.toml +46 -20
  185. agox-3.10.0rc1/setup.py +21 -0
  186. agox-3.8.0/agox/__init__.py +0 -25
  187. agox-3.8.0/agox/acquisitors/ABC_acquisitor.py +0 -211
  188. agox-3.8.0/agox/acquisitors/EI.py +0 -53
  189. agox-3.8.0/agox/acquisitors/LCB.py +0 -100
  190. agox-3.8.0/agox/acquisitors/LCB_penalty.py +0 -135
  191. agox-3.8.0/agox/acquisitors/LCB_power.py +0 -17
  192. agox-3.8.0/agox/acquisitors/__init__.py +0 -31
  193. agox-3.8.0/agox/acquisitors/meta_acquisitor.py +0 -28
  194. agox-3.8.0/agox/candidates/ABC_candidate.py +0 -376
  195. agox-3.8.0/agox/candidates/__init__.py +0 -12
  196. agox-3.8.0/agox/candidates/standard.py +0 -21
  197. agox-3.8.0/agox/cli/__init__.py +0 -6
  198. agox-3.8.0/agox/cli/cli_analysis.py +0 -152
  199. agox-3.8.0/agox/cli/cli_convert.py +0 -82
  200. agox-3.8.0/agox/cli/cli_example.py +0 -16
  201. agox-3.8.0/agox/cli/cli_graph_sorting.py +0 -134
  202. agox-3.8.0/agox/cli/cli_notebook.py +0 -116
  203. agox-3.8.0/agox/cli/main.py +0 -15
  204. agox-3.8.0/agox/collectors/ABC_collector.py +0 -152
  205. agox-3.8.0/agox/collectors/__init__.py +0 -10
  206. agox-3.8.0/agox/collectors/parallel_tempering.py +0 -165
  207. agox-3.8.0/agox/collectors/ray_collector.py +0 -97
  208. agox-3.8.0/agox/collectors/standard.py +0 -77
  209. agox-3.8.0/agox/databases/ABC_database.py +0 -103
  210. agox-3.8.0/agox/databases/__init__.py +0 -14
  211. agox-3.8.0/agox/databases/concurrent_ordered.py +0 -34
  212. agox-3.8.0/agox/databases/database.py +0 -458
  213. agox-3.8.0/agox/databases/database_concurrent.py +0 -216
  214. agox-3.8.0/agox/databases/database_utilities.py +0 -115
  215. agox-3.8.0/agox/environments/ABC_environment.py +0 -139
  216. agox-3.8.0/agox/environments/__init__.py +0 -16
  217. agox-3.8.0/agox/environments/environment.py +0 -138
  218. agox-3.8.0/agox/evaluators/ABC_evaluator.py +0 -119
  219. agox-3.8.0/agox/evaluators/__init__.py +0 -16
  220. agox-3.8.0/agox/evaluators/local_optimization.py +0 -127
  221. agox-3.8.0/agox/evaluators/rattle.py +0 -26
  222. agox-3.8.0/agox/evaluators/single_point.py +0 -19
  223. agox-3.8.0/agox/generators/ABC_generator.py +0 -219
  224. agox-3.8.0/agox/generators/MD.py +0 -154
  225. agox-3.8.0/agox/generators/__init__.py +0 -49
  226. agox-3.8.0/agox/generators/block_generators/ABC_block.py +0 -185
  227. agox-3.8.0/agox/generators/block_generators/__init__.py +0 -2
  228. agox-3.8.0/agox/generators/block_generators/random.py +0 -63
  229. agox-3.8.0/agox/generators/block_generators/rattle.py +0 -104
  230. agox-3.8.0/agox/generators/ce_generator.py +0 -132
  231. agox-3.8.0/agox/generators/cog.py +0 -57
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  233. agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_another_structure.py +0 -57
  234. agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_current_structure.py +0 -53
  235. agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_interpolation.py +0 -61
  236. agox-3.8.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_kmeans.py +0 -68
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  239. agox-3.8.0/agox/generators/random.py +0 -77
  240. agox-3.8.0/agox/generators/rattle.py +0 -69
  241. agox-3.8.0/agox/generators/replace.py +0 -74
  242. agox-3.8.0/agox/generators/reuse.py +0 -60
  243. agox-3.8.0/agox/generators/sampling.py +0 -27
  244. agox-3.8.0/agox/generators/steepest_descent.py +0 -55
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  247. agox-3.8.0/agox/generators/symmetry_rattle.py +0 -475
  248. agox-3.8.0/agox/generators/symmetry_utils/symmetry_enforcer.py +0 -1758
  249. agox-3.8.0/agox/generators/symmetry_utils/symmetry_groups.py +0 -933
  250. agox-3.8.0/agox/helpers/__init__.py +0 -5
  251. agox-3.8.0/agox/helpers/confinement.py +0 -79
  252. agox-3.8.0/agox/helpers/gpaw_io.py +0 -169
  253. agox-3.8.0/agox/helpers/gpaw_subprocess.py +0 -58
  254. agox-3.8.0/agox/main.py +0 -305
  255. agox-3.8.0/agox/models/ABC_model.py +0 -618
  256. agox-3.8.0/agox/models/GPR/GPR.py +0 -895
  257. agox-3.8.0/agox/models/GPR/__init__.py +0 -5
  258. agox-3.8.0/agox/models/GPR/kernels/__init__.py +0 -1
  259. agox-3.8.0/agox/models/GPR/kernels/kernels.py +0 -149
  260. agox-3.8.0/agox/models/GPR/local_mean.py +0 -44
  261. agox-3.8.0/agox/models/GPR/priors/__init__.py +0 -1
  262. agox-3.8.0/agox/models/GPR/priors/setup.py +0 -5
  263. agox-3.8.0/agox/models/GPR/sGPR.py +0 -873
  264. agox-3.8.0/agox/models/GPR/sGPR_ensemble.py +0 -114
  265. agox-3.8.0/agox/models/__init__.py +0 -9
  266. agox-3.8.0/agox/models/datasets/__init__.py +0 -1
  267. agox-3.8.0/agox/models/datasets/loader.py +0 -10
  268. agox-3.8.0/agox/models/descriptors/ABC_descriptor.py +0 -155
  269. agox-3.8.0/agox/models/descriptors/__init__.py +0 -10
  270. agox-3.8.0/agox/models/descriptors/acsf.py +0 -176
  271. agox-3.8.0/agox/models/descriptors/exponential_density.py +0 -147
  272. agox-3.8.0/agox/models/descriptors/fingerprint.py +0 -130
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  274. agox-3.8.0/agox/models/descriptors/fingerprint_cython/setup.py +0 -5
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  278. agox-3.8.0/agox/models/descriptors/fingerprint_jax/utils.py +0 -355
  279. agox-3.8.0/agox/models/descriptors/scale_select_descriptor.py +0 -79
  280. agox-3.8.0/agox/models/descriptors/simple_fingerprint.py +0 -64
  281. agox-3.8.0/agox/models/descriptors/soap.py +0 -166
  282. agox-3.8.0/agox/models/descriptors/spectral_graph_descriptor.py +0 -78
  283. agox-3.8.0/agox/models/descriptors/type_descriptor.py +0 -47
  284. agox-3.8.0/agox/models/descriptors/voronoi.py +0 -264
  285. agox-3.8.0/agox/models/descriptors/voronoi_site.py +0 -124
  286. agox-3.8.0/agox/models/priors/constant.py +0 -12
  287. agox-3.8.0/agox/models/schnetpack/__init__.py +0 -0
  288. agox-3.8.0/agox/models/schnetpack/schnetpack.py +0 -432
  289. agox-3.8.0/agox/module.py +0 -130
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  295. agox-3.8.0/agox/postprocessors/immunizer.py +0 -24
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  300. agox-3.8.0/agox/postprocessors/relax.py +0 -91
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  304. agox-3.8.0/agox/samplers/__init__.py +0 -29
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  308. agox-3.8.0/agox/samplers/kernel_similarity.py +0 -144
  309. agox-3.8.0/agox/samplers/kmeans.py +0 -214
  310. agox-3.8.0/agox/samplers/metropolis.py +0 -93
  311. agox-3.8.0/agox/samplers/parallel_tempering.py +0 -316
  312. agox-3.8.0/agox/samplers/spectral_graph.py +0 -151
  313. agox-3.8.0/agox/test/__init__.py +0 -0
  314. agox-3.8.0/agox/test/conftest.py +0 -24
  315. agox-3.8.0/agox/test/generator_tests/test_cog.py +0 -42
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  317. agox-3.8.0/agox/test/model_tests/descriptors_api.py +0 -23
  318. agox-3.8.0/agox/test/model_tests/test_global_gpr.py +0 -73
  319. agox-3.8.0/agox/test/model_tests/test_global_gpr_jax.py +0 -74
  320. agox-3.8.0/agox/test/postprocessor_tests/postprocessor_test.py +0 -38
  321. agox-3.8.0/agox/test/postprocessor_tests/test_survive_empty.py +0 -34
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  323. agox-3.8.0/agox/test/run_tests/tests_ea/test_ea.py +0 -5
  324. agox-3.8.0/agox/test/run_tests/tests_graph_filt/test_graph_filtering_gofee.py +0 -7
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  326. agox-3.8.0/agox/test/run_tests/tests_pt/expected_outputs/pt_test/db0_tracker.npz +0 -0
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  329. agox-3.8.0/agox/test/run_tests/tests_schnet/test_schnet_bh.py +0 -9
  330. agox-3.8.0/agox/test/test_utils.py +0 -144
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  332. agox-3.8.0/agox/test/utils_tests/plot_tests/utils_test.py +0 -23
  333. agox-3.8.0/agox/test/utils_tests/test_sparsifiers.py +0 -38
  334. agox-3.8.0/agox/test/utils_tests/tracker_test.py +0 -94
  335. agox-3.8.0/agox/tracker.py +0 -377
  336. agox-3.8.0/agox/utils/__init__.py +0 -1
  337. agox-3.8.0/agox/utils/batch_analysis.py +0 -843
  338. agox-3.8.0/agox/utils/cache.py +0 -74
  339. agox-3.8.0/agox/utils/constraints/__init__.py +0 -1
  340. agox-3.8.0/agox/utils/constraints/box_constraint.py +0 -173
  341. agox-3.8.0/agox/utils/convert_database.py +0 -100
  342. agox-3.8.0/agox/utils/data_selection.py +0 -110
  343. agox-3.8.0/agox/utils/decorators.py +0 -20
  344. agox-3.8.0/agox/utils/filters/ABC_filter.py +0 -102
  345. agox-3.8.0/agox/utils/filters/__init__.py +0 -26
  346. agox-3.8.0/agox/utils/filters/all.py +0 -25
  347. agox-3.8.0/agox/utils/filters/energy.py +0 -34
  348. agox-3.8.0/agox/utils/filters/feature_distance.py +0 -93
  349. agox-3.8.0/agox/utils/filters/filter.py +0 -57
  350. agox-3.8.0/agox/utils/filters/kmeans_energy.py +0 -57
  351. agox-3.8.0/agox/utils/filters/none.py +0 -25
  352. agox-3.8.0/agox/utils/filters/random.py +0 -29
  353. agox-3.8.0/agox/utils/filters/sparse_filter.py +0 -73
  354. agox-3.8.0/agox/utils/filters/voronoi.py +0 -119
  355. agox-3.8.0/agox/utils/graph_sorting.py +0 -136
  356. agox-3.8.0/agox/utils/jupyter_interactive.py +0 -310
  357. agox-3.8.0/agox/utils/matplotlib_utils.py +0 -14
  358. agox-3.8.0/agox/utils/metrics/__init__.py +0 -17
  359. agox-3.8.0/agox/utils/metrics/calibration.py +0 -285
  360. agox-3.8.0/agox/utils/metrics/metrics.py +0 -22
  361. agox-3.8.0/agox/utils/numerical_derivative.py +0 -25
  362. agox-3.8.0/agox/utils/plot/__init__.py +0 -4
  363. agox-3.8.0/agox/utils/plot/colors.py +0 -267
  364. agox-3.8.0/agox/utils/plot/plot_atoms.py +0 -150
  365. agox-3.8.0/agox/utils/plot/plot_cell.py +0 -82
  366. agox-3.8.0/agox/utils/plot/plot_parity.py +0 -188
  367. agox-3.8.0/agox/utils/plot/utils.py +0 -60
  368. agox-3.8.0/agox/utils/ray/__init__.py +0 -4
  369. agox-3.8.0/agox/utils/ray/actor.py +0 -68
  370. agox-3.8.0/agox/utils/ray/pool.py +0 -567
  371. agox-3.8.0/agox/utils/ray/pool_startup.py +0 -83
  372. agox-3.8.0/agox/utils/ray/pool_user.py +0 -191
  373. agox-3.8.0/agox/utils/ray/startup.py +0 -160
  374. agox-3.8.0/agox/utils/ray/testing/__init__.py +0 -2
  375. agox-3.8.0/agox/utils/ray/testing/log_reader.py +0 -103
  376. agox-3.8.0/agox/utils/ray/testing/slurm_test_functions.py +0 -81
  377. agox-3.8.0/agox/utils/sparsifiers/ABC_sparsifier.py +0 -125
  378. agox-3.8.0/agox/utils/sparsifiers/CUR.py +0 -23
  379. agox-3.8.0/agox/utils/sparsifiers/CUR_old.py +0 -24
  380. agox-3.8.0/agox/utils/sparsifiers/MBkmeans.py +0 -69
  381. agox-3.8.0/agox/utils/sparsifiers/__init__.py +0 -10
  382. agox-3.8.0/agox/utils/sparsifiers/random.py +0 -18
  383. agox-3.8.0/agox/writer.py +0 -153
  384. agox-3.8.0/setup.py +0 -19
  385. {agox-3.8.0 → agox-3.10.0rc1}/LICENSE.txt +0 -0
  386. {agox-3.8.0 → agox-3.10.0rc1}/MANIFEST.in +0 -0
  387. {agox-3.8.0 → agox-3.10.0rc1}/README.md +0 -0
  388. {agox-3.8.0 → agox-3.10.0rc1}/agox/models/GPR/priors/repulsive.pyx +0 -0
  389. {agox-3.8.0 → agox-3.10.0rc1}/agox/models/datasets/Ag5O3-dataset.traj +0 -0
  390. {agox-3.8.0 → agox-3.10.0rc1}/agox/models/descriptors/fingerprint_cython/angular_fingerprintFeature_cy.pyx +0 -0
  391. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/.coveragerc +0 -0
  392. {agox-3.8.0/agox/generators/complementary_energy → agox-3.10.0rc1/agox/test}/__init__.py +0 -0
  393. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/AgO-dataset.traj +0 -0
  394. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/B12-dataset.traj +0 -0
  395. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/C30-dataset.traj +0 -0
  396. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/databases/mos2_databases/db1.db +0 -0
  397. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/datasets/databases/mos2_databases/db2.db +0 -0
  398. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_AgO.pckl +0 -0
  399. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_B12.pckl +0 -0
  400. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_C30.pckl +0 -0
  401. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter0.pckl +0 -0
  402. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter1.pckl +0 -0
  403. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter2.pckl +0 -0
  404. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter0.pckl +0 -0
  405. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter1.pckl +0 -0
  406. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter2.pckl +0 -0
  407. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter0.pckl +0 -0
  408. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter1.pckl +0 -0
  409. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter2.pckl +0 -0
  410. {agox-3.8.0 → agox-3.10.0rc1}/agox/test/generator_tests/expected_outputs/PermutationGenerator_dataAgO_parameter0.pckl +0 -0
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@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.4
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  Name: agox
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- Version: 3.8.0
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+ Version: 3.10.0rc1
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  Summary: Atomistic Global Optimziation X is a framework for structure optimization in materials science.
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  Author: AGOX Developers
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  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
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  Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
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  Classifier: Intended Audience :: Science/Research
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  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
- Requires-Python: >=3.8
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<=1.26.4
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