scikit-complexity 0.2.0__py3-none-any.whl

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  1. scikit_complexity-0.2.0.dist-info/METADATA +317 -0
  2. scikit_complexity-0.2.0.dist-info/RECORD +1748 -0
  3. scikit_complexity-0.2.0.dist-info/WHEEL +4 -0
  4. scikit_complexity-0.2.0.dist-info/entry_points.txt +4 -0
  5. scikit_complexity-0.2.0.dist-info/licenses/LICENSE +21 -0
  6. skcomplex/__init__.py +1 -0
  7. skcomplex/analysis/__init__.py +101 -0
  8. skcomplex/analysis/_alignment.py +263 -0
  9. skcomplex/analysis/_automata.py +658 -0
  10. skcomplex/analysis/_base.py +841 -0
  11. skcomplex/analysis/_clusters.py +298 -0
  12. skcomplex/analysis/_coarse_grain.py +183 -0
  13. skcomplex/analysis/_collapse.py +318 -0
  14. skcomplex/analysis/_complexity.py +129 -0
  15. skcomplex/analysis/_computational_mechanics.py +220 -0
  16. skcomplex/analysis/_correlation.py +364 -0
  17. skcomplex/analysis/_defects.py +111 -0
  18. skcomplex/analysis/_discovery.py +101 -0
  19. skcomplex/analysis/_displacement.py +135 -0
  20. skcomplex/analysis/_distribution.py +327 -0
  21. skcomplex/analysis/_domains.py +220 -0
  22. skcomplex/analysis/_embedding.py +235 -0
  23. skcomplex/analysis/_emergence.py +503 -0
  24. skcomplex/analysis/_entropy.py +425 -0
  25. skcomplex/analysis/_ergodicity.py +228 -0
  26. skcomplex/analysis/_events.py +301 -0
  27. skcomplex/analysis/_fit.py +368 -0
  28. skcomplex/analysis/_groups.py +205 -0
  29. skcomplex/analysis/_information.py +488 -0
  30. skcomplex/analysis/_invariants.py +409 -0
  31. skcomplex/analysis/_irreversibility.py +421 -0
  32. skcomplex/analysis/_kramers_moyal.py +104 -0
  33. skcomplex/analysis/_large_deviations.py +378 -0
  34. skcomplex/analysis/_linearization.py +231 -0
  35. skcomplex/analysis/_local_information.py +166 -0
  36. skcomplex/analysis/_loops.py +394 -0
  37. skcomplex/analysis/_lyapunov.py +342 -0
  38. skcomplex/analysis/_markov.py +303 -0
  39. skcomplex/analysis/_mode_decomposition.py +209 -0
  40. skcomplex/analysis/_motifs.py +239 -0
  41. skcomplex/analysis/_neighbors.py +303 -0
  42. skcomplex/analysis/_networks.py +286 -0
  43. skcomplex/analysis/_operator.py +312 -0
  44. skcomplex/analysis/_partial_information.py +118 -0
  45. skcomplex/analysis/_passage.py +244 -0
  46. skcomplex/analysis/_recurrence.py +202 -0
  47. skcomplex/analysis/_reservoirs.py +387 -0
  48. skcomplex/analysis/_rolling.py +168 -0
  49. skcomplex/analysis/_scaling.py +370 -0
  50. skcomplex/analysis/_sections.py +225 -0
  51. skcomplex/analysis/_signatures.py +250 -0
  52. skcomplex/analysis/_sparse_identification.py +398 -0
  53. skcomplex/analysis/_spectrum.py +164 -0
  54. skcomplex/analysis/_stability.py +547 -0
  55. skcomplex/analysis/_surrogates.py +127 -0
  56. skcomplex/analysis/_symbolic.py +639 -0
  57. skcomplex/analysis/types.py +43 -0
  58. skcomplex/base.py +159 -0
  59. skcomplex/core/__init__.py +1 -0
  60. skcomplex/core/base.py +150 -0
  61. skcomplex/core/elements/__init__.py +21 -0
  62. skcomplex/core/elements/_base.py +84 -0
  63. skcomplex/core/elements/_compartment.py +52 -0
  64. skcomplex/core/elements/_density.py +52 -0
  65. skcomplex/core/elements/_element.py +80 -0
  66. skcomplex/core/elements/_field.py +192 -0
  67. skcomplex/core/elements/_group.py +241 -0
  68. skcomplex/core/elements/_lattice.py +115 -0
  69. skcomplex/core/elements/_point.py +66 -0
  70. skcomplex/core/interactions/__init__.py +89 -0
  71. skcomplex/core/interactions/_advection.py +134 -0
  72. skcomplex/core/interactions/_base.py +361 -0
  73. skcomplex/core/interactions/_cascade.py +195 -0
  74. skcomplex/core/interactions/_choice.py +320 -0
  75. skcomplex/core/interactions/_conservation.py +164 -0
  76. skcomplex/core/interactions/_coupling.py +741 -0
  77. skcomplex/core/interactions/_crossing.py +136 -0
  78. skcomplex/core/interactions/_diffusion.py +99 -0
  79. skcomplex/core/interactions/_encounter.py +201 -0
  80. skcomplex/core/interactions/_euler_lagrange.py +183 -0
  81. skcomplex/core/interactions/_evolution.py +520 -0
  82. skcomplex/core/interactions/_feedback.py +79 -0
  83. skcomplex/core/interactions/_gradient.py +293 -0
  84. skcomplex/core/interactions/_grouping.py +399 -0
  85. skcomplex/core/interactions/_hamiltonian.py +191 -0
  86. skcomplex/core/interactions/_hyperedge.py +96 -0
  87. skcomplex/core/interactions/_imitation.py +357 -0
  88. skcomplex/core/interactions/_impulse.py +133 -0
  89. skcomplex/core/interactions/_interaction.py +58 -0
  90. skcomplex/core/interactions/_jump.py +201 -0
  91. skcomplex/core/interactions/_life_cycle.py +424 -0
  92. skcomplex/core/interactions/_local_rule.py +134 -0
  93. skcomplex/core/interactions/_map.py +239 -0
  94. skcomplex/core/interactions/_matching.py +701 -0
  95. skcomplex/core/interactions/_movement.py +377 -0
  96. skcomplex/core/interactions/_neighbor.py +88 -0
  97. skcomplex/core/interactions/_optimization.py +206 -0
  98. skcomplex/core/interactions/_pair.py +82 -0
  99. skcomplex/core/interactions/_pair_coupling.py +169 -0
  100. skcomplex/core/interactions/_rate.py +240 -0
  101. skcomplex/core/interactions/_reaction.py +466 -0
  102. skcomplex/core/interactions/_reinforcement.py +226 -0
  103. skcomplex/core/interactions/_relaxation.py +103 -0
  104. skcomplex/core/interactions/_sampling.py +177 -0
  105. skcomplex/core/interactions/_satisfiability.py +145 -0
  106. skcomplex/core/interactions/_sign_adjustment.py +222 -0
  107. skcomplex/core/interactions/_topology.py +215 -0
  108. skcomplex/core/interactions/_training.py +184 -0
  109. skcomplex/core/interactions/_transfer.py +669 -0
  110. skcomplex/core/interactions/_transition.py +427 -0
  111. skcomplex/core/laws/__init__.py +60 -0
  112. skcomplex/core/laws/_base.py +194 -0
  113. skcomplex/core/laws/_bilinear.py +91 -0
  114. skcomplex/core/laws/_boundary.py +59 -0
  115. skcomplex/core/laws/_cascade.py +79 -0
  116. skcomplex/core/laws/_crossing.py +87 -0
  117. skcomplex/core/laws/_dissipator.py +79 -0
  118. skcomplex/core/laws/_drive.py +56 -0
  119. skcomplex/core/laws/_emission.py +81 -0
  120. skcomplex/core/laws/_encounter.py +96 -0
  121. skcomplex/core/laws/_equation.py +105 -0
  122. skcomplex/core/laws/_extremal.py +94 -0
  123. skcomplex/core/laws/_flux.py +108 -0
  124. skcomplex/core/laws/_fractional_noise.py +65 -0
  125. skcomplex/core/laws/_generator.py +66 -0
  126. skcomplex/core/laws/_gradient_step.py +89 -0
  127. skcomplex/core/laws/_jump.py +137 -0
  128. skcomplex/core/laws/_local_rule.py +92 -0
  129. skcomplex/core/laws/_match.py +321 -0
  130. skcomplex/core/laws/_noise.py +125 -0
  131. skcomplex/core/laws/_rate.py +82 -0
  132. skcomplex/core/laws/_rule.py +82 -0
  133. skcomplex/core/laws/_sample.py +65 -0
  134. skcomplex/core/laws/_transfer.py +165 -0
  135. skcomplex/core/laws/_transition.py +77 -0
  136. skcomplex/core/laws/_update.py +121 -0
  137. skcomplex/core/laws/utils/__init__.py +142 -0
  138. skcomplex/core/laws/utils/_agents.py +127 -0
  139. skcomplex/core/laws/utils/_components.py +63 -0
  140. skcomplex/core/laws/utils/_conditions.py +198 -0
  141. skcomplex/core/laws/utils/_contractions.py +74 -0
  142. skcomplex/core/laws/utils/_delays.py +170 -0
  143. skcomplex/core/laws/utils/_history.py +167 -0
  144. skcomplex/core/laws/utils/_local_operators.py +68 -0
  145. skcomplex/core/laws/utils/_lookups.py +40 -0
  146. skcomplex/core/laws/utils/_moments.py +122 -0
  147. skcomplex/core/laws/utils/_operators.py +237 -0
  148. skcomplex/core/laws/utils/_phase.py +126 -0
  149. skcomplex/core/laws/utils/_pointwise.py +160 -0
  150. skcomplex/core/laws/utils/_reductions.py +942 -0
  151. skcomplex/core/laws/utils/_signals.py +214 -0
  152. skcomplex/core/laws/utils/_tables.py +4 -0
  153. skcomplex/core/laws/utils/_tensors.py +235 -0
  154. skcomplex/core/spaces/__init__.py +52 -0
  155. skcomplex/core/spaces/_adjacency.py +34 -0
  156. skcomplex/core/spaces/_base.py +218 -0
  157. skcomplex/core/spaces/_box.py +41 -0
  158. skcomplex/core/spaces/_cayley.py +352 -0
  159. skcomplex/core/spaces/_cone.py +65 -0
  160. skcomplex/core/spaces/_continuous.py +93 -0
  161. skcomplex/core/spaces/_continuous_time.py +27 -0
  162. skcomplex/core/spaces/_discrete_time.py +53 -0
  163. skcomplex/core/spaces/_generator.py +51 -0
  164. skcomplex/core/spaces/_lattice.py +194 -0
  165. skcomplex/core/spaces/_lattice_neighborhood.py +50 -0
  166. skcomplex/core/spaces/_memory.py +45 -0
  167. skcomplex/core/spaces/_mesh.py +71 -0
  168. skcomplex/core/spaces/_moore.py +49 -0
  169. skcomplex/core/spaces/_nearest.py +41 -0
  170. skcomplex/core/spaces/_network.py +256 -0
  171. skcomplex/core/spaces/_phase.py +136 -0
  172. skcomplex/core/spaces/_radius.py +40 -0
  173. skcomplex/core/spaces/_static_time.py +34 -0
  174. skcomplex/core/spaces/_triangular.py +37 -0
  175. skcomplex/core/spaces/_von_neumann.py +51 -0
  176. skcomplex/core/specs/__init__.py +25 -0
  177. skcomplex/core/specs/_census_record_spec.py +72 -0
  178. skcomplex/core/specs/_census_spec.py +40 -0
  179. skcomplex/core/specs/_compiled_agents_spec.py +62 -0
  180. skcomplex/core/specs/_compiled_element_spec.py +59 -0
  181. skcomplex/core/specs/_compiled_interaction_spec.py +33 -0
  182. skcomplex/core/specs/_lattice_context_spec.py +40 -0
  183. skcomplex/core/specs/_lattice_state_spec.py +49 -0
  184. skcomplex/core/specs/_node_spec.py +64 -0
  185. skcomplex/core/specs/_operator_view_spec.py +135 -0
  186. skcomplex/core/specs/_scenario_spec.py +45 -0
  187. skcomplex/core/specs/_subsystem_spec.py +24 -0
  188. skcomplex/core/system.py +140 -0
  189. skcomplex/core/types.py +249 -0
  190. skcomplex/engine/__init__.py +5 -0
  191. skcomplex/engine/_utils.py +278 -0
  192. skcomplex/engine/backends/__init__.py +13 -0
  193. skcomplex/engine/backends/_base.py +329 -0
  194. skcomplex/engine/backends/_jax.py +285 -0
  195. skcomplex/engine/backends/_numba.py +601 -0
  196. skcomplex/engine/backends/_numba_components.py +67 -0
  197. skcomplex/engine/backends/_numba_loops.py +163 -0
  198. skcomplex/engine/backends/_numba_neighbours.py +435 -0
  199. skcomplex/engine/backends/_numba_printer.py +1023 -0
  200. skcomplex/engine/backends/_numba_stencils.py +66 -0
  201. skcomplex/engine/backends/_numpy.py +215 -0
  202. skcomplex/engine/compile/__init__.py +27 -0
  203. skcomplex/engine/compile/_base.py +582 -0
  204. skcomplex/engine/compile/_bound_renewal_spec.py +47 -0
  205. skcomplex/engine/compile/_compilation.py +351 -0
  206. skcomplex/engine/compile/_compile.py +100 -0
  207. skcomplex/engine/compile/_complex.py +216 -0
  208. skcomplex/engine/compile/_draw_lowering.py +373 -0
  209. skcomplex/engine/compile/_field_lowering.py +1668 -0
  210. skcomplex/engine/compile/_flows.py +691 -0
  211. skcomplex/engine/compile/_forms.py +48 -0
  212. skcomplex/engine/compile/_laws.py +42 -0
  213. skcomplex/engine/compile/_learning_compiler.py +481 -0
  214. skcomplex/engine/compile/_member_reductions.py +206 -0
  215. skcomplex/engine/compile/_members.py +244 -0
  216. skcomplex/engine/compile/_observables.py +940 -0
  217. skcomplex/engine/compile/_observer.py +185 -0
  218. skcomplex/engine/compile/_pass_compiler.py +1534 -0
  219. skcomplex/engine/compile/_probe.py +78 -0
  220. skcomplex/engine/compile/_renewal_law.py +70 -0
  221. skcomplex/engine/compile/passes/__init__.py +34 -0
  222. skcomplex/engine/compile/passes/_agents.py +111 -0
  223. skcomplex/engine/compile/passes/_agents_problem.py +143 -0
  224. skcomplex/engine/compile/passes/_census.py +808 -0
  225. skcomplex/engine/compile/passes/_check_fractional_noise.py +107 -0
  226. skcomplex/engine/compile/passes/_collect.py +31 -0
  227. skcomplex/engine/compile/passes/_compile_encounters.py +301 -0
  228. skcomplex/engine/compile/passes/_complex.py +198 -0
  229. skcomplex/engine/compile/passes/_conserved_noise.py +224 -0
  230. skcomplex/engine/compile/passes/_core.py +116 -0
  231. skcomplex/engine/compile/passes/_declare_renewals.py +84 -0
  232. skcomplex/engine/compile/passes/_draws.py +29 -0
  233. skcomplex/engine/compile/passes/_encounter_functions.py +60 -0
  234. skcomplex/engine/compile/passes/_encounter_jacobian.py +25 -0
  235. skcomplex/engine/compile/passes/_encounter_problem.py +32 -0
  236. skcomplex/engine/compile/passes/_events.py +204 -0
  237. skcomplex/engine/compile/passes/_expand_flows.py +32 -0
  238. skcomplex/engine/compile/passes/_field_functions.py +647 -0
  239. skcomplex/engine/compile/passes/_field_jacobian.py +38 -0
  240. skcomplex/engine/compile/passes/_field_problem.py +106 -0
  241. skcomplex/engine/compile/passes/_flatten.py +339 -0
  242. skcomplex/engine/compile/passes/_flows_problem.py +29 -0
  243. skcomplex/engine/compile/passes/_form.py +82 -0
  244. skcomplex/engine/compile/passes/_fractional_form.py +172 -0
  245. skcomplex/engine/compile/passes/_fractional_problem.py +91 -0
  246. skcomplex/engine/compile/passes/_functions.py +485 -0
  247. skcomplex/engine/compile/passes/_hilbert_space_error.py +10 -0
  248. skcomplex/engine/compile/passes/_hyperedges.py +598 -0
  249. skcomplex/engine/compile/passes/_jacobian.py +38 -0
  250. skcomplex/engine/compile/passes/_kernels.py +407 -0
  251. skcomplex/engine/compile/passes/_lattices.py +818 -0
  252. skcomplex/engine/compile/passes/_layout.py +667 -0
  253. skcomplex/engine/compile/passes/_lower_fields.py +225 -0
  254. skcomplex/engine/compile/passes/_lower_flows.py +28 -0
  255. skcomplex/engine/compile/passes/_markov.py +329 -0
  256. skcomplex/engine/compile/passes/_mask_requests.py +121 -0
  257. skcomplex/engine/compile/passes/_members.py +30 -0
  258. skcomplex/engine/compile/passes/_noise.py +196 -0
  259. skcomplex/engine/compile/passes/_operator_compiler.py +843 -0
  260. skcomplex/engine/compile/passes/_orders.py +409 -0
  261. skcomplex/engine/compile/passes/_owners.py +90 -0
  262. skcomplex/engine/compile/passes/_particles.py +69 -0
  263. skcomplex/engine/compile/passes/_plan.py +130 -0
  264. skcomplex/engine/compile/passes/_problem.py +802 -0
  265. skcomplex/engine/compile/passes/_reduction_lowering.py +1193 -0
  266. skcomplex/engine/compile/passes/_reductions.py +84 -0
  267. skcomplex/engine/compile/passes/_renewal_problem.py +357 -0
  268. skcomplex/engine/compile/passes/_request_jumps.py +51 -0
  269. skcomplex/engine/compile/passes/_residences.py +140 -0
  270. skcomplex/engine/compile/passes/_rows.py +162 -0
  271. skcomplex/engine/compile/passes/_set_renewals_apart.py +29 -0
  272. skcomplex/engine/compile/passes/_set_rules_apart.py +28 -0
  273. skcomplex/engine/compile/passes/_specs.py +1317 -0
  274. skcomplex/engine/compile/passes/_split_requests.py +44 -0
  275. skcomplex/engine/compile/passes/_topology_functions.py +265 -0
  276. skcomplex/engine/compile/passes/_topology_problem.py +27 -0
  277. skcomplex/engine/compile/passes/_towards.py +66 -0
  278. skcomplex/engine/compile/passes/_unpack_matches.py +29 -0
  279. skcomplex/engine/compile/passes/_unpack_renewals.py +41 -0
  280. skcomplex/engine/problems/__init__.py +61 -0
  281. skcomplex/engine/problems/_base.py +150 -0
  282. skcomplex/engine/problems/_base_problem_spec.py +153 -0
  283. skcomplex/engine/problems/_block_spec.py +48 -0
  284. skcomplex/engine/problems/_born_spec.py +24 -0
  285. skcomplex/engine/problems/_cascade_kernel.py +134 -0
  286. skcomplex/engine/problems/_collision_kernel.py +147 -0
  287. skcomplex/engine/problems/_compiled_delay_spec.py +21 -0
  288. skcomplex/engine/problems/_compiled_request_spec.py +46 -0
  289. skcomplex/engine/problems/_control_problem_spec.py +90 -0
  290. skcomplex/engine/problems/_declarations_spec.py +126 -0
  291. skcomplex/engine/problems/_delayed_state_spec.py +50 -0
  292. skcomplex/engine/problems/_diffusive_limit_spec.py +50 -0
  293. skcomplex/engine/problems/_draw_kernel.py +128 -0
  294. skcomplex/engine/problems/_drive_kernel.py +65 -0
  295. skcomplex/engine/problems/_dynamics_spec.py +28 -0
  296. skcomplex/engine/problems/_edge_row_search.py +78 -0
  297. skcomplex/engine/problems/_edge_search.py +64 -0
  298. skcomplex/engine/problems/_encounter_kernel.py +200 -0
  299. skcomplex/engine/problems/_event_kernel.py +70 -0
  300. skcomplex/engine/problems/_expression_printer.py +410 -0
  301. skcomplex/engine/problems/_extremal_kernel.py +125 -0
  302. skcomplex/engine/problems/_field_operator_kernel.py +105 -0
  303. skcomplex/engine/problems/_finite_volume_kernel.py +423 -0
  304. skcomplex/engine/problems/_flow_term_spec.py +45 -0
  305. skcomplex/engine/problems/_frame_spec.py +105 -0
  306. skcomplex/engine/problems/_jacobian_kernel.py +575 -0
  307. skcomplex/engine/problems/_kernel_spec.py +130 -0
  308. skcomplex/engine/problems/_kinetic_problem_spec.py +23 -0
  309. skcomplex/engine/problems/_law_kernel.py +604 -0
  310. skcomplex/engine/problems/_learning_problem_spec.py +67 -0
  311. skcomplex/engine/problems/_linear_term_spec.py +50 -0
  312. skcomplex/engine/problems/_loop_term_spec.py +44 -0
  313. skcomplex/engine/problems/_lowered_kernels_spec.py +59 -0
  314. skcomplex/engine/problems/_markov_kernel.py +68 -0
  315. skcomplex/engine/problems/_metric_search.py +155 -0
  316. skcomplex/engine/problems/_monte_carlo_kernel.py +213 -0
  317. skcomplex/engine/problems/_neighborhood_kernel.py +594 -0
  318. skcomplex/engine/problems/_noise_term_spec.py +26 -0
  319. skcomplex/engine/problems/_observed_spec.py +22 -0
  320. skcomplex/engine/problems/_operator_kernel.py +102 -0
  321. skcomplex/engine/problems/_operator_lowering.py +323 -0
  322. skcomplex/engine/problems/_operator_problem_spec.py +138 -0
  323. skcomplex/engine/problems/_output_spec.py +78 -0
  324. skcomplex/engine/problems/_pair_search.py +86 -0
  325. skcomplex/engine/problems/_partials_spec.py +27 -0
  326. skcomplex/engine/problems/_partition_spec.py +39 -0
  327. skcomplex/engine/problems/_printed_spec.py +24 -0
  328. skcomplex/engine/problems/_problem_functions_spec.py +102 -0
  329. skcomplex/engine/problems/_problem_spec.py +365 -0
  330. skcomplex/engine/problems/_random_stream.py +49 -0
  331. skcomplex/engine/problems/_record_spec.py +22 -0
  332. skcomplex/engine/problems/_recorded_spec.py +21 -0
  333. skcomplex/engine/problems/_reduction_kernel.py +254 -0
  334. skcomplex/engine/problems/_reduction_schedule_spec.py +97 -0
  335. skcomplex/engine/problems/_reference_spec.py +114 -0
  336. skcomplex/engine/problems/_relation_spec.py +29 -0
  337. skcomplex/engine/problems/_renewal_kernel.py +250 -0
  338. skcomplex/engine/problems/_request_spec.py +27 -0
  339. skcomplex/engine/problems/_rule_kernel.py +227 -0
  340. skcomplex/engine/problems/_set_symbol_spec.py +28 -0
  341. skcomplex/engine/problems/_source_loader.py +113 -0
  342. skcomplex/engine/problems/_static_search.py +42 -0
  343. skcomplex/engine/problems/_steps.py +39 -0
  344. skcomplex/engine/problems/_sweep_spec.py +26 -0
  345. skcomplex/engine/problems/_symmetry_spec.py +29 -0
  346. skcomplex/engine/problems/_too_dense.py +8 -0
  347. skcomplex/engine/problems/_topology_kernel.py +589 -0
  348. skcomplex/engine/problems/_transfer_network.py +4 -0
  349. skcomplex/engine/problems/_transfer_network_spec.py +50 -0
  350. skcomplex/engine/problems/_transfer_state_spec.py +68 -0
  351. skcomplex/engine/runtime/__init__.py +22 -0
  352. skcomplex/engine/runtime/_as_fast_as_possible.py +17 -0
  353. skcomplex/engine/runtime/_base.py +137 -0
  354. skcomplex/engine/runtime/_conservation.py +125 -0
  355. skcomplex/engine/runtime/_invariants.py +100 -0
  356. skcomplex/engine/runtime/_real_time.py +55 -0
  357. skcomplex/engine/runtime/_recorder.py +84 -0
  358. skcomplex/engine/runtime/_simulations.py +665 -0
  359. skcomplex/engine/runtime/_trajectories.py +314 -0
  360. skcomplex/engine/solvers/__init__.py +95 -0
  361. skcomplex/engine/solvers/_base.py +372 -0
  362. skcomplex/engine/solvers/_caputo.py +194 -0
  363. skcomplex/engine/solvers/_collocation.py +334 -0
  364. skcomplex/engine/solvers/_convolution.py +155 -0
  365. skcomplex/engine/solvers/_cosimulation.py +400 -0
  366. skcomplex/engine/solvers/_crank_nicolson.py +32 -0
  367. skcomplex/engine/solvers/_defaults.py +34 -0
  368. skcomplex/engine/solvers/_etdrk4.py +86 -0
  369. skcomplex/engine/solvers/_euler_maruyama.py +161 -0
  370. skcomplex/engine/solvers/_event_locator.py +249 -0
  371. skcomplex/engine/solvers/_external.py +94 -0
  372. skcomplex/engine/solvers/_fractional_abm.py +126 -0
  373. skcomplex/engine/solvers/_fractional_euler_maruyama.py +322 -0
  374. skcomplex/engine/solvers/_gillespie.py +135 -0
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  1620. skcomplex/models/social/segregation/_resident_view.py +13 -0
  1621. skcomplex/models/social/segregation/_schelling.py +75 -0
  1622. skcomplex/models/social/spreading/__init__.py +37 -0
  1623. skcomplex/models/social/spreading/_cascades.py +118 -0
  1624. skcomplex/models/social/spreading/_exposure.py +166 -0
  1625. skcomplex/models/social/spreading/_growing_word.py +55 -0
  1626. skcomplex/models/social/spreading/_growing_word_view.py +13 -0
  1627. skcomplex/models/social/spreading/_growth.py +52 -0
  1628. skcomplex/models/social/spreading/_infective.py +55 -0
  1629. skcomplex/models/social/spreading/_listeners.py +41 -0
  1630. skcomplex/models/social/spreading/_participant.py +50 -0
  1631. skcomplex/models/social/spreading/_rumour_contacts.py +81 -0
  1632. skcomplex/models/social/spreading/_rumours.py +57 -0
  1633. skcomplex/models/social/spreading/_simplicial.py +120 -0
  1634. skcomplex/models/social/spreading/_simplicial_infection.py +64 -0
  1635. skcomplex/models/social/spreading/_threshold_activation.py +50 -0
  1636. skcomplex/models/social/spreading/_threshold_node_view.py +13 -0
  1637. skcomplex/models/social/spreading/_writing.py +86 -0
  1638. skcomplex/models/types.py +10 -0
  1639. skcomplex/specs/__init__.py +198 -0
  1640. skcomplex/specs/_accelerated_spec.py +46 -0
  1641. skcomplex/specs/_agent_snapshot_spec.py +34 -0
  1642. skcomplex/specs/_agent_state_spec.py +26 -0
  1643. skcomplex/specs/_arguments_spec.py +60 -0
  1644. skcomplex/specs/_axis_spec.py +59 -0
  1645. skcomplex/specs/_base_record_spec.py +16 -0
  1646. skcomplex/specs/_base_spec.py +73 -0
  1647. skcomplex/specs/_base_structure_spec.py +173 -0
  1648. skcomplex/specs/_batch_matching_spec.py +23 -0
  1649. skcomplex/specs/_breakpoints_spec.py +58 -0
  1650. skcomplex/specs/_call_spec.py +64 -0
  1651. skcomplex/specs/_capacity_rows_spec.py +120 -0
  1652. skcomplex/specs/_cardinality_spec.py +58 -0
  1653. skcomplex/specs/_cascade_record_spec.py +36 -0
  1654. skcomplex/specs/_clamp_spec.py +54 -0
  1655. skcomplex/specs/_clause_spec.py +42 -0
  1656. skcomplex/specs/_compiled_flow_spec.py +20 -0
  1657. skcomplex/specs/_composed_rule_spec.py +33 -0
  1658. skcomplex/specs/_continuous_matching_spec.py +48 -0
  1659. skcomplex/specs/_control_solution_spec.py +54 -0
  1660. skcomplex/specs/_control_spec.py +21 -0
  1661. skcomplex/specs/_covariance_adaptation_spec.py +25 -0
  1662. skcomplex/specs/_dataset_spec.py +85 -0
  1663. skcomplex/specs/_delay_spec.py +27 -0
  1664. skcomplex/specs/_dialect_spec.py +207 -0
  1665. skcomplex/specs/_differential_evolution_spec.py +33 -0
  1666. skcomplex/specs/_direction_spec.py +44 -0
  1667. skcomplex/specs/_draw_spec.py +273 -0
  1668. skcomplex/specs/_entry_spec.py +403 -0
  1669. skcomplex/specs/_event_record_spec.py +37 -0
  1670. skcomplex/specs/_evolution_strategy_spec.py +25 -0
  1671. skcomplex/specs/_extremal_record_spec.py +32 -0
  1672. skcomplex/specs/_fractional_rows_spec.py +33 -0
  1673. skcomplex/specs/_fractional_state_spec.py +30 -0
  1674. skcomplex/specs/_held_reduction_spec.py +29 -0
  1675. skcomplex/specs/_hilbert_spec.py +75 -0
  1676. skcomplex/specs/_hyperedge_reduction_spec.py +38 -0
  1677. skcomplex/specs/_issue_spec.py +52 -0
  1678. skcomplex/specs/_iterative_matching_spec.py +39 -0
  1679. skcomplex/specs/_jump_channels_spec.py +40 -0
  1680. skcomplex/specs/_jump_path_spec.py +29 -0
  1681. skcomplex/specs/_layer_spec.py +47 -0
  1682. skcomplex/specs/_layout_spec.py +158 -0
  1683. skcomplex/specs/_local_operator_spec.py +72 -0
  1684. skcomplex/specs/_lookup_spec.py +33 -0
  1685. skcomplex/specs/_loop_spec.py +17 -0
  1686. skcomplex/specs/_lowered_functions_spec.py +71 -0
  1687. skcomplex/specs/_match_spec.py +37 -0
  1688. skcomplex/specs/_matrix_law_spec.py +31 -0
  1689. skcomplex/specs/_move_spec.py +69 -0
  1690. skcomplex/specs/_neighbor_read_spec.py +83 -0
  1691. skcomplex/specs/_neighbor_reduction_spec.py +39 -0
  1692. skcomplex/specs/_network_rows_spec.py +124 -0
  1693. skcomplex/specs/_network_snapshot_spec.py +61 -0
  1694. skcomplex/specs/_noise_process_spec.py +41 -0
  1695. skcomplex/specs/_objective_spec.py +39 -0
  1696. skcomplex/specs/_observable_spec.py +79 -0
  1697. skcomplex/specs/_operator_spec.py +170 -0
  1698. skcomplex/specs/_orders_spec.py +16 -0
  1699. skcomplex/specs/_outer_totalistic_spec.py +38 -0
  1700. skcomplex/specs/_owners_spec.py +28 -0
  1701. skcomplex/specs/_pair_read_spec.py +38 -0
  1702. skcomplex/specs/_parameter_spec.py +81 -0
  1703. skcomplex/specs/_parameters_spec.py +26 -0
  1704. skcomplex/specs/_particle_swarm_spec.py +33 -0
  1705. skcomplex/specs/_partner_spec.py +98 -0
  1706. skcomplex/specs/_partner_switch_spec.py +39 -0
  1707. skcomplex/specs/_phase_spec.py +61 -0
  1708. skcomplex/specs/_phases_schedule_spec.py +59 -0
  1709. skcomplex/specs/_plan_spec.py +18 -0
  1710. skcomplex/specs/_planned_partition_spec.py +30 -0
  1711. skcomplex/specs/_queue_spec.py +46 -0
  1712. skcomplex/specs/_radius_spec.py +66 -0
  1713. skcomplex/specs/_random_search_spec.py +51 -0
  1714. skcomplex/specs/_read_spec.py +45 -0
  1715. skcomplex/specs/_reduction_spec.py +48 -0
  1716. skcomplex/specs/_renewal_record_spec.py +49 -0
  1717. skcomplex/specs/_requirement_spec.py +32 -0
  1718. skcomplex/specs/_role_spec.py +54 -0
  1719. skcomplex/specs/_run_result_spec.py +52 -0
  1720. skcomplex/specs/_run_state_spec.py +41 -0
  1721. skcomplex/specs/_sampled_draw_spec.py +32 -0
  1722. skcomplex/specs/_sampler_spec.py +57 -0
  1723. skcomplex/specs/_samples_spec.py +29 -0
  1724. skcomplex/specs/_schedule_spec.py +17 -0
  1725. skcomplex/specs/_sector_spec.py +31 -0
  1726. skcomplex/specs/_segment_spec.py +21 -0
  1727. skcomplex/specs/_series_spec.py +29 -0
  1728. skcomplex/specs/_signature_spec.py +55 -0
  1729. skcomplex/specs/_snapshots_spec.py +56 -0
  1730. skcomplex/specs/_stable_matching_spec.py +58 -0
  1731. skcomplex/specs/_state_spec.py +138 -0
  1732. skcomplex/specs/_step_spec.py +39 -0
  1733. skcomplex/specs/_structure_state_spec.py +30 -0
  1734. skcomplex/specs/_support_spec.py +76 -0
  1735. skcomplex/specs/_symmetry_spec.py +59 -0
  1736. skcomplex/specs/_table_spec.py +42 -0
  1737. skcomplex/specs/_table_values_spec.py +36 -0
  1738. skcomplex/specs/_tensor_spec.py +197 -0
  1739. skcomplex/specs/_topology_request_spec.py +97 -0
  1740. skcomplex/specs/_totalistic_spec.py +37 -0
  1741. skcomplex/specs/_unknown_spec.py +22 -0
  1742. skcomplex/specs/_validation_report_spec.py +62 -0
  1743. skcomplex/specs/_variable_spec.py +124 -0
  1744. skcomplex/specs/_visual_spec.py +30 -0
  1745. skcomplex/specs/_weight_spec.py +16 -0
  1746. skcomplex/specs/_wiener_block_spec.py +31 -0
  1747. skcomplex/specs/_wiener_process_spec.py +54 -0
  1748. skcomplex/types.py +140 -0
@@ -0,0 +1,399 @@
1
+ """Define groupings, which draw groups of the members of a group every step and act on each group."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ from collections.abc import Callable, Sequence
7
+ from types import SimpleNamespace
8
+ from typing import Annotated, cast
9
+
10
+ from sage.all__sagemath_symbolics import SR, Expression
11
+
12
+ from ...errors import ValidationError
13
+ from ...specs import BaseSpec, PartnerSpec, ReductionSpec, RoleSpec
14
+ from ..laws import BaseLaw, MatchLaw, RuleLaw, UpdateLaw
15
+ from ..laws.utils import both, count, maximum, mean, minimum, reductions_in, total, variance
16
+ from ..spaces import BaseSpace
17
+ from ..types import AgentViewProtocol, ModelViewProtocol, Pairing
18
+ from ._interaction import Interaction
19
+
20
+ GROUPS = ('pairs', 'partition', 'neighborhood', 'state')
21
+ FORMS = ('agent', 'symbolic')
22
+ REDUCES = ('sum', 'mean')
23
+ PAIR = 2
24
+ KEYED: dict[str, Callable[..., Expression]] = {
25
+ 'sum': total,
26
+ 'mean': mean,
27
+ 'max': maximum,
28
+ 'min': minimum,
29
+ 'var': variance,
30
+ }
31
+
32
+ type Act = Callable[[list[AgentViewProtocol], ModelViewProtocol], None]
33
+ type GroupFunction = Callable[[SimpleNamespace], object]
34
+
35
+
36
+ class GroupingInteraction(Interaction):
37
+ """Grouping of the members of a group into groups drawn every step, with an action on every group.
38
+
39
+ The groups are one of four kinds:
40
+
41
+ - `'pairs'` draws disjoint random pairs, and an odd member out forms no group.
42
+ - `'partition'` draws a random partition into groups of `size` members, the last group holding the remainder.
43
+ - `'neighborhood'` forms one group per member, the member first and then the members in the cells or nodes
44
+ around it.
45
+ - `'state'` forms one group per value of the state `by`, of at most `capacity` agents drawn at random among those
46
+ that hold the value in the agent form.
47
+
48
+ In the agent form the groups act in random order, each through `act(members, model)`, a function of the list of
49
+ agent views and the model view, or the method `act_on` a subclass overrides. The grouping is an agent rule, so the
50
+ system runs in discrete time.
51
+
52
+ In the symbolic form every member of a group takes the value of `function(namespace)` for the state `write` in the
53
+ next step, reduced by `reduce` over the groups that hold it, and a member in no group keeps its value. The
54
+ namespace of a group holds `member`, the member the value is for, `others`, the other members in the order of the
55
+ group, `members`, which `total`, `mean`, `count`, `maximum`, and `minimum` reduce with `over=namespace.members`,
56
+ the time `t`, and the parameters of the interaction. Pairs and partitions are drawn again at every step from the
57
+ random stream of the simulation, and neighbourhoods are those of the space. The groups by state hold no `others`,
58
+ and their reductions over the members are keyed by the state. Within a step, the grouping runs in its `phase` and
59
+ reads the states the phases before it set.
60
+
61
+ Args:
62
+ label:
63
+ The label of the interaction, unique among the parts of its system.
64
+
65
+ target:
66
+ The path of the group whose members are grouped.
67
+
68
+ groups:
69
+ The kind of groups, `'pairs'`, `'partition'`, `'neighborhood'`, or `'state'`, or in the agent form a
70
+ `PartnerSpec` or a function `pairing(members, members, rng, capacity)` that returns pairs, which group
71
+ every member with its partners. `'pairs'` is a shorthand of `PartnerSpec('all', 'uniform', capacity=1)`.
72
+
73
+ act:
74
+ The function of the members of a group and the model view that acts on the group in the agent form, used
75
+ when a subclass does not override `act_on`.
76
+
77
+ size:
78
+ The number of members of a group of a partition.
79
+
80
+ by:
81
+ The name of the state whose values the groups `'state'` share.
82
+
83
+ capacity:
84
+ The largest number of agents of a group `'state'` in the agent form, or `None` for no limit.
85
+
86
+ phase:
87
+ The phase of the step the grouping runs in, or `None` for the default phase.
88
+
89
+ form:
90
+ `'agent'` for an action on the agents of every group, or `'symbolic'` for a function of every group.
91
+
92
+ write:
93
+ The name of the state that the symbolic form sets.
94
+
95
+ function:
96
+ The function of the namespace of one group that returns the value of `write` for its member, in the
97
+ symbolic form.
98
+
99
+ reduce:
100
+ `'sum'` or `'mean'`, how the symbolic form combines the values of the groups that hold a member.
101
+
102
+ Raises:
103
+ ValidationError:
104
+ The kind of groups, the form, or the reduction is unknown, the size is below two, the groups `'state'` have
105
+ no state, the capacity is not positive, the symbolic form has no state or function, or a setting of one
106
+ form is given to the other, raised by `check`.
107
+
108
+ Examples:
109
+ >>> from typing import Annotated
110
+ >>> from skcomplex.core.elements import Element, GroupElement
111
+ >>> from skcomplex.core.interactions import GroupingInteraction
112
+ >>> from skcomplex.core.system import System
113
+ >>> from skcomplex.engine.runtime import Simulation
114
+ >>> from skcomplex.specs import StateSpec
115
+ >>> class VoterElement(Element):
116
+ ... def __init__(self, label, visual=None, *, s: Annotated[float, StateSpec()] = 0.0):
117
+ ... super().__init__(label, visual=visual)
118
+ ... self.s = s
119
+ >>> def adopt_majority(members, model):
120
+ ... majority = float(2 * sum(member.s for member in members) > len(members))
121
+ ... for member in members:
122
+ ... member.s = majority
123
+ >>> voters = GroupElement('voters', element=VoterElement, size=3, values={'s': [1.0, 1.0, 0.0]})
124
+ >>> galam = GroupingInteraction('galam', target='voters', groups='partition', size=3, act=adopt_majority)
125
+ >>> trajectory = Simulation(System(elements=[voters], interactions=[galam])).check().prepare().run(until=1)
126
+ >>> trajectory.trajectory_.agents('voters', 1).values['s'].tolist()
127
+ [1.0, 1.0, 1.0]
128
+
129
+ In the symbolic form every group of the partition takes the opinion of its majority:
130
+
131
+ >>> from skcomplex.core.laws.utils import mean, where
132
+ >>> galam = GroupingInteraction(
133
+ ... 'galam',
134
+ ... target='voters',
135
+ ... groups='partition',
136
+ ... size=3,
137
+ ... form='symbolic',
138
+ ... write='s',
139
+ ... function=lambda g: where(mean(g.members.s, over=g.members) > 1 / 2, 1, 0),
140
+ ... )
141
+ >>> simulation = Simulation(System(elements=[voters], interactions=[galam]), random_state=0)
142
+ >>> simulation.check().prepare().run(until=1).trajectory_.values('voters.s')[-1].tolist()
143
+ [1.0, 1.0, 1.0]
144
+ """
145
+
146
+ def __init__(
147
+ self,
148
+ label: str,
149
+ *,
150
+ target: Annotated[str, RoleSpec()],
151
+ groups: str = 'pairs',
152
+ act: Act | None = None,
153
+ size: int = 2,
154
+ by: str | None = None,
155
+ capacity: int | None = None,
156
+ phase: str | None = None,
157
+ form: str = 'agent',
158
+ write: str | None = None,
159
+ function: GroupFunction | None = None,
160
+ reduce: str = 'sum',
161
+ ) -> None:
162
+ super().__init__(label)
163
+ self.target = target
164
+ self.groups = groups
165
+ self.act = act
166
+ self.size = size
167
+ self.by = by
168
+ self.capacity = capacity
169
+ self.phase = phase
170
+ self.form = form
171
+ self.write = write
172
+ self.function = function
173
+ self.reduce = reduce
174
+
175
+ def _check_symbolic(self) -> None:
176
+ """Raise an error for a symbolic form without its state or function, or with a setting of the agent form.
177
+
178
+ Raises:
179
+ ValidationError:
180
+ The reduction is unknown, the state or the function is missing, or `act` or `capacity` is given.
181
+ """
182
+ if self.reduce not in REDUCES:
183
+ error_msg = f'Unknown reduction {self.reduce!r} of {self.label!r}. Use one of {", ".join(REDUCES)}.'
184
+ raise ValidationError(error_msg)
185
+ for name, value in (('act', self.act), ('capacity', self.capacity)):
186
+ if value is not None:
187
+ error_msg = (
188
+ f'The grouping {self.label!r} is symbolic, but it was given `{name}`, a setting of the agent form. '
189
+ f'Remove `{name}`, or use form `agent`.'
190
+ )
191
+ raise ValidationError(error_msg)
192
+ if not isinstance(self.write, str) or not callable(self.function):
193
+ error_msg = (
194
+ f'The symbolic grouping {self.label!r} sets a state to a function of every group. Pass the name of the '
195
+ 'state as `write` and the function as `function`.'
196
+ )
197
+ raise ValidationError(error_msg)
198
+
199
+ def _check_space(self, space: BaseSpace | None) -> None:
200
+ """Raise an error for groups of neighbouring cells or nodes in a continuous space."""
201
+ if self.groups == 'neighborhood':
202
+ self._check_grid('groups', self.groups, space, "groups='pairs', 'partition', 'state', or a radius")
203
+ self._check_partners(self.groups, space)
204
+
205
+ def _check(self) -> None:
206
+ """Raise an error for an unknown kind of groups, a size below two, a missing state, or a capacity below one.
207
+
208
+ Raises:
209
+ ValidationError:
210
+ The kind of groups, the form, or the reduction is unknown, the size is below two, the groups `'state'`
211
+ have no state, the capacity is not positive, the symbolic form has no state or function, or a setting
212
+ of one form is given to the other.
213
+ """
214
+ super()._check()
215
+ if self.form not in FORMS:
216
+ error_msg = f'Unknown form {self.form!r} of {self.label!r}. Use one of {", ".join(FORMS)}.'
217
+ raise ValidationError(error_msg)
218
+ self._check_variant('groups', self.groups, GROUPS, (BaseSpec,), functions=True)
219
+ if isinstance(self.groups, PartnerSpec):
220
+ self.groups.check()
221
+ if isinstance(self.size, bool) or not isinstance(self.size, int) or self.size < PAIR:
222
+ error_msg = f'The size of the groups of {self.label!r} is {self.size!r}. Give a whole number of at least 2.'
223
+ raise ValidationError(error_msg)
224
+ if self.groups == 'state' and not isinstance(self.by, str):
225
+ error_msg = f'The groups `state` of {self.label!r} share the value of a state. Pass its name as `by`.'
226
+ raise ValidationError(error_msg)
227
+ if self.capacity is not None and (isinstance(self.capacity, bool) or self.capacity < 1):
228
+ error_msg = f'The capacity of {self.label!r} is {self.capacity!r}. Give a positive whole number, or None.'
229
+ raise ValidationError(error_msg)
230
+ if self.act is not None and not callable(self.act):
231
+ error_msg = f'The action of {self.label!r} is {self.act!r}. Give a function, or None.'
232
+ raise ValidationError(error_msg)
233
+ if self.form == 'symbolic':
234
+ if not isinstance(self.groups, str):
235
+ error_msg = (
236
+ f'The symbolic form of {self.label!r} compiles the named groups, so it cannot run {self.groups!r}. '
237
+ 'Use `form="agent"`, whose groups `_get_groups` draws.'
238
+ )
239
+ raise ValidationError(error_msg)
240
+ self._check_symbolic()
241
+ return
242
+ if self.write is not None or self.function is not None:
243
+ error_msg = (
244
+ f'The grouping {self.label!r} acts on agents, but it was given `write` or `function`, settings of the '
245
+ 'symbolic form. Remove them, or use form `symbolic`.'
246
+ )
247
+ raise ValidationError(error_msg)
248
+
249
+ def _get_partition(
250
+ self,
251
+ agents: Sequence[AgentViewProtocol],
252
+ size: int,
253
+ model: ModelViewProtocol,
254
+ ) -> list[list[AgentViewProtocol]]:
255
+ """Return a random partition of agents into groups of a size, with the remainder in the last group."""
256
+ order = [agents[int(index)] for index in model.rng.permutation(len(agents))]
257
+ return [order[start : start + size] for start in range(0, len(order), size)]
258
+
259
+ def _get_neighborhoods(self, agents: Sequence[AgentViewProtocol]) -> list[list[AgentViewProtocol]]:
260
+ """Return every agent followed by the agents in the cells or nodes around it."""
261
+ located: dict[object, list[AgentViewProtocol]] = {}
262
+ for agent in agents:
263
+ located.setdefault(agent.location_key, []).append(agent)
264
+ return [
265
+ [agent, *(other for cell in agent.neighbor_cells() for other in located.get(cell, []))] for agent in agents
266
+ ]
267
+
268
+ def _get_shared(
269
+ self,
270
+ agents: Sequence[AgentViewProtocol],
271
+ model: ModelViewProtocol,
272
+ ) -> list[list[AgentViewProtocol]]:
273
+ """Return the groups of agents that share a value of the state `by`, each cut at random to the capacity."""
274
+ shared: dict[float, list[AgentViewProtocol]] = {}
275
+ for agent in agents:
276
+ shared.setdefault(float(getattr(agent, str(self.by))), []).append(agent)
277
+ groups = []
278
+ for value in sorted(shared):
279
+ members = shared[value]
280
+ order = [members[int(index)] for index in model.rng.permutation(len(members))]
281
+ groups.append(order if self.capacity is None else order[: self.capacity])
282
+ return groups
283
+
284
+ def _get_partners(
285
+ self,
286
+ pairing: PartnerSpec | Pairing,
287
+ agents: Sequence[AgentViewProtocol],
288
+ model: ModelViewProtocol,
289
+ ) -> list[list[AgentViewProtocol]]:
290
+ """Return the groups of every agent with the partners a selection of partners or a function gives it."""
291
+ law = MatchLaw(self.target, pairing=pairing, capacity=self.capacity or 1)
292
+ groups: dict[int, list[AgentViewProtocol]] = {}
293
+ for first, second in law.get_pairs(agents, agents, model.rng):
294
+ member, partner = cast(AgentViewProtocol, first), cast(AgentViewProtocol, second)
295
+ groups.setdefault(member.id, [member]).append(partner)
296
+ return list(groups.values())
297
+
298
+ def _get_groups(self, model: ModelViewProtocol) -> list[list[AgentViewProtocol]]:
299
+ """Return the groups of one step."""
300
+ agents = [agent for agent in model.agents(self._get_role('target')) if agent.alive]
301
+ if self.groups == 'pairs':
302
+ return self._get_partners(PartnerSpec('all', 'uniform', capacity=1), agents, model)
303
+ if callable(self.groups) or isinstance(self.groups, PartnerSpec):
304
+ return self._get_partners(self.groups, agents, model)
305
+ if self.groups == 'partition':
306
+ return self._get_partition(agents, self.size, model)
307
+ if self.groups == 'neighborhood':
308
+ return self._get_neighborhoods(agents)
309
+ if self.groups == 'state':
310
+ return self._get_shared(agents, model)
311
+ raise self._get_variant_error(self.groups, 'groups', '_get_groups')
312
+
313
+ def _act_on_groups(self, model: ModelViewProtocol) -> None:
314
+ """Act on every group of one step in random order."""
315
+ groups = self._get_groups(model)
316
+ for index in model.rng.permutation(len(groups)):
317
+ self.act_on(groups[int(index)], model)
318
+
319
+ def _keyed(self, reduction: ReductionSpec, member: SimpleNamespace, members: SimpleNamespace) -> Expression:
320
+ """Return a reduction over the members of a group restricted to the members that share the value of `by`.
321
+
322
+ Args:
323
+ reduction:
324
+ The reduction over the members of the group.
325
+
326
+ member:
327
+ The symbols of the member.
328
+
329
+ members:
330
+ The symbols of the members of the group.
331
+
332
+ Returns:
333
+ reduction:
334
+ The reduction restricted to the members that share the value of `by`.
335
+
336
+ Raises:
337
+ ValidationError:
338
+ The reduction has weights.
339
+ """
340
+ if reduction.weights is not None:
341
+ error_msg = f'The reduction {reduction.call} of the grouping {self.label!r} takes no weights.'
342
+ raise ValidationError(error_msg)
343
+ shared = SR(getattr(members, str(self.by))) == SR(getattr(member, str(self.by)))
344
+ condition = shared if reduction.condition is None else both(reduction.condition, shared)
345
+ if reduction.kind == 'count':
346
+ return count(over=reduction.over, where=condition)
347
+ return KEYED[reduction.kind](reduction.argument, over=reduction.over, where=condition)
348
+
349
+ def _get_keyed_group(self, namespace: SimpleNamespace) -> tuple[SimpleNamespace, Expression]:
350
+ """Return the namespace of the group by state of a member and the value of the group, its reductions keyed."""
351
+ target = self._get_member(namespace, 'target')
352
+ names = {name: value for name, value in vars(namespace).items() if name != self._get_role('target')}
353
+ group = SimpleNamespace(**names, member=target, members=target.other, others=())
354
+ value = SR(self.function(group)) if self.function is not None else SR(0)
355
+ keyed = {
356
+ reduction.call: self._keyed(reduction, target, target.other)
357
+ for reduction in reductions_in(value)
358
+ if reduction.over is not None
359
+ }
360
+ return group, value.subs(keyed) if keyed else value
361
+
362
+ def _get_laws(self, namespace: SimpleNamespace) -> list[BaseLaw]:
363
+ """Return the rule of the agent form, or the update of the state of the member of a group.
364
+
365
+ Args:
366
+ namespace:
367
+ The namespace of the symbols the laws can use, of one group in the symbolic form, and of the target for
368
+ groups by state.
369
+
370
+ Returns:
371
+ laws:
372
+ The rule that draws the groups and acts on them every step, or the update of `write`.
373
+ """
374
+ if self.form == 'agent':
375
+ return [RuleLaw(self._act_on_groups, phase=self.phase)]
376
+ if self.groups == 'state':
377
+ group, value = self._get_keyed_group(namespace)
378
+ return [UpdateLaw(getattr(group.member, str(self.write)), value, phase=self.phase)]
379
+ value = self.function(namespace) if self.function is not None else 0
380
+ return [UpdateLaw(getattr(namespace.member, str(self.write)), value, phase=self.phase)]
381
+
382
+ def act_on(self, members: list[AgentViewProtocol], model: ModelViewProtocol) -> None:
383
+ """Act on the members of one group.
384
+
385
+ Args:
386
+ members:
387
+ The agent views of the members of the group.
388
+
389
+ model:
390
+ The model view of the rule.
391
+
392
+ Raises:
393
+ ValidationError:
394
+ The grouping has neither an action nor its own `act_on`.
395
+ """
396
+ if self.act is None:
397
+ error_msg = f'The grouping {self.label!r} has no action. Pass `act` or override `act_on`.'
398
+ raise ValidationError(error_msg)
399
+ self.act(members, model)
@@ -0,0 +1,191 @@
1
+ """Define Hamiltonian interactions, Hamilton's equations of canonical coordinates and momenta."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ from collections.abc import Callable, Sequence
7
+ from types import SimpleNamespace
8
+ from typing import Annotated
9
+
10
+ from sage.all__sagemath_symbolics import SR, Expression, vector
11
+ from sage.modules.free_module_element import FreeModuleElement
12
+
13
+ from ...errors import ValidationError
14
+ from ...specs import RoleSpec
15
+ from ..base import BasePart
16
+ from ..laws import RateLaw
17
+ from ..types import Target
18
+ from ._interaction import Interaction
19
+
20
+
21
+ class HamiltonianInteraction(Interaction):
22
+ """Hamilton's equations `q' = dH/dp` and `p' = -dH/dq` of the canonical pairs `(q, p)` of a Hamiltonian `H(ns)`.
23
+
24
+ The coordinates and the momenta are states of order 1, which may be angles, of every role that binds one element or
25
+ group, `target` by default, and the coordinates pair with the momenta in order. Every component of a vector state
26
+ is a coordinate or a momentum. The interaction returns one rate law per coordinate and per momentum, and the rates
27
+ of one state add, so the Hamiltonians of separate interactions sum: a coupling between two oscillators is an
28
+ interaction of its own whose Hamiltonian holds only the coupling energy. Dissipation or forcing is a rate
29
+ interaction on the momenta.
30
+
31
+ A Hamiltonian function takes the namespace of the interaction, with the namespaces of the roles, the time `t`, and
32
+ the symbols of the parameters a subclass declares.
33
+
34
+ Args:
35
+ label:
36
+ The label of the interaction, unique among the parts of its system.
37
+
38
+ target:
39
+ The path of the element or group whose states are the canonical pairs.
40
+
41
+ coordinates:
42
+ The name of the state of order 1 that is a coordinate, or the names of several states.
43
+
44
+ momenta:
45
+ The name of the state of order 1 that is the momentum of the coordinate, or the names of several states in
46
+ the order of the coordinates.
47
+
48
+ hamiltonian:
49
+ A function of the namespace that returns the Hamiltonian.
50
+
51
+ Raises:
52
+ ValidationError:
53
+ A state is not a name, the coordinates and the momenta differ in count, the Hamiltonian is not callable,
54
+ or a coordinate and its momentum differ in size or are not of order 1.
55
+
56
+ Examples:
57
+ >>> from typing import Annotated
58
+ >>> from skcomplex.core.elements import Element
59
+ >>> from skcomplex.core.interactions import HamiltonianInteraction
60
+ >>> from skcomplex.core.system import System
61
+ >>> from skcomplex.engine.runtime import Simulation
62
+ >>> from skcomplex.specs import StateSpec
63
+ >>> class OscillatorElement(Element):
64
+ ... def __init__(self, label, q: Annotated[float, StateSpec()] = 1.0, p: Annotated[float, StateSpec()] = 0):
65
+ ... super().__init__(label)
66
+ ... self.q = q
67
+ ... self.p = p
68
+ >>> energy = lambda s: (s.target.p**2 + s.target.q**2) / 2
69
+ >>> spring = HamiltonianInteraction('spring', target='mass', hamiltonian=energy)
70
+ >>> system = System(elements=[OscillatorElement('mass')], interactions=[spring])
71
+ >>> trajectory = Simulation(system, dt=0.01).check().prepare().run(until=3.14159).trajectory_
72
+ >>> round(float(trajectory.values('mass.q')[-1]), 3)
73
+ -1.0
74
+ """
75
+
76
+ def __init__(
77
+ self,
78
+ label: str,
79
+ *,
80
+ target: Annotated[str, RoleSpec()],
81
+ coordinates: str | Sequence[str] = 'q',
82
+ momenta: str | Sequence[str] = 'p',
83
+ hamiltonian: Callable[[SimpleNamespace], object] | None = None,
84
+ ) -> None:
85
+ super().__init__(label)
86
+ self.target = target
87
+ self.coordinates = coordinates
88
+ self.momenta = momenta
89
+ self.hamiltonian = hamiltonian
90
+
91
+ def _get_names(self, names: str | Sequence[str]) -> tuple[str, ...]:
92
+ """Return the names of the states of one side of the canonical pairs."""
93
+ return (names,) if isinstance(names, str) else tuple(names)
94
+
95
+ def _check(self) -> None:
96
+ """Raise an error for a state that is not a name, an unpaired state, or a Hamiltonian that is not callable.
97
+
98
+ Raises:
99
+ ValidationError:
100
+ The type declares states, a state is not a name, the coordinates and the momenta differ in count, or
101
+ the Hamiltonian is not callable.
102
+ """
103
+ super()._check()
104
+ for side in ('coordinates', 'momenta'):
105
+ names = self._get_names(getattr(self, side))
106
+ if not names or not all(isinstance(name, str) and name.isidentifier() for name in names):
107
+ error_msg = f'The {side} of {self.label!r} are {getattr(self, side)!r}. Give names of states.'
108
+ raise ValidationError(error_msg)
109
+ coordinates, momenta = self._get_names(self.coordinates), self._get_names(self.momenta)
110
+ if len(coordinates) != len(momenta):
111
+ unpaired = coordinates[len(momenta) :] or momenta[len(coordinates) :]
112
+ error_msg = (
113
+ f'{type(self).__name__} {self.label!r} pairs the coordinates {coordinates} with the momenta {momenta}, '
114
+ f'so {", ".join(unpaired)} has no partner. Give one momentum per coordinate.'
115
+ )
116
+ raise ValidationError(error_msg)
117
+ if self.hamiltonian is not None and not callable(self.hamiltonian):
118
+ error_msg = f'The hamiltonian of {self.label!r} is {self.hamiltonian!r}. Give a function of the namespace.'
119
+ raise ValidationError(error_msg)
120
+
121
+ def _get_hamiltonian(self, namespace: SimpleNamespace) -> object:
122
+ """Return the Hamiltonian, the hook a subclass overrides to derive it from its parameters."""
123
+ if self.hamiltonian is None:
124
+ error_msg = f'{type(self).__name__} {self.label!r} has no Hamiltonian. Give a function of the namespace.'
125
+ raise ValidationError(error_msg)
126
+ return self.hamiltonian(namespace)
127
+
128
+ def _get_members(self, namespace: SimpleNamespace) -> list[SimpleNamespace]:
129
+ """Return the namespaces of the members whose states are canonical pairs, those of every role of one path."""
130
+ return [
131
+ getattr(namespace, name)
132
+ for name, spec in self._get_specs().items()
133
+ if isinstance(spec, RoleSpec) and not spec.variadic and not spec.noise
134
+ ]
135
+
136
+ def _get_state(self, member: SimpleNamespace, name: str) -> Target:
137
+ """Return a canonical state of a member, after checking that it has order 1."""
138
+ if hasattr(member, f'{name}_d1'):
139
+ error_msg = (
140
+ f'{type(self).__name__} {self.label!r} reads the state {name} of order above 1, but canonical '
141
+ 'coordinates and momenta have order 1. Declare it with `StateSpec(order=1)`, or derive the equations '
142
+ 'of a coordinate of order 2 with `EulerLagrangeInteraction`.'
143
+ )
144
+ raise ValidationError(error_msg)
145
+ state: Target = getattr(member, name)
146
+ return state
147
+
148
+ def _get_pairs(self, namespace: SimpleNamespace) -> list[tuple[Target, Target]]:
149
+ """Return the canonical pairs of every member, after checking that each coordinate matches its momentum."""
150
+ pairs = []
151
+ names = list(zip(self._get_names(self.coordinates), self._get_names(self.momenta), strict=True))
152
+ for member in self._get_members(namespace):
153
+ for coordinate, momentum in names:
154
+ q, p = self._get_state(member, coordinate), self._get_state(member, momentum)
155
+ if len(self._get_components(q)) != len(self._get_components(p)):
156
+ error_msg = (
157
+ f'The coordinate {coordinate} and the momentum {momentum} of {self.label!r} differ in size. '
158
+ 'Give a momentum of the size of its coordinate.'
159
+ )
160
+ raise ValidationError(error_msg)
161
+ pairs.append((q, p))
162
+ return pairs
163
+
164
+ def _get_components(self, state: Target) -> list[Expression]:
165
+ """Return the components of a state, the state itself for a scalar."""
166
+ return list(state) if isinstance(state, FreeModuleElement) else [state]
167
+
168
+ def _get_derivative(self, hamiltonian: Expression, state: Target) -> Target:
169
+ """Return the derivative of the Hamiltonian with respect to a state, every component of a vector state."""
170
+ if isinstance(state, FreeModuleElement):
171
+ return vector(SR, [hamiltonian.diff(component) for component in state])
172
+ return hamiltonian.diff(state)
173
+
174
+ def _get_laws(self, namespace: SimpleNamespace) -> list[BasePart]:
175
+ """Return the rate of every coordinate, `dH/dp`, and of every momentum, `-dH/dq`.
176
+
177
+ Args:
178
+ namespace:
179
+ The namespace of the symbols the laws can use, with the namespaces of the roles.
180
+
181
+ Returns:
182
+ laws:
183
+ The rate laws of the coordinates and the momenta.
184
+ """
185
+ pairs = self._get_pairs(namespace)
186
+ hamiltonian = SR(self._get_hamiltonian(namespace))
187
+ laws: list[BasePart] = []
188
+ for q, p in pairs:
189
+ laws.append(RateLaw(q, self._get_derivative(hamiltonian, p)))
190
+ laws.append(RateLaw(p, -self._get_derivative(hamiltonian, q)))
191
+ return laws