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 +1,409 @@
1
+ """Read derivatives and lags of states through their companion states, and solve equations for highest derivatives."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ from __future__ import annotations
7
+
8
+ import itertools
9
+ from collections.abc import Callable
10
+ from types import SimpleNamespace
11
+
12
+ import numpy as np
13
+ import numpy.typing as npt
14
+ from sage.all__sagemath_symbolics import SR, Expression, matrix, solve
15
+ from sage.modules.free_module_element import FreeModuleElement
16
+
17
+ from ....core.laws import BaseLaw, BoundaryLaw, CrossingLaw, EquationLaw, JumpLaw, NoiseLaw, RateLaw, UpdateLaw
18
+ from ....core.laws.utils import reductions_in
19
+ from ....core.spaces import StaticTime
20
+ from ....errors import ValidationError
21
+ from ....specs import CallSpec
22
+ from ....specs._orders_spec import _OrdersSpec
23
+ from ....types import Array, VariableKind
24
+ from ..._utils import components_of, declarations_of, symbol, vector
25
+ from ...problems import BlockSpec, KernelSpec
26
+ from ...problems._relation_spec import _RelationSpec
27
+ from .._base import BasePass
28
+ from .._compilation import Compilation
29
+ from .._laws import _KERNEL_FREE_LAWS
30
+ from .._renewal_law import RenewalLaw
31
+ from ._complex import LowerComplexPass
32
+
33
+ _EQUATION_UNKNOWNS = 6
34
+
35
+
36
+ class OrdersPass(BasePass):
37
+ """Pass that reads derivatives and lags through companion states, adds their chains, and solves equations."""
38
+
39
+ def _get_reads(self) -> tuple[str, ...]:
40
+ """Return the fields of the compilation the pass reads."""
41
+ return ('lowered', 'layout')
42
+
43
+ def _get_writes(self) -> tuple[str, ...]:
44
+ """Return the fields of the compilation the pass writes."""
45
+ return ('ordered',)
46
+
47
+ def _run(self, inputs: object = None) -> None:
48
+ """Lower the orders and lags of the laws and solve their equations."""
49
+ compilation = self.compilation_
50
+ blocks = list(Compilation._required(compilation.layout, 'layout').blocks.values())
51
+ orders = self._orders_of(blocks)
52
+ specs = [
53
+ (spec, self._with_orders(spec, laws, block, orders))
54
+ for spec, laws, block in Compilation._required(compilation.lowered, 'lowered')
55
+ ]
56
+ static = isinstance(compilation.system.time, StaticTime)
57
+ compilation.ordered = self._solve_static(specs) if static else self._solve_equations(specs)
58
+
59
+ @staticmethod
60
+ def _orders_of(blocks: list[BlockSpec]) -> _OrdersSpec:
61
+ """Return the orders above 1 and the lags of every state of the blocks."""
62
+ orders, lags = {}, {}
63
+ for block in blocks:
64
+ if block.node.interaction or block.node.is_agent:
65
+ continue
66
+ declarations = declarations_of(block.node.component_type, VariableKind.STATE)
67
+ for variable, entry in block.entries.items():
68
+ declaration = declarations.get(variable)
69
+ if declaration is not None and declaration.derivatives:
70
+ orders[entry.name] = declaration.derivatives + 1
71
+ if declaration is not None and declaration.lags:
72
+ lags[entry.name] = declaration.lags
73
+ return _OrdersSpec(orders, lags)
74
+
75
+ @staticmethod
76
+ def _companion_symbol(spec: KernelSpec, item: Expression, suffix: str) -> Expression:
77
+ """Return the symbol of a companion state of the state a symbol reads, in the same namespace and column."""
78
+ reference = spec.references[item]
79
+ name = f'{reference.entry.name}{suffix}'
80
+ for other, candidate in spec.references.items():
81
+ if (
82
+ candidate.entry.name == name
83
+ and candidate.column == reference.column
84
+ and candidate.source == reference.source
85
+ ):
86
+ return other
87
+ error_msg = f'A law of {spec.owner} reads {name}, which the namespace does not hold.'
88
+ raise ValidationError(error_msg)
89
+
90
+ @staticmethod
91
+ def _substitute(
92
+ value: object,
93
+ spec: KernelSpec,
94
+ orders: _OrdersSpec,
95
+ owner: str,
96
+ highest: dict[Expression, Expression] | None = None,
97
+ ) -> object:
98
+ """Return a law value with derivatives and lags of states replaced by their companion symbols.
99
+
100
+ When `highest` is given, derivatives of a state's own order become placeholders that map to the symbol of the
101
+ state's highest derivative, which an equation solves for.
102
+ """
103
+ if isinstance(value, FreeModuleElement):
104
+ return vector(OrdersPass._substitute(item, spec, orders, owner, highest) for item in value)
105
+ if not isinstance(value, Expression):
106
+ return value
107
+ replacements = {}
108
+ for call in BasePass._calls_of(value, 'derivative'):
109
+ item, degree = call.operands()
110
+ reference = spec.references.get(item)
111
+ order = orders.orders.get(reference.entry.name, 1) if reference is not None else 1
112
+ if highest is not None and reference is not None and degree.is_integer() and int(degree) == order:
113
+ top = item if order == 1 else OrdersPass._companion_symbol(spec, item, f'_d{order - 1}')
114
+ placeholder = symbol(f'_highest_{top}')
115
+ highest[placeholder] = top
116
+ replacements[call] = placeholder
117
+ continue
118
+ if reference is None or not degree.is_integer() or not 0 < int(degree) < order:
119
+ error_msg = (
120
+ f'{owner} uses {call}, but laws read derivatives of a state only below its declared order, here '
121
+ f'{order}. Declare a higher order with `state(order=...)`, or state the highest derivative with an '
122
+ '`EquationLaw`.'
123
+ )
124
+ raise ValidationError(error_msg)
125
+ replacements[call] = OrdersPass._companion_symbol(spec, item, f'_d{int(degree)}')
126
+ for call in BasePass._calls_of(value, 'lag'):
127
+ item, steps = call.operands()
128
+ reference = spec.references.get(item)
129
+ kept = orders.lags.get(reference.entry.name, 0) if reference is not None else 0
130
+ if reference is None or not steps.is_integer() or not 0 < int(steps) <= kept:
131
+ error_msg = (
132
+ f'{owner} uses {call}, but the state keeps {kept} past values. Declare more with `state(lags=...)`.'
133
+ )
134
+ raise ValidationError(error_msg)
135
+ replacements[call] = OrdersPass._companion_symbol(spec, item, f'_lag{int(steps)}')
136
+ return value.subs(replacements) if replacements else value
137
+
138
+ @staticmethod
139
+ def _retarget(law: RateLaw | NoiseLaw, spec: KernelSpec, orders: _OrdersSpec) -> RateLaw | NoiseLaw:
140
+ """Return a rate or noise law that targets the highest derivative of its state, after checking its order."""
141
+ items = components_of(law._get_targets()[0])
142
+ references = [spec.references.get(item) for item in items]
143
+ declared = {orders.orders.get(reference.entry.name, 1) for reference in references if reference is not None}
144
+ order = max(declared, default=1)
145
+ if law.order is not None and law.order != order:
146
+ names = ', '.join(sorted({reference.entry.name for reference in references if reference is not None}))
147
+ error_msg = (
148
+ f'A {type(law).__name__} of {spec.owner} on {names} gives the derivative of order {law.order}, but the '
149
+ f'state has order {order}. Match the law to the order declared with `state(order=...)`.'
150
+ )
151
+ raise ValidationError(error_msg)
152
+ if order == 1:
153
+ return law
154
+ tops = [OrdersPass._companion_symbol(spec, item, f'_d{order - 1}') for item in items]
155
+ target = vector(tops) if isinstance(law._get_targets()[0], FreeModuleElement) else tops[0]
156
+ return BasePass._replaced(law, target=target)
157
+
158
+ @staticmethod
159
+ def _intrinsic_laws(spec: KernelSpec, block: BlockSpec, orders: _OrdersSpec) -> list[BaseLaw]:
160
+ """Return the chain `x' = x_d1, ...` of every higher-order state and the shifts of every lagged state."""
161
+ laws: list[BaseLaw] = []
162
+ for variable, entry in block.entries.items():
163
+ names = [variable, *(f'{variable}_d{index}' for index in range(1, orders.orders.get(entry.name, 1)))]
164
+ laws += [
165
+ RateLaw(getattr(spec.namespace, lower), getattr(spec.namespace, upper))
166
+ for lower, upper in itertools.pairwise(names)
167
+ ]
168
+ shifted = [variable, *(f'{variable}_lag{index}' for index in range(1, orders.lags.get(entry.name, 0) + 1))]
169
+ laws += [
170
+ UpdateLaw(getattr(spec.namespace, older), getattr(spec.namespace, newer))
171
+ for newer, older in itertools.pairwise(shifted)
172
+ ]
173
+ return laws
174
+
175
+ @staticmethod
176
+ def _relation(spec: KernelSpec, law: EquationLaw, orders: _OrdersSpec) -> _RelationSpec:
177
+ """Return an equation law as a relation in placeholders of the highest derivatives it contains."""
178
+ description = f'the equation {law.lhs_} == {law.rhs_} of {spec.owner}'
179
+ if spec.pairs is not None:
180
+ error_msg = f'Pair interaction {spec.owner} returns {description}. Pair interactions take only rate laws.'
181
+ raise ValidationError(error_msg)
182
+ highest: dict[Expression, Expression] = {}
183
+ lhs = OrdersPass._substitute(SR(law.lhs_), spec, orders, f'In {description}, it', highest)
184
+ rhs = OrdersPass._substitute(SR(law.rhs_), spec, orders, f'In {description}, it', highest)
185
+ reference = spec.references.get(law.target) if isinstance(law.target, Expression) else None
186
+ key = None if reference is None else (reference.entry.name, reference.column)
187
+ target = None if key is None else law.target
188
+ return _RelationSpec(spec, SR(lhs) - SR(rhs), highest, description, key, target)
189
+
190
+ @staticmethod
191
+ def _check_relation(relation: _RelationSpec) -> None:
192
+ """Raise an error for a relation with no highest derivative of a state to solve for."""
193
+ if not relation.highest:
194
+ description = relation.description
195
+ error_msg = (
196
+ f'{description[0].upper()}{description[1:]} contains no highest derivative of a state to solve for.'
197
+ )
198
+ raise ValidationError(error_msg)
199
+
200
+ @staticmethod
201
+ def _summed(relations: list[_RelationSpec]) -> list[_RelationSpec]:
202
+ """Return the relations with those of one target added into one."""
203
+ groups: dict[tuple[str, int] | int, list[_RelationSpec]] = {}
204
+ for index, relation in enumerate(relations):
205
+ groups.setdefault(index if relation.key is None else relation.key, []).append(relation)
206
+ summed = []
207
+ for group in groups.values():
208
+ first = group[0]
209
+ if len(group) > 1:
210
+ references = {key: value for item in group for key, value in item.spec.references.items()}
211
+ owner = ', '.join(dict.fromkeys(item.spec.owner for item in group))
212
+ spec = KernelSpec(owner, SimpleNamespace(), references, max(item.spec.rows for item in group))
213
+ first = _RelationSpec(
214
+ spec,
215
+ sum((item.expression for item in group), SR(0)),
216
+ {key: value for item in group for key, value in item.highest.items()},
217
+ ' + '.join(item.description for item in group),
218
+ first.key,
219
+ first.target,
220
+ )
221
+ summed.append(first)
222
+ return summed
223
+
224
+ @staticmethod
225
+ def _ordered_law(spec: KernelSpec, law: BaseLaw, orders: _OrdersSpec) -> BaseLaw:
226
+ """Return a jump, event, renewal, or assignment law with derivatives and lags replaced and rates retargeted."""
227
+ owner = f'A {type(law).__name__} of {spec.owner}'
228
+ if isinstance(law, JumpLaw):
229
+ return JumpLaw(OrdersPass._substitute(law.rate, spec, orders, owner), law.changes)
230
+ if isinstance(law, CrossingLaw | RenewalLaw):
231
+ reset = {
232
+ OrdersPass._substitute(SR(target), spec, orders, owner): (
233
+ value if BaseLaw._is_function(value) else OrdersPass._substitute(SR(value), spec, orders, owner)
234
+ )
235
+ for target, value in (law.reset or {}).items()
236
+ }
237
+ reset_value = reset if law.reset is not None else None
238
+ if isinstance(law, RenewalLaw):
239
+ return BasePass._replaced(
240
+ law,
241
+ waiting=(
242
+ law.waiting
243
+ if BaseLaw._is_function(law.waiting)
244
+ else OrdersPass._substitute(SR(law.waiting), spec, orders, owner)
245
+ ),
246
+ reset=reset_value,
247
+ )
248
+ return BasePass._replaced(
249
+ law,
250
+ guard=(
251
+ law.guard
252
+ if BaseLaw._is_function(law.guard)
253
+ else OrdersPass._substitute(SR(law.guard), spec, orders, owner)
254
+ ),
255
+ reset=reset_value,
256
+ )
257
+ if not isinstance(law, RateLaw | NoiseLaw | UpdateLaw | BoundaryLaw):
258
+ return law
259
+ value = OrdersPass._substitute(law.value, spec, orders, owner)
260
+ if isinstance(law, RateLaw | NoiseLaw):
261
+ return OrdersPass._retarget(BasePass._replaced(law, value=value), spec, orders)
262
+ return BasePass._replaced(law, value=value)
263
+
264
+ @staticmethod
265
+ def _with_orders(
266
+ spec: KernelSpec,
267
+ laws: list[BaseLaw],
268
+ block: BlockSpec,
269
+ orders: _OrdersSpec,
270
+ ) -> list[BaseLaw | _RelationSpec]:
271
+ """Return laws with derivatives and lags replaced, rates retargeted, equations as relations, chains added."""
272
+ if not orders.orders and not orders.lags and not any(isinstance(law, EquationLaw) for law in laws):
273
+ return list(laws)
274
+ result: list[BaseLaw | _RelationSpec] = []
275
+ for law in laws:
276
+ if isinstance(law, _KERNEL_FREE_LAWS):
277
+ result.append(law)
278
+ elif isinstance(law, EquationLaw):
279
+ result.append(OrdersPass._relation(spec, law, orders))
280
+ else:
281
+ result.append(OrdersPass._ordered_law(spec, law, orders))
282
+ if not block.node.interaction:
283
+ result += [
284
+ item
285
+ for law in OrdersPass._intrinsic_laws(spec, block, orders)
286
+ for item in LowerComplexPass._split_law(
287
+ law,
288
+ spec.owner,
289
+ spec._state_name,
290
+ )
291
+ ]
292
+ return result
293
+
294
+ @staticmethod
295
+ def _numeric_solution(rows: int, size: int, index: int) -> Callable[..., Array]:
296
+ """Return a function of the matrix and right side entries that solves the linear system for one unknown."""
297
+
298
+ def solve(t: float, *entries: npt.ArrayLike) -> Array:
299
+ del t
300
+ values = [np.broadcast_to(np.asarray(entry, dtype=float), (rows,)) for entry in entries]
301
+ matrix_ = np.stack(values[: size * size], axis=-1).reshape(rows, size, size)
302
+ right = np.stack(values[size * size :], axis=-1)
303
+ return np.linalg.solve(matrix_, right[..., None])[..., 0][:, index]
304
+
305
+ return solve
306
+
307
+ @staticmethod
308
+ def _checked_relations(specs: list[tuple[KernelSpec, list[BaseLaw | _RelationSpec]]]) -> list[_RelationSpec]:
309
+ """Return the relations of specs with those of one target added, each checked for a highest derivative."""
310
+ relations = OrdersPass._summed([item for _, laws in specs for item in laws if isinstance(item, _RelationSpec)])
311
+ for relation in relations:
312
+ OrdersPass._check_relation(relation)
313
+ return relations
314
+
315
+ @staticmethod
316
+ def _solve_equations(
317
+ specs: list[tuple[KernelSpec, list[BaseLaw | _RelationSpec]]],
318
+ ) -> list[tuple[KernelSpec, list[BaseLaw]]]:
319
+ """Return specs whose equations are replaced by rate laws on the highest derivatives they solve for jointly."""
320
+ relations = OrdersPass._checked_relations(specs)
321
+ kept = [(spec, [law for law in laws if not isinstance(law, _RelationSpec)]) for spec, laws in specs]
322
+ if not relations:
323
+ return kept
324
+ highest: dict[Expression, Expression] = {}
325
+ for relation in relations:
326
+ highest.update(relation.highest)
327
+ unknowns = list(highest)
328
+ for relation in relations:
329
+ for first in unknowns:
330
+ for second in unknowns:
331
+ if not relation.expression.diff(first).diff(second).is_trivial_zero():
332
+ error_msg = (
333
+ f'{relation.description[0].upper()}{relation.description[1:]} is not linear in the highest '
334
+ f'derivative {highest[first]}. Write the equation so that highest derivatives appear '
335
+ 'linearly.'
336
+ )
337
+ raise ValidationError(error_msg)
338
+ descriptions = '; '.join(relation.description for relation in relations)
339
+ if len(relations) != len(unknowns):
340
+ error_msg = (
341
+ f'{len(relations)} equations give {len(unknowns)} highest derivatives, '
342
+ f'{", ".join(str(highest[item]) for item in unknowns)}, in {descriptions}. Give one equation per '
343
+ 'derivative.'
344
+ )
345
+ raise ValidationError(error_msg)
346
+ zero = dict.fromkeys(unknowns, 0)
347
+ coefficients = [[relation.expression.diff(item) for item in unknowns] for relation in relations]
348
+ right = [-relation.expression.subs(zero) for relation in relations]
349
+ references = {key: value for relation in relations for key, value in relation.spec.references.items()}
350
+ rows = max(relation.spec.rows for relation in relations)
351
+ owner = ', '.join(dict.fromkeys(relation.spec.owner for relation in relations))
352
+ merged = KernelSpec(owner, SimpleNamespace(), references, rows)
353
+ laws: list[BaseLaw]
354
+ if len(unknowns) <= _EQUATION_UNKNOWNS:
355
+ system = matrix(SR, coefficients)
356
+ if system.det().simplify_full().is_trivial_zero():
357
+ error_msg = f'The highest derivatives of {descriptions} cannot be solved for: the system is singular.'
358
+ raise ValidationError(error_msg)
359
+ solution = system.solve_right(vector([SR(item) for item in right]), check=False)
360
+ laws = [RateLaw(highest[item], value) for item, value in zip(unknowns, solution, strict=True)]
361
+ else:
362
+ entries = [entry for row in coefficients for entry in row] + right
363
+ laws = [
364
+ RateLaw(
365
+ highest[item],
366
+ CallSpec(OrdersPass._numeric_solution(rows, len(unknowns), index), tuple(entries)),
367
+ )
368
+ for index, item in enumerate(unknowns)
369
+ ]
370
+ return [*kept, (merged, laws)]
371
+
372
+ @staticmethod
373
+ def _exact_solution(relations: list[_RelationSpec]) -> list[Expression] | None:
374
+ """Return the unique explicit solution of static equations for their targets, or `None` when Sage finds none."""
375
+ unknowns = [item.target for item in relations]
376
+ reduced = {
377
+ name for item in relations for call in reductions_in(item.expression) for name in call.call.variables()
378
+ }
379
+ if len(relations) > _EQUATION_UNKNOWNS or reduced & set(unknowns):
380
+ return None
381
+ known = {name for item in relations for name in item.expression.variables()}
382
+ try:
383
+ solutions = solve([item.expression == 0 for item in relations], unknowns, solution_dict=True)
384
+ except TypeError:
385
+ return None
386
+ if len(solutions) != 1 or any(item not in solutions[0] for item in unknowns):
387
+ return None
388
+ values = [SR(solutions[0][item]) for item in unknowns]
389
+ explicit = all(set(value.variables()) <= known - set(unknowns) for value in values)
390
+ return values if explicit else None
391
+
392
+ @staticmethod
393
+ def _solve_static(
394
+ specs: list[tuple[KernelSpec, list[BaseLaw | _RelationSpec]]],
395
+ ) -> list[tuple[KernelSpec, list[BaseLaw]]]:
396
+ """Return specs whose equations are replaced by updates of an exact solution, or else rates of their residuals.
397
+
398
+ An equation without a state as its target is left out, since the compiler reports it.
399
+ """
400
+ declared = [item for _, laws in specs for item in laws if isinstance(item, _RelationSpec)]
401
+ relations = OrdersPass._summed([item for item in declared if item.key is not None])
402
+ kept = [(spec, [law for law in laws if not isinstance(law, _RelationSpec)]) for spec, laws in specs]
403
+ if not relations:
404
+ return kept
405
+ values = OrdersPass._exact_solution(relations)
406
+ if values is None:
407
+ return [*kept, *((item.spec, [RateLaw(item.target, item.expression)]) for item in relations)]
408
+ pairs = zip(relations, values, strict=True)
409
+ return [*kept, *((item.spec, [UpdateLaw(item.target, value)]) for item, value in pairs)]
@@ -0,0 +1,90 @@
1
+ """Keep the laws of the owners a compilation compiles, masked to the rows present of capacity groups."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ from collections import defaultdict
7
+
8
+ from sage.all__sagemath_symbolics import SR, Expression
9
+ from sage.modules.free_module_element import FreeModuleElement
10
+
11
+ from ....core.laws import BaseLaw, JumpLaw, NoiseLaw, RateLaw, UpdateLaw
12
+ from ..._utils import vector
13
+ from ...problems import DeclarationsSpec, KernelSpec
14
+ from .._base import BasePass
15
+ from .._compilation import Compilation, Laws
16
+ from ._census import CensusPass
17
+ from ._kernels import KernelsPass
18
+ from ._mask_requests import MaskRequestsPass
19
+
20
+
21
+ class OwnersPass(BasePass):
22
+ """Pass that keeps the laws of the compiled owners, masks them to the rows present, and finds their kinds."""
23
+
24
+ def _get_reads(self) -> tuple[str, ...]:
25
+ """Return the fields of the compilation the pass reads."""
26
+ return ('shifted', 'apart', 'nodes', 'layout')
27
+
28
+ def _get_writes(self) -> tuple[str, ...]:
29
+ """Return the fields of the compilation the pass writes."""
30
+ return ('drawn', 'kinds', 'drawn_apart')
31
+
32
+ def _run(self, inputs: object = None) -> None:
33
+ """Keep the laws of the owners of the compilation and find their kinds."""
34
+ compilation = self.compilation_
35
+ declarations = Compilation._required(compilation.layout, 'layout')
36
+ agents = {node.path for node in Compilation._required(compilation.nodes, 'nodes') if node.is_agent}
37
+ owned = self._owned(Compilation._required(compilation.shifted, 'shifted'), compilation.owners, agents)
38
+ compilation.drawn = [(spec, self._masked(spec, laws, declarations)) for spec, laws in owned]
39
+ apart = Compilation._required(compilation.apart, 'apart')
40
+ compilation.drawn_apart = self._owned(apart, compilation.owners, agents)
41
+ compilation.kinds = self._law_kinds([*compilation.drawn, *compilation.drawn_apart], agents)
42
+
43
+ @staticmethod
44
+ def _kept_update(law: UpdateLaw, mask: Expression) -> UpdateLaw:
45
+ """Return an update law that keeps the value of its target on the free rows of a capacity layout."""
46
+ value, kept = (
47
+ MaskRequestsPass._masked_value(law.value, mask),
48
+ MaskRequestsPass._masked_value(law._get_targets()[0], 1 - mask),
49
+ )
50
+ if isinstance(value, FreeModuleElement) and isinstance(kept, FreeModuleElement):
51
+ return BasePass._replaced(law, value=vector(a + b for a, b in zip(value, kept, strict=True)))
52
+ return BasePass._replaced(law, value=SR(value) + SR(kept))
53
+
54
+ @staticmethod
55
+ def _masked(spec: KernelSpec, laws: list[BaseLaw], declarations: DeclarationsSpec) -> list[BaseLaw]:
56
+ """Return laws that leave the free rows of a capacity layout unchanged and fire no event for them."""
57
+ mask = MaskRequestsPass._mask_of(spec, declarations)
58
+ if mask is None:
59
+ return laws
60
+ masked: list[BaseLaw] = []
61
+ for law in laws:
62
+ if isinstance(law, RateLaw | NoiseLaw):
63
+ masked.append(BasePass._replaced(law, value=MaskRequestsPass._masked_value(law.value, mask)))
64
+ elif isinstance(law, JumpLaw) and law.rate is not None:
65
+ masked.append(BasePass._replaced(law, rate=MaskRequestsPass._masked_value(law.rate, mask)))
66
+ elif isinstance(law, UpdateLaw) and isinstance(law.value, Expression | FreeModuleElement | int | float):
67
+ masked.append(OwnersPass._kept_update(law, mask))
68
+ else:
69
+ masked.append(law)
70
+ return masked
71
+
72
+ @staticmethod
73
+ def _owned(specs: Laws, owners: frozenset[str] | None, agents: set[str]) -> Laws:
74
+ """Return the laws of the components in `owners`, or every law."""
75
+ return [
76
+ (
77
+ spec,
78
+ laws if owners is None else [law for law in laws if CensusPass._law_owner(spec, law, agents) in owners],
79
+ )
80
+ for spec, laws in specs
81
+ ]
82
+
83
+ @staticmethod
84
+ def _law_kinds(specs: list[tuple[KernelSpec, list[BaseLaw]]], agents: set[str]) -> dict[str, set[type]]:
85
+ """Return the kinds of the laws of every component."""
86
+ kinds: dict[str, set[type]] = defaultdict(set)
87
+ for spec, laws in specs:
88
+ for law in laws:
89
+ kinds[CensusPass._law_owner(spec, law, agents)].add(KernelsPass._kind_of(law))
90
+ return kinds
@@ -0,0 +1,69 @@
1
+ """Compile particles: pair interactions within a cutoff and the boundaries of the continuous space they move in."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+
7
+ from sage.all__sagemath_symbolics import SR
8
+
9
+ from ....core.laws import BaseLaw, BoundaryLaw
10
+ from ....core.laws.utils import either, mod, where
11
+ from ....core.spaces import ContinuousSpace
12
+ from ....types import VariableKind
13
+ from ..._utils import components_of, declarations_of
14
+ from ...problems import BlockSpec, KernelSpec
15
+ from .._base import BasePass
16
+ from .._compilation import Compilation
17
+
18
+
19
+ class BoundaryLawsPass(BasePass):
20
+ """Pass that adds the laws by which the boundary of a continuous space acts on the positions of components."""
21
+
22
+ def _get_reads(self) -> tuple[str, ...]:
23
+ """Return the fields of the compilation the pass reads."""
24
+ return ('collected',)
25
+
26
+ def _get_writes(self) -> tuple[str, ...]:
27
+ """Return the fields of the compilation the pass writes."""
28
+ return ('collected',)
29
+
30
+ def _run(self, inputs: object = None) -> None:
31
+ """Add the boundary laws of continuous spaces."""
32
+ compilation = self.compilation_
33
+ compilation.collected = [
34
+ (spec, [*laws, *self._space_boundary_laws(block, spec)], block)
35
+ for spec, laws, block in Compilation._required(compilation.collected, 'collected')
36
+ ]
37
+
38
+ @staticmethod
39
+ def _space_boundary_laws(block: BlockSpec, spec: KernelSpec) -> list[BaseLaw]:
40
+ """Return the laws by which the boundary of a continuous space acts on the position states of a component.
41
+
42
+ A periodic boundary wraps every position component into the box. A reflecting boundary mirrors a position that
43
+ crossed a wall back into the box and reverses the velocity component across the wall, where the velocity is the
44
+ first derivative of a position of order 2.
45
+ """
46
+ space = block.node.space
47
+ if block.node.interaction or not isinstance(space, ContinuousSpace) or space.boundary == 'open':
48
+ return []
49
+ declarations = declarations_of(block.node.component_type, VariableKind.STATE)
50
+ laws: list[BaseLaw] = []
51
+ for name, declaration in declarations.items():
52
+ if not declaration.is_place:
53
+ continue
54
+ velocity_name = f'{name}_d1' if declaration.order > 1 else None
55
+ positions = [SR(item) for item in components_of(getattr(spec.namespace, name))]
56
+ velocities = (
57
+ [SR(item) for item in components_of(getattr(spec.namespace, velocity_name))]
58
+ if velocity_name
59
+ else [None] * len(positions)
60
+ )
61
+ for position, velocity, side in zip(positions, velocities, space.extent_, strict=True):
62
+ if space.boundary == 'periodic':
63
+ laws.append(BoundaryLaw(position, mod(position, side)))
64
+ continue
65
+ below, above = position < 0, position > side
66
+ laws.append(BoundaryLaw(position, where(below, -position, where(above, 2 * side - position, position))))
67
+ if velocity is not None:
68
+ laws.append(BoundaryLaw(velocity, where(either(below, above), -velocity, velocity)))
69
+ return laws