diff-grok 1.1.0 → 1.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (487) hide show
  1. package/LICENSE +1 -1
  2. package/README.MD +80 -31
  3. package/dist/index.d.ts +6 -0
  4. package/{index.js → dist/index.js} +2 -1
  5. package/dist/index.js.map +1 -0
  6. package/dist/src/examples/basic-use.d.ts +10 -0
  7. package/dist/src/examples/basic-use.js.map +1 -0
  8. package/dist/src/examples/check-methods.d.ts +1 -0
  9. package/{src → dist/src}/examples/check-methods.js +15 -3
  10. package/dist/src/examples/check-methods.js.map +1 -0
  11. package/dist/src/examples/corr-probs.d.ts +15 -0
  12. package/{src → dist/src}/examples/corr-probs.js +2 -2
  13. package/dist/src/examples/corr-probs.js.map +1 -0
  14. package/dist/src/examples/cyclic-model.d.ts +6 -0
  15. package/dist/src/examples/cyclic-model.js.map +1 -0
  16. package/dist/src/examples/e5.d.ts +15 -0
  17. package/dist/src/examples/e5.js.map +1 -0
  18. package/dist/src/examples/hires.d.ts +15 -0
  19. package/dist/src/examples/hires.js.map +1 -0
  20. package/dist/src/examples/index.d.ts +22 -0
  21. package/dist/src/examples/index.js.map +1 -0
  22. package/dist/src/examples/model-updates.d.ts +6 -0
  23. package/dist/src/examples/model-updates.js.map +1 -0
  24. package/dist/src/examples/orego.d.ts +15 -0
  25. package/dist/src/examples/orego.js.map +1 -0
  26. package/dist/src/examples/pipeline-use.d.ts +6 -0
  27. package/dist/src/examples/pipeline-use.js.map +1 -0
  28. package/dist/src/examples/pollution.d.ts +15 -0
  29. package/dist/src/examples/pollution.js.map +1 -0
  30. package/{src/examples/print-benchmark.ts → dist/src/examples/print-benchmark.d.ts} +8 -58
  31. package/dist/src/examples/print-benchmark.js.map +1 -0
  32. package/dist/src/examples/robertson.d.ts +15 -0
  33. package/{src → dist/src}/examples/robertson.js +2 -2
  34. package/dist/src/examples/robertson.js.map +1 -0
  35. package/dist/src/examples/scripting.d.ts +1 -0
  36. package/dist/src/examples/scripting.js.map +1 -0
  37. package/dist/src/examples/vdpol.d.ts +15 -0
  38. package/dist/src/examples/vdpol.js.map +1 -0
  39. package/dist/src/latex-export/examples/advanced-to-latex.d.ts +2 -0
  40. package/dist/src/latex-export/examples/advanced-to-latex.js +41 -0
  41. package/dist/src/latex-export/examples/advanced-to-latex.js.map +1 -0
  42. package/dist/src/latex-export/examples/basic-to-latex.d.ts +2 -0
  43. package/dist/src/latex-export/examples/basic-to-latex.js +17 -0
  44. package/dist/src/latex-export/examples/basic-to-latex.js.map +1 -0
  45. package/dist/src/latex-export/examples/bioreactor-to-latex-selective.d.ts +2 -0
  46. package/dist/src/latex-export/examples/bioreactor-to-latex-selective.js +145 -0
  47. package/dist/src/latex-export/examples/bioreactor-to-latex-selective.js.map +1 -0
  48. package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.d.ts +2 -0
  49. package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.js +41 -0
  50. package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.js.map +1 -0
  51. package/dist/src/latex-export/examples/energy-n-control-to-markdown.d.ts +2 -0
  52. package/dist/src/latex-export/examples/energy-n-control-to-markdown.js +58 -0
  53. package/dist/src/latex-export/examples/energy-n-control-to-markdown.js.map +1 -0
  54. package/dist/src/latex-export/examples/extended-to-markdown.d.ts +2 -0
  55. package/dist/src/latex-export/examples/extended-to-markdown.js +37 -0
  56. package/dist/src/latex-export/examples/extended-to-markdown.js.map +1 -0
  57. package/dist/src/latex-export/examples/fermentation-to-latex.d.ts +2 -0
  58. package/dist/src/latex-export/examples/fermentation-to-latex.js +32 -0
  59. package/dist/src/latex-export/examples/fermentation-to-latex.js.map +1 -0
  60. package/dist/src/latex-export/examples/ga-production-to-markdown.d.ts +2 -0
  61. package/dist/src/latex-export/examples/ga-production-to-markdown.js +58 -0
  62. package/dist/src/latex-export/examples/ga-production-to-markdown.js.map +1 -0
  63. package/dist/src/latex-export/examples/nimotuzumab-to-latex.d.ts +2 -0
  64. package/dist/src/latex-export/examples/nimotuzumab-to-latex.js +53 -0
  65. package/dist/src/latex-export/examples/nimotuzumab-to-latex.js.map +1 -0
  66. package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.d.ts +2 -0
  67. package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.js +50 -0
  68. package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.js.map +1 -0
  69. package/dist/src/latex-export/examples/pk-to-markdown.d.ts +2 -0
  70. package/dist/src/latex-export/examples/pk-to-markdown.js +35 -0
  71. package/dist/src/latex-export/examples/pk-to-markdown.js.map +1 -0
  72. package/dist/src/latex-export/examples/pollution-to-latex.d.ts +2 -0
  73. package/dist/src/latex-export/examples/pollution-to-latex.js +141 -0
  74. package/dist/src/latex-export/examples/pollution-to-latex.js.map +1 -0
  75. package/dist/src/latex-export/examples/robertson-to-latex-no-meta.d.ts +2 -0
  76. package/dist/src/latex-export/examples/robertson-to-latex-no-meta.js +25 -0
  77. package/dist/src/latex-export/examples/robertson-to-latex-no-meta.js.map +1 -0
  78. package/dist/src/latex-export/generator/bracket-manager.d.ts +19 -0
  79. package/dist/src/latex-export/generator/bracket-manager.js +58 -0
  80. package/dist/src/latex-export/generator/bracket-manager.js.map +1 -0
  81. package/dist/src/latex-export/generator/document-builder.d.ts +13 -0
  82. package/dist/src/latex-export/generator/document-builder.js +433 -0
  83. package/dist/src/latex-export/generator/document-builder.js.map +1 -0
  84. package/dist/src/latex-export/generator/latex-generator.d.ts +23 -0
  85. package/dist/src/latex-export/generator/latex-generator.js +176 -0
  86. package/dist/src/latex-export/generator/latex-generator.js.map +1 -0
  87. package/dist/src/latex-export/index.d.ts +8 -0
  88. package/dist/src/latex-export/index.js +25 -0
  89. package/dist/src/latex-export/index.js.map +1 -0
  90. package/dist/src/latex-export/output/md-formatter.d.ts +16 -0
  91. package/dist/src/latex-export/output/md-formatter.js +27 -0
  92. package/dist/src/latex-export/output/md-formatter.js.map +1 -0
  93. package/dist/src/latex-export/output/tex-formatter.d.ts +5 -0
  94. package/dist/src/latex-export/output/tex-formatter.js +20 -0
  95. package/dist/src/latex-export/output/tex-formatter.js.map +1 -0
  96. package/dist/src/latex-export/parser/ast-parser.d.ts +7 -0
  97. package/dist/src/latex-export/parser/ast-parser.js +153 -0
  98. package/dist/src/latex-export/parser/ast-parser.js.map +1 -0
  99. package/dist/src/latex-export/parser/ivp-parser.d.ts +6 -0
  100. package/dist/src/latex-export/parser/ivp-parser.js +219 -0
  101. package/dist/src/latex-export/parser/ivp-parser.js.map +1 -0
  102. package/dist/src/latex-export/parser/line-joiner.d.ts +25 -0
  103. package/dist/src/latex-export/parser/line-joiner.js +80 -0
  104. package/dist/src/latex-export/parser/line-joiner.js.map +1 -0
  105. package/dist/src/latex-export/parser/tokenizer.d.ts +7 -0
  106. package/dist/src/latex-export/parser/tokenizer.js +143 -0
  107. package/dist/src/latex-export/parser/tokenizer.js.map +1 -0
  108. package/dist/src/latex-export/transformer/functions.d.ts +12 -0
  109. package/dist/src/latex-export/transformer/functions.js +47 -0
  110. package/dist/src/latex-export/transformer/functions.js.map +1 -0
  111. package/dist/src/latex-export/transformer/identifier.d.ts +23 -0
  112. package/dist/src/latex-export/transformer/identifier.js +194 -0
  113. package/dist/src/latex-export/transformer/identifier.js.map +1 -0
  114. package/dist/src/latex-export/transformer/operators.d.ts +9 -0
  115. package/dist/src/latex-export/transformer/operators.js +41 -0
  116. package/dist/src/latex-export/transformer/operators.js.map +1 -0
  117. package/dist/src/latex-export/types.d.ts +122 -0
  118. package/dist/src/latex-export/types.js +10 -0
  119. package/dist/src/latex-export/types.js.map +1 -0
  120. package/{src/pipeline/basic-pipeline-creator.ts → dist/src/pipeline/basic-pipeline-creator.d.ts} +11 -28
  121. package/dist/src/pipeline/basic-pipeline-creator.js.map +1 -0
  122. package/dist/src/pipeline/constants.d.ts +14 -0
  123. package/dist/src/pipeline/constants.js.map +1 -0
  124. package/dist/src/pipeline/index.d.ts +7 -0
  125. package/dist/src/pipeline/index.js.map +1 -0
  126. package/dist/src/pipeline/input.d.ts +3 -0
  127. package/dist/src/pipeline/input.js.map +1 -0
  128. package/dist/src/pipeline/loops-pipeline-creator.d.ts +124 -0
  129. package/dist/src/pipeline/loops-pipeline-creator.js.map +1 -0
  130. package/dist/src/pipeline/output.d.ts +10 -0
  131. package/{src → dist/src}/pipeline/output.js +1 -1
  132. package/dist/src/pipeline/output.js.map +1 -0
  133. package/dist/src/pipeline/pipeline-creator.d.ts +12 -0
  134. package/{src → dist/src}/pipeline/pipeline-creator.js +2 -0
  135. package/dist/src/pipeline/pipeline-creator.js.map +1 -0
  136. package/{src/pipeline/pipeline.ts → dist/src/pipeline/pipeline.d.ts} +10 -97
  137. package/dist/src/pipeline/pipeline.js.map +1 -0
  138. package/{src/pipeline/updates-pipeline-creator.ts → dist/src/pipeline/updates-pipeline-creator.d.ts} +15 -131
  139. package/dist/src/pipeline/updates-pipeline-creator.js.map +1 -0
  140. package/dist/src/scripting-tools/constants.d.ts +59 -0
  141. package/dist/src/scripting-tools/constants.js.map +1 -0
  142. package/dist/src/scripting-tools/index.d.ts +3 -0
  143. package/dist/src/scripting-tools/index.js.map +1 -0
  144. package/dist/src/scripting-tools/model-error.d.ts +10 -0
  145. package/{src → dist/src}/scripting-tools/model-error.js +2 -1
  146. package/dist/src/scripting-tools/model-error.js.map +1 -0
  147. package/dist/src/scripting-tools/scripting-tools.d.ts +277 -0
  148. package/{src → dist/src}/scripting-tools/scripting-tools.js +2 -4
  149. package/dist/src/scripting-tools/scripting-tools.js.map +1 -0
  150. package/dist/src/solver-tools/ab4-method.d.ts +46 -0
  151. package/{src → dist/src}/solver-tools/ab4-method.js +3 -3
  152. package/dist/src/solver-tools/ab4-method.js.map +1 -0
  153. package/dist/src/solver-tools/ab5-method.d.ts +46 -0
  154. package/{src → dist/src}/solver-tools/ab5-method.js +3 -3
  155. package/dist/src/solver-tools/ab5-method.js.map +1 -0
  156. package/dist/src/solver-tools/callbacks/callback-base.d.ts +8 -0
  157. package/dist/src/solver-tools/callbacks/callback-base.js.map +1 -0
  158. package/dist/src/solver-tools/callbacks/callback-tools.d.ts +6 -0
  159. package/dist/src/solver-tools/callbacks/callback-tools.js.map +1 -0
  160. package/dist/src/solver-tools/callbacks/iter-checker-callback.d.ts +12 -0
  161. package/{src → dist/src}/solver-tools/callbacks/iter-checker-callback.js +2 -0
  162. package/dist/src/solver-tools/callbacks/iter-checker-callback.js.map +1 -0
  163. package/dist/src/solver-tools/callbacks/time-checker-callback.d.ts +12 -0
  164. package/{src → dist/src}/solver-tools/callbacks/time-checker-callback.js +2 -2
  165. package/dist/src/solver-tools/callbacks/time-checker-callback.js.map +1 -0
  166. package/dist/src/solver-tools/cvode/common.d.ts +395 -0
  167. package/dist/src/solver-tools/cvode/common.js +483 -0
  168. package/dist/src/solver-tools/cvode/common.js.map +1 -0
  169. package/dist/src/solver-tools/cvode/cvode.d.ts +23 -0
  170. package/dist/src/solver-tools/cvode/cvode.js +1062 -0
  171. package/dist/src/solver-tools/cvode/cvode.js.map +1 -0
  172. package/dist/src/solver-tools/cvode/cvode_adams.d.ts +22 -0
  173. package/dist/src/solver-tools/cvode/cvode_adams.js +124 -0
  174. package/dist/src/solver-tools/cvode/cvode_adams.js.map +1 -0
  175. package/dist/src/solver-tools/cvode/cvode_bdf.d.ts +37 -0
  176. package/dist/src/solver-tools/cvode/cvode_bdf.js +153 -0
  177. package/dist/src/solver-tools/cvode/cvode_bdf.js.map +1 -0
  178. package/dist/src/solver-tools/cvode/cvode_class.d.ts +116 -0
  179. package/dist/src/solver-tools/cvode/cvode_class.js +163 -0
  180. package/dist/src/solver-tools/cvode/cvode_class.js.map +1 -0
  181. package/dist/src/solver-tools/cvode/cvode_hin.d.ts +24 -0
  182. package/dist/src/solver-tools/cvode/cvode_hin.js +119 -0
  183. package/dist/src/solver-tools/cvode/cvode_hin.js.map +1 -0
  184. package/dist/src/solver-tools/cvode/cvode_io.d.ts +98 -0
  185. package/dist/src/solver-tools/cvode/cvode_io.js +202 -0
  186. package/dist/src/solver-tools/cvode/cvode_io.js.map +1 -0
  187. package/dist/src/solver-tools/cvode/cvode_ls.d.ts +23 -0
  188. package/dist/src/solver-tools/cvode/cvode_ls.js +210 -0
  189. package/dist/src/solver-tools/cvode/cvode_ls.js.map +1 -0
  190. package/dist/src/solver-tools/cvode/cvode_nls.d.ts +25 -0
  191. package/dist/src/solver-tools/cvode/cvode_nls.js +220 -0
  192. package/dist/src/solver-tools/cvode/cvode_nls.js.map +1 -0
  193. package/dist/src/solver-tools/cvode/cvode_root.d.ts +64 -0
  194. package/dist/src/solver-tools/cvode/cvode_root.js +415 -0
  195. package/dist/src/solver-tools/cvode/cvode_root.js.map +1 -0
  196. package/dist/src/solver-tools/cvode/dense_linalg.d.ts +50 -0
  197. package/dist/src/solver-tools/cvode/dense_linalg.js +131 -0
  198. package/dist/src/solver-tools/cvode/dense_linalg.js.map +1 -0
  199. package/dist/src/solver-tools/cvode/index.d.ts +24 -0
  200. package/dist/src/solver-tools/cvode/index.js +26 -0
  201. package/dist/src/solver-tools/cvode/index.js.map +1 -0
  202. package/dist/src/solver-tools/cvode-method.d.ts +47 -0
  203. package/dist/src/solver-tools/cvode-method.js +114 -0
  204. package/dist/src/solver-tools/cvode-method.js.map +1 -0
  205. package/dist/src/solver-tools/index.d.ts +16 -0
  206. package/{src → dist/src}/solver-tools/index.js +1 -0
  207. package/dist/src/solver-tools/index.js.map +1 -0
  208. package/dist/src/solver-tools/lin-alg-tools.d.ts +6 -0
  209. package/dist/src/solver-tools/lin-alg-tools.js.map +1 -0
  210. package/dist/src/solver-tools/lsoda/blas.d.ts +59 -0
  211. package/{src → dist/src}/solver-tools/lsoda/blas.js +11 -0
  212. package/dist/src/solver-tools/lsoda/blas.js.map +1 -0
  213. package/dist/src/solver-tools/lsoda/cfode.d.ts +18 -0
  214. package/{src → dist/src}/solver-tools/lsoda/cfode.js +11 -0
  215. package/dist/src/solver-tools/lsoda/cfode.js.map +1 -0
  216. package/dist/src/solver-tools/lsoda/common.d.ts +85 -0
  217. package/dist/src/solver-tools/lsoda/common.js +96 -0
  218. package/dist/src/solver-tools/lsoda/common.js.map +1 -0
  219. package/dist/src/solver-tools/lsoda/corfailure.d.ts +18 -0
  220. package/{src → dist/src}/solver-tools/lsoda/corfailure.js +11 -0
  221. package/dist/src/solver-tools/lsoda/corfailure.js.map +1 -0
  222. package/dist/src/solver-tools/lsoda/correction.d.ts +23 -0
  223. package/{src → dist/src}/solver-tools/lsoda/correction.js +11 -0
  224. package/dist/src/solver-tools/lsoda/correction.js.map +1 -0
  225. package/dist/src/solver-tools/lsoda/dense.d.ts +47 -0
  226. package/{src → dist/src}/solver-tools/lsoda/dense.js +13 -0
  227. package/dist/src/solver-tools/lsoda/dense.js.map +1 -0
  228. package/dist/src/solver-tools/lsoda/index.d.ts +16 -0
  229. package/dist/src/solver-tools/lsoda/index.js +15 -0
  230. package/dist/src/solver-tools/lsoda/index.js.map +1 -0
  231. package/dist/src/solver-tools/lsoda/intdy.d.ts +19 -0
  232. package/{src → dist/src}/solver-tools/lsoda/intdy.js +11 -0
  233. package/dist/src/solver-tools/lsoda/intdy.js.map +1 -0
  234. package/dist/src/solver-tools/lsoda/lsoda.d.ts +66 -0
  235. package/{src → dist/src}/solver-tools/lsoda/lsoda.js +24 -5
  236. package/dist/src/solver-tools/lsoda/lsoda.js.map +1 -0
  237. package/dist/src/solver-tools/lsoda/methodswitch.d.ts +21 -0
  238. package/{src → dist/src}/solver-tools/lsoda/methodswitch.js +11 -0
  239. package/dist/src/solver-tools/lsoda/methodswitch.js.map +1 -0
  240. package/dist/src/solver-tools/lsoda/orderswitch.d.ts +21 -0
  241. package/{src → dist/src}/solver-tools/lsoda/orderswitch.js +11 -0
  242. package/dist/src/solver-tools/lsoda/orderswitch.js.map +1 -0
  243. package/dist/src/solver-tools/lsoda/prja.d.ts +18 -0
  244. package/{src → dist/src}/solver-tools/lsoda/prja.js +11 -0
  245. package/dist/src/solver-tools/lsoda/prja.js.map +1 -0
  246. package/dist/src/solver-tools/lsoda/scaleh.d.ts +16 -0
  247. package/{src → dist/src}/solver-tools/lsoda/scaleh.js +11 -0
  248. package/dist/src/solver-tools/lsoda/scaleh.js.map +1 -0
  249. package/dist/src/solver-tools/lsoda/solsy.d.ts +17 -0
  250. package/dist/src/solver-tools/lsoda/solsy.js +25 -0
  251. package/dist/src/solver-tools/lsoda/solsy.js.map +1 -0
  252. package/dist/src/solver-tools/lsoda/stoda.d.ts +19 -0
  253. package/{src → dist/src}/solver-tools/lsoda/stoda.js +11 -0
  254. package/dist/src/solver-tools/lsoda/stoda.js.map +1 -0
  255. package/dist/src/solver-tools/lsoda-method.d.ts +46 -0
  256. package/{src → dist/src}/solver-tools/lsoda-method.js +23 -9
  257. package/dist/src/solver-tools/lsoda-method.js.map +1 -0
  258. package/dist/src/solver-tools/mrt-method.d.ts +47 -0
  259. package/{src → dist/src}/solver-tools/mrt-method.js +2 -2
  260. package/dist/src/solver-tools/mrt-method.js.map +1 -0
  261. package/dist/src/solver-tools/rk3-method.d.ts +46 -0
  262. package/{src → dist/src}/solver-tools/rk3-method.js +2 -2
  263. package/dist/src/solver-tools/rk3-method.js.map +1 -0
  264. package/dist/src/solver-tools/rk4-method.d.ts +46 -0
  265. package/{src → dist/src}/solver-tools/rk4-method.js +2 -2
  266. package/dist/src/solver-tools/rk4-method.js.map +1 -0
  267. package/dist/src/solver-tools/rkdp-method.d.ts +46 -0
  268. package/{src → dist/src}/solver-tools/rkdp-method.js +2 -2
  269. package/dist/src/solver-tools/rkdp-method.js.map +1 -0
  270. package/dist/src/solver-tools/ros34prw-method.d.ts +46 -0
  271. package/{src → dist/src}/solver-tools/ros34prw-method.js +2 -2
  272. package/dist/src/solver-tools/ros34prw-method.js.map +1 -0
  273. package/dist/src/solver-tools/ros3prw-method.d.ts +46 -0
  274. package/{src → dist/src}/solver-tools/ros3prw-method.js +2 -2
  275. package/dist/src/solver-tools/ros3prw-method.js.map +1 -0
  276. package/{src/solver-tools/solver-defs.ts → dist/src/solver-tools/solver-defs.d.ts} +45 -84
  277. package/{src → dist/src}/solver-tools/solver-defs.js +1 -0
  278. package/dist/src/solver-tools/solver-defs.js.map +1 -0
  279. package/dist/src/worker-tools/index.d.ts +2 -0
  280. package/dist/src/worker-tools/index.js.map +1 -0
  281. package/{src/worker-tools/scripting.ts → dist/src/worker-tools/scripting.d.ts} +9 -91
  282. package/dist/src/worker-tools/scripting.js.map +1 -0
  283. package/dist/src/worker-tools/solving.d.ts +7 -0
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@@ -1,125 +0,0 @@
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- /** Example. Solve the following initial value problem
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-
3
- dx / dt = x + y - t
4
- dy / dt = x * y + t
5
- x(0) = 1
6
- y(0) = -1
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-
8
- on [0, 2] with the step 0.01.
9
- */
10
- import { lsoda } from '../../index';
11
- // constants
12
- const VLinit = 7.2;
13
- const VTV = 10;
14
- const speed = 400;
15
- const diam = 6;
16
- const power = 2.1;
17
- const pH = 7.4;
18
- const k1red = 0.05604;
19
- const k1ox = 0.0108;
20
- const k2Fd = 1.35;
21
- const k2Fa = 110400000;
22
- const k2Kd = 0.04038;
23
- const k2Ka = 120000000;
24
- const k3FKa = 181200000;
25
- const k3FKd = 0.01188;
26
- const k4ox = 0.0108;
27
- const k4red = 0.05604;
28
- const ktox = 0.005;
29
- const krcyst = 0;
30
- const pO2sat = 100;
31
- const pKa2MEA = 8.18;
32
- const H = 1.072069378;
33
- const R = 0.082;
34
- const _t0 = 0;
35
- const _t1 = 1000;
36
- const _h = 1;
37
- const FFox = 0.2;
38
- const KKox = 0.2;
39
- const FFred = 0.1;
40
- const KKred = 0.1;
41
- const Ffree = 0;
42
- const Kfree = 0;
43
- const FKred = 0;
44
- const FKox = 0;
45
- const MEAthiol = 15;
46
- const CO2 = 0.12;
47
- const yO2P = 0.209;
48
- const CYST = 0;
49
- const VL = 7.2;
50
- const qin = 1;
51
- const yO2in = 0.21;
52
- const T = 300;
53
- const P = 1;
54
- const switchTime = 135;
55
- // the problem definition
56
- const task = {
57
- name: 'Bioreactor',
58
- arg: { name: 't', start: _t0, finish: _t1, step: _h },
59
- initial: [FFox, KKox, FFred, KKred, Ffree, Kfree, FKred, FKox, MEAthiol, CO2, yO2P, CYST, VL],
60
- func: (t, _y, _output) => {
61
- // extract function values
62
- const FFox = _y[0];
63
- const KKox = _y[1];
64
- const FFred = _y[2];
65
- const KKred = _y[3];
66
- const Ffree = _y[4];
67
- const Kfree = _y[5];
68
- const FKred = _y[6];
69
- const FKox = _y[7];
70
- const MEAthiol = _y[8];
71
- const CO2 = _y[9];
72
- const yO2P = _y[10];
73
- const CYST = _y[11];
74
- const VL = _y[12];
75
- // evaluate expressions
76
- const KF = pow(VL, -0.65) * 0.065 * pow(Math.pow(speed, 3) * Math.pow(diam, 5) * power / 2.16e12, 0.361);
77
- const MA = MEAthiol * pow(10, pH - pKa2MEA);
78
- const qout = qin - KF * (yO2P * H - CO2) * VL * R * T / (P * 1000);
79
- const OTR = KF * (yO2P * H - CO2);
80
- const Fin = t < switchTime ? 0 : 0.025;
81
- const Fper = t < switchTime ? 0.025 : Fin;
82
- const E0 = VLinit / VL;
83
- const E1 = Math.pow((MA * E0), 2);
84
- const E11 = k1red * FFox * E0 * E1;
85
- const E12 = k1ox * FFred * E0;
86
- const E31 = k2Fd * FFred * E0;
87
- const E32 = k2Fa * Math.pow((Ffree * E0), 2) * E1;
88
- const E21 = k1red * KKox * E0 * E1;
89
- const E22 = k1ox * KKred * E0;
90
- const E41 = k2Kd * KKred * E0;
91
- const E42 = k2Ka * Math.pow((Kfree * E0), 2) * E1;
92
- const E51 = k3FKa * Ffree * E0 * Kfree * E0;
93
- const E52 = k3FKd * FKred * E0;
94
- const E61 = k4ox * FKred * E0 * Math.pow((CYST * E0), 2);
95
- const E62 = k4red * FKox * E0 * E1;
96
- const E70 = E0 * CO2;
97
- const E71 = Math.pow((MEAthiol * E0), 2);
98
- const E72 = (E70 >= 0) ? sqrt(E70) : 0;
99
- // compute output
100
- _output[0] = -E11 + E12;
101
- _output[1] = -E21 + E22;
102
- _output[2] = E11 - E12 - E31 + E32;
103
- _output[3] = E21 - E22 - E41 + E42;
104
- _output[4] = 2 * (E31 - E32) - E51 + E52;
105
- _output[5] = 2 * (E41 - E42) - E51 + E52;
106
- _output[6] = E51 - E52 - E61 + E62;
107
- _output[7] = E61 - E62;
108
- _output[8] = 2 * (-E11 + E12 - E21 + E22 + E31 + E41 - E32 - E42 - E62 - ktox * E71 * E72) -
109
- (MEAthiol + MA) * (Fin + Fper) / VL;
110
- _output[9] = (Fin * pO2sat * 0.0022 - 2 * Fper * CO2) / VL + OTR - 0.5 * ktox * E71 * E72;
111
- _output[10] = -OTR * (VL / (VTV - VL)) * R * T * P + yO2in * qin - yO2P * qout;
112
- _output[11] = ktox * E71 * E72 - krcyst * CYST * E0 - (Fin + Fper) * CYST / VL;
113
- _output[12] = Fin - Fper;
114
- },
115
- tolerance: 0.00005,
116
- solutionColNames: ['FFox', 'KKox', 'FFred', 'KKred', 'Ffree', 'Kfree', 'FKred',
117
- 'FKox', 'MEAthiol', 'CO2', 'yO2P', 'CYST', 'VL'],
118
- };
119
- // used Math-functions
120
- const pow = (x, y) => Math.pow(x, y);
121
- const tan = (x) => Math.tan(x);
122
- const sqrt = (x) => Math.sqrt(x);
123
- const exp = (x) => Math.exp(x);
124
- const solution = lsoda(task);
125
- //# sourceMappingURL=bioreactor.js.map
@@ -1 +0,0 @@
1
- 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@@ -1,132 +0,0 @@
1
- /** Example. Solve the following initial value problem
2
-
3
- dx / dt = x + y - t
4
- dy / dt = x * y + t
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- x(0) = 1
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- y(0) = -1
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-
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- on [0, 2] with the step 0.01.
9
- */
10
-
11
- import {ODEs, lsoda, mrt} from '../../index';
12
-
13
- // constants
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- const VLinit = 7.2;
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- const VTV = 10;
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- const speed = 400;
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- const diam = 6;
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- const power = 2.1;
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- const pH = 7.4;
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- const k1red = 0.05604;
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- const k1ox = 0.0108;
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- const k2Fd = 1.35;
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- const k2Fa = 110400000;
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- const k2Kd = 0.04038;
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- const k2Ka = 120000000;
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- const k3FKa = 181200000;
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- const k3FKd = 0.01188;
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- const k4ox = 0.0108;
29
- const k4red = 0.05604;
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- const ktox = 0.005;
31
- const krcyst = 0;
32
- const pO2sat = 100;
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- const pKa2MEA = 8.18;
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- const H = 1.072069378;
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- const R = 0.082;
36
-
37
- const _t0 = 0;
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- const _t1 = 1000;
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- const _h = 1;
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- const FFox = 0.2;
41
- const KKox = 0.2;
42
- const FFred = 0.1;
43
- const KKred = 0.1;
44
- const Ffree = 0;
45
- const Kfree = 0;
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- const FKred = 0;
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- const FKox = 0;
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- const MEAthiol = 15;
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- const CO2 = 0.12;
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- const yO2P = 0.209;
51
- const CYST = 0;
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- const VL = 7.2;
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- const qin = 1;
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- const yO2in = 0.21;
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- const T = 300;
56
- const P = 1;
57
- const switchTime = 135;
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-
59
- // the problem definition
60
- const task = {
61
- name: 'Bioreactor',
62
- arg: {name: 't', start: _t0, finish: _t1, step: _h},
63
- initial: [FFox, KKox, FFred, KKred, Ffree, Kfree, FKred, FKox, MEAthiol, CO2, yO2P, CYST, VL],
64
- func: (t: number, _y: Float64Array, _output: Float64Array) => {
65
- // extract function values
66
- const FFox = _y[0];
67
- const KKox = _y[1];
68
- const FFred = _y[2];
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- const KKred = _y[3];
70
- const Ffree = _y[4];
71
- const Kfree = _y[5];
72
- const FKred = _y[6];
73
- const FKox = _y[7];
74
- const MEAthiol = _y[8];
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- const CO2 = _y[9];
76
- const yO2P = _y[10];
77
- const CYST = _y[11];
78
- const VL = _y[12];
79
-
80
- // evaluate expressions
81
- const KF = pow(VL, -0.65) * 0.065 * pow(speed**3 * diam**5 * power / 2.16e12, 0.361);
82
- const MA = MEAthiol * pow(10, pH - pKa2MEA);
83
- const qout = qin - KF * (yO2P * H - CO2) * VL * R * T / (P * 1000);
84
- const OTR = KF * (yO2P * H - CO2);
85
- const Fin = t < switchTime ? 0 : 0.025;
86
- const Fper = t < switchTime ? 0.025 : Fin;
87
- const E0 = VLinit / VL;
88
- const E1 = (MA * E0)**2;
89
- const E11 = k1red * FFox * E0 * E1;
90
- const E12 = k1ox * FFred * E0;
91
- const E31 = k2Fd * FFred * E0;
92
- const E32 = k2Fa * (Ffree * E0)**2 * E1;
93
- const E21 = k1red * KKox * E0 * E1;
94
- const E22 = k1ox * KKred * E0;
95
- const E41 = k2Kd * KKred * E0;
96
- const E42 = k2Ka * (Kfree * E0)**2 * E1;
97
- const E51 = k3FKa * Ffree * E0 * Kfree * E0;
98
- const E52 = k3FKd * FKred * E0;
99
- const E61 = k4ox * FKred * E0 * (CYST * E0)**2;
100
- const E62 = k4red * FKox * E0 * E1;
101
- const E70 = E0 * CO2;
102
- const E71 = (MEAthiol * E0)**2;
103
- const E72 = (E70 >= 0) ? sqrt(E70) : 0;
104
-
105
- // compute output
106
- _output[0] = -E11 + E12;
107
- _output[1] = -E21 + E22;
108
- _output[2] = E11 - E12 - E31 + E32;
109
- _output[3] = E21 - E22 - E41 + E42;
110
- _output[4] = 2 * (E31 - E32) - E51 + E52;
111
- _output[5] = 2 * (E41 - E42) - E51 + E52;
112
- _output[6] = E51 - E52 - E61 + E62;
113
- _output[7] = E61 - E62;
114
- _output[8] = 2 * (-E11 + E12 - E21 + E22 + E31 + E41 - E32 - E42 - E62 - ktox * E71 * E72) -
115
- (MEAthiol + MA) * (Fin + Fper) / VL;
116
- _output[9] = (Fin * pO2sat * 0.0022 - 2 * Fper * CO2) / VL + OTR - 0.5 * ktox * E71 * E72;
117
- _output[10] = -OTR * (VL / (VTV - VL)) * R * T * P + yO2in * qin - yO2P * qout;
118
- _output[11] = ktox * E71 * E72 - krcyst * CYST * E0 - (Fin + Fper) * CYST / VL;
119
- _output[12] = Fin - Fper;
120
- },
121
- tolerance: 0.00005,
122
- solutionColNames: ['FFox', 'KKox', 'FFred', 'KKred', 'Ffree', 'Kfree', 'FKred',
123
- 'FKox', 'MEAthiol', 'CO2', 'yO2P', 'CYST', 'VL'],
124
- };
125
-
126
- // used Math-functions
127
- const pow = (x: number, y: number) => Math.pow(x, y);
128
- const tan = (x: number) => Math.tan(x);
129
- const sqrt = (x: number) => Math.sqrt(x);
130
- const exp = (x: number) => Math.exp(x);
131
-
132
- const solution = lsoda(task);
@@ -1 +0,0 @@
1
- {"version":3,"file":"check-methods.js","sourceRoot":"","sources":["check-methods.ts"],"names":[],"mappings":"AAAA,oCAAoC;AAEpC,OAAO,EAAO,SAAS,EAAe,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,SAAS,EAAC,MAAM,aAAa,CAAC;AAEvG,wGAAwG;AACxG,SAAS,QAAQ,CAAC,MAAsC,EAAE,OAAoB;IAC5E,IAAI,KAAK,GAAG,CAAC,CAAC;IAEd,yBAAyB;IACzB,MAAM,cAAc,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IAE5C,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC;IAE5B,MAAM,GAAG,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC;IAE9B,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,CAAC;IAC/B,MAAM,UAAU,GAAG,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC;IAE7C,gBAAgB;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,EAAE,CAAC,EAAE,CAAC;QACrC,MAAM,aAAa,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;QAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,EAAE,CAAC;YACjC,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACnF,CAAC;IAED,OAAO,KAAK,CAAC;AACf,CAAC,CAAC,WAAW;AAEb,SAAS,8BAA8B,CAAC,QAAwB,EAAE,QAAsB;IACtF,IAAI,QAAQ,GAAG,CAAC,CAAC;IACjB,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;IACvC,IAAI,GAAG,GAAG,CAAC,CAAC;IAEZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE,CAAC;QACzC,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;QACnD,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;IACrC,CAAC;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC,CAAC,iCAAiC;AAEnC,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC;IACtB,CAAC,KAAK,EAAE,GAAG,CAAC;IACZ,CAAC,SAAS,EAAE,OAAO,CAAC;IACpB,CAAC,UAAU,EAAE,QAAQ,CAAC;CACvB,CAAC,CAAC;AAEH,OAAO,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC;AAE7B,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE;IAC/B,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;IAEvB,OAAO,CAAC,GAAG,CAAC,qCAAqC,CAAC,CAAC;IAEnD,SAAS,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE;QAC9B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QACzB,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC;QAC9B,MAAM,MAAM,GAAG,8BAA8B,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC;QAClG,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAC1B,OAAO,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,IAAI,QAAQ,MAAM,GAAG,KAAK,QAAQ,MAAM,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;IACjF,CAAC,CAAC,CAAC;IAEH,OAAO,CAAC,GAAG,EAAE,CAAC;AAChB,CAAC,CAAC,CAAC;AAEH,OAAO,CAAC,GAAG,CAAC,mDAAmD,CAAC,CAAC;AAEjE,OAAO,CAAC,GAAG,CAAC,mEAAmE,CAAC,CAAC;AAEjF,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE;IAC/B,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC;IACxB,OAAO,CAAC,GAAG,CAAC,yBAAyB,CAAC,CAAC;IAEvC,SAAS,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QAC5B,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QACxC,OAAO,CAAC,GAAG,CAAC,QAAQ,OAAO,CAAC,IAAI,CAAC,IAAI,OAAO,KAAK,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;IACrF,CAAC,CAAC,CAAC;IAEH,OAAO,CAAC,GAAG,EAAE,CAAC;AAChB,CAAC,CAAC,CAAC"}
@@ -1,81 +0,0 @@
1
- // A script for checking performance
2
-
3
- import {ODEs, corrProbs, CorrProblem, mrt, ros3prw, ros34prw, perfProbs, refPoints} from '../../index';
4
-
5
- /** Return numerical solution error: maximum absolute deviation between approximate & exact solutions */
6
- function getError(method: (odes: ODEs) => Float64Array[], corProb: CorrProblem): number {
7
- let error = 0;
8
-
9
- // Get numerical solution
10
- const approxSolution = method(corProb.odes);
11
-
12
- const exact = corProb.exact;
13
-
14
- const arg = approxSolution[0];
15
-
16
- const pointsCount = arg.length;
17
- const funcsCount = approxSolution.length - 1;
18
-
19
- // Compute error
20
- for (let i = 0; i < pointsCount; ++i) {
21
- const exactSolution = exact(arg[i]);
22
-
23
- for (let j = 0; j < funcsCount; ++j)
24
- error = Math.max(error, Math.abs(exactSolution[j] - approxSolution[j + 1][i]));
25
- }
26
-
27
- return error;
28
- } // getError
29
-
30
- function getDeviationFromReferencePoint(solution: Float64Array[], refPoint: Float64Array): number {
31
- let absolute = 0;
32
- const lastIdx = solution[0].length - 1;
33
- let cur = 0;
34
-
35
- for (let k = 0; k < solution.length; ++k) {
36
- cur = Math.abs(solution[k][lastIdx] - refPoint[k]);
37
- absolute = Math.max(cur, absolute);
38
- }
39
-
40
- return absolute;
41
- } // getDeviationFromReferencePoint
42
-
43
- const methods = new Map([
44
- ['MRT', mrt],
45
- ['ROS3PRw', ros3prw],
46
- ['ROS34PRw', ros34prw],
47
- ]);
48
-
49
- console.log('Performance\n');
50
-
51
- methods.forEach((method, name) => {
52
- console.log(' ', name);
53
-
54
- console.log(' PROBLEM TIME,MS ERR*');
55
-
56
- perfProbs.forEach((odes, idx) => {
57
- const start = Date.now();
58
- const solution = method(odes);
59
- const absErr = getDeviationFromReferencePoint(solution.slice(1), refPoints[idx]).toExponential(2);
60
- const finish = Date.now();
61
- console.log(` ${odes.name} ${finish - start} ${absErr}`.padStart(37));
62
- });
63
-
64
- console.log();
65
- });
66
-
67
- console.log('* approximate vs. reference (also, numerical)\n\n');
68
-
69
- console.log('Correctness (maximum absolute deviation): approximate vs. exact\n');
70
-
71
- methods.forEach((method, name) => {
72
- console.log(' ', name);
73
- console.log(' PROBLEM ERR');
74
-
75
- corrProbs.forEach((problem) => {
76
- const error = getError(method, problem);
77
- console.log(` ${problem.odes.name} ${error.toExponential(2)}`.padStart(28));
78
- });
79
-
80
- console.log();
81
- });
@@ -1 +0,0 @@
1
- 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@@ -1,155 +0,0 @@
1
- // Problems with known exact solution (for testing correctness)
2
-
3
- import {ODEs} from '../../index';
4
-
5
- /** Non-stiff 1D test problem: equation (see [1], p. 736) */
6
- const nonStiff1D: ODEs = {
7
- name: 'non-stiff 1D',
8
- arg: {name: 't', start: 0, finish: 4, step: 0.01},
9
- initial: [2],
10
- func: (t: number, y: Float64Array, output: Float64Array) => {
11
- output[0] = 4 * Math.exp(0.8 * t) - 0.5 * y[0];
12
- },
13
- tolerance: 0.00001,
14
- solutionColNames: ['y'],
15
- };
16
-
17
- /** Non-stiff 1D test problem: exact solution (see [1], p. 736) */
18
- const exactNonStiff1D = (t: number) => {
19
- return new Float64Array([
20
- (Math.exp(0.8 * t) - Math.exp(-0.5 * t)) * 4 / 1.3 + 2 * Math.exp(-0.5 * t),
21
- ]);
22
- };
23
-
24
- /** Non-stiff 2D test problem: equation */
25
- const nonStiff2D: ODEs = {
26
- name: 'non-stiff 2D',
27
- arg: {name: 't', start: 0, finish: 4, step: 0.01},
28
- initial: [1, 1],
29
- func: (t: number, y: Float64Array, output: Float64Array) => {
30
- output[0] = y[0] + y[1];
31
- output[1] = y[1] - y[0];
32
- },
33
- tolerance: 0.000000001,
34
- solutionColNames: ['x', 'y'],
35
- };
36
-
37
- /** Non-stiff 2D test problem: exact solution */
38
- const exactNonStiff2D = (t: number) => {
39
- return new Float64Array([
40
- Math.exp(t) * (Math.cos(t) + Math.sin(t)),
41
- Math.exp(t) * (Math.cos(t) - Math.sin(t)),
42
- ]);
43
- };
44
-
45
- /** Non-stiff 3D test problem: equations */
46
- const nonStiff3D: ODEs = {
47
- name: 'non-stiff 3D',
48
- arg: {name: 't', start: 0, finish: 2, step: 0.001},
49
- initial: [0.3, -0.8, 0],
50
- func: (t: number, y: Float64Array, output: Float64Array) => {
51
- output[0] = 5 * y[0] + 2 * y[1] + Math.sin(t);
52
- output[1] = -4 * y[0] - y[1] + Math.exp(2 * t);
53
- output[2] = 5 * t**4 - 3 * t**2 + 2 * t;
54
- },
55
- tolerance: 0.00000001,
56
- solutionColNames: ['x', 'y', 'z'],
57
- };
58
-
59
- /** Non-stiff 3D test problem: exact solution */
60
- const exactNonStiff3D = (t: number) => {
61
- const e1 = Math.exp(t);
62
- const e2 = Math.exp(2 * t);
63
- const e3 = Math.exp(3 * t);
64
- const c = Math.cos(t);
65
- const s = Math.sin(t);
66
-
67
- return new Float64Array([
68
- e1 + e3 + 0.1 * (3 * c - s) - 2 * e2,
69
- -2 * e1 - e3 - 0.2 * (2 * s + 4 * c) + 3 * e2,
70
- t**5 - t**3 + t**2,
71
- ]);
72
- };
73
-
74
- /** Stiff 1D test problem: equation (see [1], p. 767) */
75
- const stiff1D: ODEs = {
76
- name: 'stiff 1D',
77
- arg: {name: 't', start: 0, finish: 4, step: 0.01},
78
- initial: [0],
79
- func: (t: number, y: Float64Array, output: Float64Array) => {
80
- output[0] = -1000 * y[0] + 3000 - 2000 * Math.exp(-t);
81
- },
82
- tolerance: 0.0000005,
83
- solutionColNames: ['y'],
84
- };
85
-
86
- /** Stiff 1D test problem: exact solution (see [1], p. 767) */
87
- const exactStiff1D = (t: number) => {
88
- return new Float64Array([
89
- 3 - 0.998 * Math.exp(-1000 * t) - 2.002 * Math.exp(-t),
90
- ]);
91
- };
92
-
93
- /** Stiff 2D test problem: equations (see [1], p. 770) */
94
- const stiff2D: ODEs = {
95
- name: 'stiff 2D',
96
- arg: {name: 't', start: 0, finish: 4, step: 0.01},
97
- initial: [52.29, 83.82],
98
- func: (t: number, y: Float64Array, output: Float64Array) => {
99
- output[0] = -5 * y[0] + 3 * y[1];
100
- output[1] = 100 * y[0] - 301 * y[1];
101
- },
102
- tolerance: 0.0000005,
103
- solutionColNames: ['x', 'y'],
104
- };
105
-
106
- /** Stiff 2D test problem: exact solution (see [1], p. 770) */
107
- const exactStiff2D = (t: number) => {
108
- return new Float64Array([
109
- 52.96 * Math.exp(-3.9899 * t) - 0.67 * Math.exp(-302.0101 * t),
110
- 17.83 * Math.exp(-3.9899 * t) + 65.99 * Math.exp(-302.0101 * t),
111
- ]);
112
- };
113
-
114
- /** Stiff 3D test problem: equations */
115
- const stiff3D: ODEs = {
116
- name: 'stiff 3D',
117
- arg: {name: 't', start: 0, finish: 4, step: 0.01},
118
- initial: [2, 1, 0],
119
- func: (t: number, y: Float64Array, output: Float64Array) => {
120
- output[0] = -100 * y[0] + 100 * y[1] + y[2];
121
- output[1] = y[2];
122
- output[2] = -y[1];
123
- },
124
- tolerance: 0.00000001,
125
- solutionColNames: ['x', 'y', 'z'],
126
- };
127
-
128
- /** Stiff 3D test problem: exact solution */
129
- const exactStiff3D = (t: number) => {
130
- return new Float64Array([
131
- Math.exp(-100 * t) + Math.cos(t),
132
- Math.cos(t),
133
- -Math.sin(t),
134
- ]);
135
- };
136
-
137
- /** Correctness problem
138
- * @internal
139
- */
140
- export type CorrProblem = {
141
- odes: ODEs,
142
- exact: (t: number) => Float64Array,
143
- };
144
-
145
- /** Problems for testing correctness
146
- * @internal
147
- */
148
- export const corrProbs = [
149
- {odes: nonStiff1D, exact: exactNonStiff1D},
150
- {odes: nonStiff2D, exact: exactNonStiff2D},
151
- {odes: nonStiff3D, exact: exactNonStiff3D},
152
- {odes: stiff1D, exact: exactStiff1D},
153
- {odes: stiff2D, exact: exactStiff2D},
154
- {odes: stiff3D, exact: exactStiff3D},
155
- ];
@@ -1 +0,0 @@
1
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@@ -1,112 +0,0 @@
1
- /* eslint-disable max-len */
2
- /** This example shows how to apply pipelines and cyclic models.
3
- This approach can be used for in-webworkers analysis of models.
4
-
5
- Here, we consider pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model.
6
- */
7
-
8
- import * as DGL from '../../index';
9
-
10
- /** 1. Model specification */
11
- const model = `#name: PK-PD
12
- #tags: model
13
- #description: Pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model
14
- #equations:
15
- d(depot)/dt = -KA * depot
16
- d(centr)/dt = KA * depot - CL * C2 - Q * C2 + Q * C3
17
- d(peri)/dt = Q * C2 - Q * C3
18
- d(eff)/dt = Kin - Kout * (1 - C2/(EC50 + C2)) * eff
19
-
20
- #expressions:
21
- C2 = centr / V2
22
- C3 = peri / V3
23
-
24
- #loop:
25
- _count = 10 {caption: count; category: Dosing; min: 1; max: 20} [Number of doses]
26
- depot += dose
27
-
28
- #argument: t
29
- _t0 = 0 {units: h; caption: begin; category: Dosing; min: 0; max: 1} [Begin of dosing interval]
30
- _t1 = 12 {units: h; caption: end; category: Dosing; min: 5; max: 15} [End of dosing interval]
31
- _h = 1 {units: h; caption: step; category: Dosing; min: 0.01; max: 0.1} [Time step of simulation]
32
-
33
- #inits:
34
- depot = 0 {category: Initial values}
35
- centr = 0 {category: Initial values} [Central]
36
- peri = 0 {category: Initial values} [Peripheral]
37
- eff = 0.2 {category: Initial values} [Effective compartment rate]
38
-
39
- #parameters:
40
- dose = 1e4 {category: Dosing; min: 1e3; max: 2e4; step: 1e3} [Dosage]
41
- KA = 0.3 {caption: rate constant; category: Parameters; min: 0.1; max: 1}
42
- CL = 2 {caption: clearance; category: Parameters; min: 1; max: 5}
43
- V2 = 4 {caption: central volume; category: Parameters; min: 1; max: 10} [Central compartment volume]
44
- Q = 1 {caption: inter rate; category: Parameters; min: 0.1; max: 1} [Intercompartmental rate]
45
- V3 = 30 {caption: peri volume; category: Parameters; min: 20; max: 40} [Peripheral compartment volume]
46
- EC50 = 8 {caption: effect; category: Parameters; min: 1; max: 10}
47
- Kin = 0.2 {caption: Kin; category: Parameters; min: 0.1; max: 0.5} [The first-order production constant]
48
- Kout = 0.2 {caption: Kout; category: Parameters; min: 0.1; max: 0.5} [The first-order dissipation rate constant]
49
-
50
- #tolerance: 1e-9
51
-
52
- #meta.solver: {method: 'rkdp'; maxTimeMs: 5000}`;
53
-
54
- /** 2. Generate IVP-objects: for the main thread & for computations in webworkers */
55
- const ivp = DGL.getIVP(model);
56
- const ivpWW = DGL.getIvp2WebWorker(ivp);
57
-
58
- /** 3. Perform computations */
59
- try {
60
- // 3.1) Extract names of outputs
61
- const outputNames = DGL.getOutputNames(ivp);
62
- const outSize = outputNames.length;
63
-
64
- // 3.2) Set model inputs
65
- const inputs = {
66
- _count: 10,
67
- _t0: 0,
68
- _t1: 16,
69
- _h: 1,
70
- depot: 0,
71
- centr: 0,
72
- peri: 0,
73
- eff: 0.2,
74
- dose: 10000,
75
- KA: 0.63,
76
- CL: 3.2,
77
- V2: 6.58,
78
- Q: 0.622,
79
- V3: 35.6,
80
- EC50: 5.41,
81
- Kin: 0.272,
82
- Kout: 0.276,
83
- };
84
- const inputVector = DGL.getInputVector(inputs, ivp);
85
-
86
- // 3.3) Create a pipeline
87
- const creator = DGL.getPipelineCreator(ivp);
88
- const pipeline = creator.getPipeline(inputVector);
89
-
90
- // 3.4) Apply pipeline to perform computations
91
- const solution = DGL.applyPipeline(pipeline, ivpWW, inputVector);
92
-
93
- // 3.5) Print results
94
-
95
- // 3.5.1) Table header
96
- let line = ' ';
97
- outputNames.forEach((name) => line += name + ' ');
98
- console.log(line);
99
-
100
- // 3.5.2) Table with solution
101
- const length = solution[0].length;
102
- for (let i = 0; i < length; ++i) {
103
- line = '';
104
-
105
- for (let j = 0; j < outSize; ++j)
106
- line += solution[j][i].toFixed(8) + ' ';
107
-
108
- console.log(line);
109
- }
110
- } catch (err) {
111
- console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
112
- }
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