rexafs 0.1.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (361) hide show
  1. rexafs-0.1.0/Cargo.lock +11695 -0
  2. rexafs-0.1.0/Cargo.toml +79 -0
  3. rexafs-0.1.0/LICENSE +12 -0
  4. rexafs-0.1.0/LICENSE-APACHE +201 -0
  5. rexafs-0.1.0/LICENSE-MIT +21 -0
  6. rexafs-0.1.0/PKG-INFO +76 -0
  7. rexafs-0.1.0/crates/rexafs/.gitignore +4 -0
  8. rexafs-0.1.0/crates/rexafs/Cargo.toml +84 -0
  9. rexafs-0.1.0/crates/rexafs/LICENSE-APACHE +201 -0
  10. rexafs-0.1.0/crates/rexafs/LICENSE-MIT +21 -0
  11. rexafs-0.1.0/crates/rexafs/README.md +163 -0
  12. rexafs-0.1.0/crates/rexafs/benches/autobk_stage_benchmark.rs +89 -0
  13. rexafs-0.1.0/crates/rexafs/benches/feff_fitting_batch_benchmark.rs +178 -0
  14. rexafs-0.1.0/crates/rexafs/benches/perf.rs +72 -0
  15. rexafs-0.1.0/crates/rexafs/benches/xas_group_benchmark_parallel.rs +66 -0
  16. rexafs-0.1.0/crates/rexafs/benches/xas_group_benchmark_single.rs +66 -0
  17. rexafs-0.1.0/crates/rexafs/benchmarks/baseline.json +25 -0
  18. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ag.cif +252 -0
  19. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ag.json +18 -0
  20. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ag2o.cif +117 -0
  21. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ag2o.json +18 -0
  22. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/al.cif +262 -0
  23. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/al.json +18 -0
  24. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/al2o3_corundum.cif +216 -0
  25. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/al2o3_corundum.json +18 -0
  26. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/aspirin.cif +162 -0
  27. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/aspirin.json +18 -0
  28. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/au.cif +259 -0
  29. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/au.json +18 -0
  30. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/caf2_fluorite.cif +6261 -0
  31. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/caf2_fluorite.json +18 -0
  32. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/catalog.json +1118 -0
  33. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ceo2.cif +452 -0
  34. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ceo2.json +18 -0
  35. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/co3o4.cif +248 -0
  36. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/co3o4.json +18 -0
  37. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/co_hcp.cif +86 -0
  38. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/co_hcp.json +18 -0
  39. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/coo.cif +261 -0
  40. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/coo.json +18 -0
  41. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cos2_cattierite.cif +99 -0
  42. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cos2_cattierite.json +18 -0
  43. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cr.cif +156 -0
  44. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cr.json +18 -0
  45. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cr2o3_eskolaite.cif +181 -0
  46. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cr2o3_eskolaite.json +18 -0
  47. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cu.cif +377 -0
  48. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cu.json +18 -0
  49. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cu2o_cuprite.cif +126 -0
  50. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cu2o_cuprite.json +18 -0
  51. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cufes2_chalcopyrite.cif +136 -0
  52. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cufes2_chalcopyrite.json +18 -0
  53. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cuo_tenorite.cif +141 -0
  54. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/cuo_tenorite.json +18 -0
  55. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/fe2o3_hematite.cif +114 -0
  56. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/fe2o3_hematite.json +18 -0
  57. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/fe3o4_magnetite.cif +305 -0
  58. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/fe3o4_magnetite.json +18 -0
  59. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/fe_bcc.cif +252 -0
  60. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/fe_bcc.json +18 -0
  61. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/feo_wustite.cif +259 -0
  62. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/feo_wustite.json +18 -0
  63. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/fes2_pyrite.cif +1009 -0
  64. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/fes2_pyrite.json +18 -0
  65. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ir.cif +249 -0
  66. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ir.json +18 -0
  67. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/licoo2.cif +384 -0
  68. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/licoo2.json +18 -0
  69. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/lifepo4_triphylite.cif +278 -0
  70. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/lifepo4_triphylite.json +18 -0
  71. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mn2o3_bixbyite.cif +119 -0
  72. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mn2o3_bixbyite.json +18 -0
  73. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mn_alpha.cif +114 -0
  74. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mn_alpha.json +18 -0
  75. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mno.cif +266 -0
  76. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mno.json +18 -0
  77. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mno2_pyrolusite.cif +102 -0
  78. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mno2_pyrolusite.json +18 -0
  79. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mo.cif +238 -0
  80. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mo.json +18 -0
  81. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/moo3.cif +73 -0
  82. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/moo3.json +18 -0
  83. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mos2_2h.cif +89 -0
  84. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/mos2_2h.json +18 -0
  85. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/nacl_halite.cif +903 -0
  86. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/nacl_halite.json +18 -0
  87. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/nb.cif +245 -0
  88. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/nb.json +18 -0
  89. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ni.cif +272 -0
  90. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ni.json +18 -0
  91. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/nio.cif +342 -0
  92. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/nio.json +18 -0
  93. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/nis_millerite.cif +90 -0
  94. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/nis_millerite.json +18 -0
  95. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/os.cif +91 -0
  96. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/os.json +18 -0
  97. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/pd.cif +249 -0
  98. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/pd.json +18 -0
  99. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/pdo.cif +93 -0
  100. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/pdo.json +18 -0
  101. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/pt.cif +317 -0
  102. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/pt.json +18 -0
  103. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/pto2_alpha.cif +70 -0
  104. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/pto2_alpha.json +18 -0
  105. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/re.cif +85 -0
  106. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/re.json +18 -0
  107. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/rh.cif +274 -0
  108. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/rh.json +18 -0
  109. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ru_hcp.cif +91 -0
  110. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ru_hcp.json +18 -0
  111. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ruo2.cif +136 -0
  112. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ruo2.json +18 -0
  113. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/sn_beta.cif +171 -0
  114. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/sn_beta.json +18 -0
  115. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/sno2_cassiterite.cif +134 -0
  116. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/sno2_cassiterite.json +18 -0
  117. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ta.cif +152 -0
  118. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ta.json +18 -0
  119. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ti_hcp.cif +93 -0
  120. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/ti_hcp.json +18 -0
  121. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/tio2_anatase.cif +114 -0
  122. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/tio2_anatase.json +18 -0
  123. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/tio2_rutile.cif +119 -0
  124. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/tio2_rutile.json +18 -0
  125. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/urea.cif +90 -0
  126. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/urea.json +18 -0
  127. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/v.cif +225 -0
  128. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/v.json +18 -0
  129. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/v2o5.cif +71 -0
  130. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/v2o5.json +18 -0
  131. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/w.cif +156 -0
  132. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/w.json +18 -0
  133. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/wo3_monoclinic.cif +69 -0
  134. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/wo3_monoclinic.json +18 -0
  135. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/zn.cif +90 -0
  136. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/zn.json +18 -0
  137. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/zno_wurtzite.cif +170 -0
  138. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/zno_wurtzite.json +18 -0
  139. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/zns_sphalerite.cif +166 -0
  140. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/zns_sphalerite.json +18 -0
  141. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/zro2_monoclinic.cif +4250 -0
  142. rexafs-0.1.0/crates/rexafs/data/builtin_cifs/zro2_monoclinic.json +18 -0
  143. rexafs-0.1.0/crates/rexafs/doc/feff-fitting-mvp.md +79 -0
  144. rexafs-0.1.0/crates/rexafs/doc/img/flamegraph_rexafs_analytical_optimization.svg +491 -0
  145. rexafs-0.1.0/crates/rexafs/doc/img/flamegraph_rexafs_numerical_optimization.svg +491 -0
  146. rexafs-0.1.0/crates/rexafs/doc/img/flamegraph_xraylarch.svg +14588 -0
  147. rexafs-0.1.0/crates/rexafs/doc/migration-performance-logic-hardening.md +92 -0
  148. rexafs-0.1.0/crates/rexafs/doc/profiling.md +327 -0
  149. rexafs-0.1.0/crates/rexafs/examples/alloc_baseline.rs +128 -0
  150. rexafs-0.1.0/crates/rexafs/examples/feff_backend_probe.rs +57 -0
  151. rexafs-0.1.0/crates/rexafs/examples/feff_compare_export.rs +522 -0
  152. rexafs-0.1.0/crates/rexafs/examples/plot_demo.rs +439 -0
  153. rexafs-0.1.0/crates/rexafs/flamegraph.svg +491 -0
  154. rexafs-0.1.0/crates/rexafs/pythontest.py +8 -0
  155. rexafs-0.1.0/crates/rexafs/scripts/bench_regression_gate.sh +83 -0
  156. rexafs-0.1.0/crates/rexafs/scripts/build_builtin_library.py +33 -0
  157. rexafs-0.1.0/crates/rexafs/scripts/fetch_builtin_cifs.py +114 -0
  158. rexafs-0.1.0/crates/rexafs/scripts/generate_element_table.py +25 -0
  159. rexafs-0.1.0/crates/rexafs/scripts/generate_larch_fit_references.py +220 -0
  160. rexafs-0.1.0/crates/rexafs/scripts/generate_larch_fitspace_references.py +157 -0
  161. rexafs-0.1.0/crates/rexafs/scripts/generate_spacegroup_table.py +45 -0
  162. rexafs-0.1.0/crates/rexafs/scripts/generate_structure_fixtures.py +64 -0
  163. rexafs-0.1.0/crates/rexafs/src/lib.rs +18 -0
  164. rexafs-0.1.0/crates/rexafs/src/parser/mod.rs +1 -0
  165. rexafs-0.1.0/crates/rexafs/src/plot/builder.rs +553 -0
  166. rexafs-0.1.0/crates/rexafs/src/plot/config.rs +319 -0
  167. rexafs-0.1.0/crates/rexafs/src/plot/errors.rs +41 -0
  168. rexafs-0.1.0/crates/rexafs/src/plot/fitting_plots.rs +558 -0
  169. rexafs-0.1.0/crates/rexafs/src/plot/group_plots.rs +103 -0
  170. rexafs-0.1.0/crates/rexafs/src/plot/mod.rs +12 -0
  171. rexafs-0.1.0/crates/rexafs/src/plot/panels.rs +153 -0
  172. rexafs-0.1.0/crates/rexafs/src/plot/spectrum_plots.rs +351 -0
  173. rexafs-0.1.0/crates/rexafs/src/plot/traits.rs +26 -0
  174. rexafs-0.1.0/crates/rexafs/src/prelude.rs +50 -0
  175. rexafs-0.1.0/crates/rexafs/src/xafs/analysis/lcf.rs +695 -0
  176. rexafs-0.1.0/crates/rexafs/src/xafs/analysis/mod.rs +193 -0
  177. rexafs-0.1.0/crates/rexafs/src/xafs/analysis/pca.rs +336 -0
  178. rexafs-0.1.0/crates/rexafs/src/xafs/background.rs +1923 -0
  179. rexafs-0.1.0/crates/rexafs/src/xafs/background_ndarray.rs +1909 -0
  180. rexafs-0.1.0/crates/rexafs/src/xafs/bessel_i0.rs +124 -0
  181. rexafs-0.1.0/crates/rexafs/src/xafs/errors.rs +401 -0
  182. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/builder.rs +549 -0
  183. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/errors.rs +89 -0
  184. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/expression.pest +23 -0
  185. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/expression.rs +433 -0
  186. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/feffdat.rs +321 -0
  187. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/mod.rs +89 -0
  188. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/path_model.rs +472 -0
  189. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/runner.rs +1295 -0
  190. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/solver.rs +1359 -0
  191. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/template.rs +332 -0
  192. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/transform.rs +809 -0
  193. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/types.rs +1096 -0
  194. rexafs-0.1.0/crates/rexafs/src/xafs/fitting/variables.rs +225 -0
  195. rexafs-0.1.0/crates/rexafs/src/xafs/io/QAS.rs +0 -0
  196. rexafs-0.1.0/crates/rexafs/src/xafs/io/athena.rs +1517 -0
  197. rexafs-0.1.0/crates/rexafs/src/xafs/io/mod.rs +68 -0
  198. rexafs-0.1.0/crates/rexafs/src/xafs/io/xafs_bson.rs +195 -0
  199. rexafs-0.1.0/crates/rexafs/src/xafs/io/xafs_json.rs +333 -0
  200. rexafs-0.1.0/crates/rexafs/src/xafs/io/xasdatatype.rs +32 -0
  201. rexafs-0.1.0/crates/rexafs/src/xafs/io/xdi.rs +580 -0
  202. rexafs-0.1.0/crates/rexafs/src/xafs/lmutils.rs +154 -0
  203. rexafs-0.1.0/crates/rexafs/src/xafs/mathutils.rs +276 -0
  204. rexafs-0.1.0/crates/rexafs/src/xafs/mathutils_ndarray.rs +807 -0
  205. rexafs-0.1.0/crates/rexafs/src/xafs/mod.rs +140 -0
  206. rexafs-0.1.0/crates/rexafs/src/xafs/normalization.rs +776 -0
  207. rexafs-0.1.0/crates/rexafs/src/xafs/normalization_ndarray.rs +879 -0
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