xtalforge 0.0.1__tar.gz

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Files changed (331) hide show
  1. xtalforge-0.0.1/Cargo.lock +1315 -0
  2. xtalforge-0.0.1/Cargo.toml +59 -0
  3. xtalforge-0.0.1/PKG-INFO +10 -0
  4. xtalforge-0.0.1/crates/xtalforge/Cargo.toml +40 -0
  5. xtalforge-0.0.1/crates/xtalforge/src/lib.rs +53 -0
  6. xtalforge-0.0.1/crates/xtalforge/tests/hello_world.rs +41 -0
  7. xtalforge-0.0.1/crates/xtalforge-analysis/Cargo.toml +22 -0
  8. xtalforge-0.0.1/crates/xtalforge-analysis/data/rcsr_subset.json +19 -0
  9. xtalforge-0.0.1/crates/xtalforge-analysis/src/automatic.rs +189 -0
  10. xtalforge-0.0.1/crates/xtalforge-analysis/src/cells.rs +193 -0
  11. xtalforge-0.0.1/crates/xtalforge-analysis/src/fit.rs +216 -0
  12. xtalforge-0.0.1/crates/xtalforge-analysis/src/grid.rs +384 -0
  13. xtalforge-0.0.1/crates/xtalforge-analysis/src/indexing.rs +142 -0
  14. xtalforge-0.0.1/crates/xtalforge-analysis/src/instrument.rs +228 -0
  15. xtalforge-0.0.1/crates/xtalforge-analysis/src/isosurface.rs +136 -0
  16. xtalforge-0.0.1/crates/xtalforge-analysis/src/lebail.rs +323 -0
  17. xtalforge-0.0.1/crates/xtalforge-analysis/src/lib.rs +57 -0
  18. xtalforge-0.0.1/crates/xtalforge-analysis/src/merge.rs +37 -0
  19. xtalforge-0.0.1/crates/xtalforge-analysis/src/nets.rs +276 -0
  20. xtalforge-0.0.1/crates/xtalforge-analysis/src/overlay.rs +102 -0
  21. xtalforge-0.0.1/crates/xtalforge-analysis/src/pareto.rs +40 -0
  22. xtalforge-0.0.1/crates/xtalforge-analysis/src/peaks.rs +114 -0
  23. xtalforge-0.0.1/crates/xtalforge-analysis/src/profiles.rs +95 -0
  24. xtalforge-0.0.1/crates/xtalforge-analysis/src/pxrd/profile.rs +51 -0
  25. xtalforge-0.0.1/crates/xtalforge-analysis/src/pxrd/scattering.rs +65 -0
  26. xtalforge-0.0.1/crates/xtalforge-analysis/src/pxrd.rs +456 -0
  27. xtalforge-0.0.1/crates/xtalforge-analysis/src/rcsr.rs +225 -0
  28. xtalforge-0.0.1/crates/xtalforge-analysis/src/refine/fit.rs +203 -0
  29. xtalforge-0.0.1/crates/xtalforge-analysis/src/refine/model.rs +296 -0
  30. xtalforge-0.0.1/crates/xtalforge-analysis/src/refine.rs +316 -0
  31. xtalforge-0.0.1/crates/xtalforge-analysis/src/rietveld.rs +144 -0
  32. xtalforge-0.0.1/crates/xtalforge-analysis/src/rietx.rs +127 -0
  33. xtalforge-0.0.1/crates/xtalforge-analysis/src/zeo.rs +442 -0
  34. xtalforge-0.0.1/crates/xtalforge-analysis/tests/automatic.rs +83 -0
  35. xtalforge-0.0.1/crates/xtalforge-analysis/tests/cells.rs +78 -0
  36. xtalforge-0.0.1/crates/xtalforge-analysis/tests/fit.rs +49 -0
  37. xtalforge-0.0.1/crates/xtalforge-analysis/tests/indexing.rs +34 -0
  38. xtalforge-0.0.1/crates/xtalforge-analysis/tests/instrument.rs +108 -0
  39. xtalforge-0.0.1/crates/xtalforge-analysis/tests/isosurface.rs +68 -0
  40. xtalforge-0.0.1/crates/xtalforge-analysis/tests/lebail.rs +89 -0
  41. xtalforge-0.0.1/crates/xtalforge-analysis/tests/merge.rs +92 -0
  42. xtalforge-0.0.1/crates/xtalforge-analysis/tests/nets.rs +98 -0
  43. xtalforge-0.0.1/crates/xtalforge-analysis/tests/overlay.rs +77 -0
  44. xtalforge-0.0.1/crates/xtalforge-analysis/tests/pareto.rs +18 -0
  45. xtalforge-0.0.1/crates/xtalforge-analysis/tests/peaks.rs +77 -0
  46. xtalforge-0.0.1/crates/xtalforge-analysis/tests/porosity.rs +158 -0
  47. xtalforge-0.0.1/crates/xtalforge-analysis/tests/profiles.rs +53 -0
  48. xtalforge-0.0.1/crates/xtalforge-analysis/tests/pxrd.rs +255 -0
  49. xtalforge-0.0.1/crates/xtalforge-analysis/tests/rcsr.rs +63 -0
  50. xtalforge-0.0.1/crates/xtalforge-analysis/tests/refine.rs +184 -0
  51. xtalforge-0.0.1/crates/xtalforge-analysis/tests/rietveld.rs +41 -0
  52. xtalforge-0.0.1/crates/xtalforge-analysis/tests/rietx.rs +83 -0
  53. xtalforge-0.0.1/crates/xtalforge-analysis/tests/zeo.rs +141 -0
  54. xtalforge-0.0.1/crates/xtalforge-build/Cargo.toml +23 -0
  55. xtalforge-0.0.1/crates/xtalforge-build/data/c60.json +305 -0
  56. xtalforge-0.0.1/crates/xtalforge-build/data/fragments.json +300 -0
  57. xtalforge-0.0.1/crates/xtalforge-build/data/polymer_protocol.json +24 -0
  58. xtalforge-0.0.1/crates/xtalforge-build/src/carbon.rs +174 -0
  59. xtalforge-0.0.1/crates/xtalforge-build/src/embed/geometry.rs +250 -0
  60. xtalforge-0.0.1/crates/xtalforge-build/src/embed/mod.rs +223 -0
  61. xtalforge-0.0.1/crates/xtalforge-build/src/embed/relax.rs +89 -0
  62. xtalforge-0.0.1/crates/xtalforge-build/src/fragments.rs +49 -0
  63. xtalforge-0.0.1/crates/xtalforge-build/src/fullerene.rs +36 -0
  64. xtalforge-0.0.1/crates/xtalforge-build/src/guest.rs +67 -0
  65. xtalforge-0.0.1/crates/xtalforge-build/src/hydrogens/geometry.rs +186 -0
  66. xtalforge-0.0.1/crates/xtalforge-build/src/hydrogens.rs +286 -0
  67. xtalforge-0.0.1/crates/xtalforge-build/src/lib.rs +35 -0
  68. xtalforge-0.0.1/crates/xtalforge-build/src/net.rs +78 -0
  69. xtalforge-0.0.1/crates/xtalforge-build/src/polymer.rs +259 -0
  70. xtalforge-0.0.1/crates/xtalforge-build/src/ribbon.rs +51 -0
  71. xtalforge-0.0.1/crates/xtalforge-build/src/sketch/mod.rs +305 -0
  72. xtalforge-0.0.1/crates/xtalforge-build/src/sketch/writer.rs +269 -0
  73. xtalforge-0.0.1/crates/xtalforge-build/src/smiles.rs +254 -0
  74. xtalforge-0.0.1/crates/xtalforge-build/src/spiral.rs +75 -0
  75. xtalforge-0.0.1/crates/xtalforge-build/src/substitute.rs +60 -0
  76. xtalforge-0.0.1/crates/xtalforge-build/src/twist.rs +57 -0
  77. xtalforge-0.0.1/crates/xtalforge-build/src/ztc.rs +181 -0
  78. xtalforge-0.0.1/crates/xtalforge-build/tests/carbon.rs +40 -0
  79. xtalforge-0.0.1/crates/xtalforge-build/tests/embed.rs +126 -0
  80. xtalforge-0.0.1/crates/xtalforge-build/tests/fragments.rs +19 -0
  81. xtalforge-0.0.1/crates/xtalforge-build/tests/fullerene.rs +21 -0
  82. xtalforge-0.0.1/crates/xtalforge-build/tests/guest.rs +27 -0
  83. xtalforge-0.0.1/crates/xtalforge-build/tests/hydrogens.rs +223 -0
  84. xtalforge-0.0.1/crates/xtalforge-build/tests/net.rs +51 -0
  85. xtalforge-0.0.1/crates/xtalforge-build/tests/phase6_extras.rs +80 -0
  86. xtalforge-0.0.1/crates/xtalforge-build/tests/polymer.rs +72 -0
  87. xtalforge-0.0.1/crates/xtalforge-build/tests/ribbon.rs +47 -0
  88. xtalforge-0.0.1/crates/xtalforge-build/tests/sketch.rs +153 -0
  89. xtalforge-0.0.1/crates/xtalforge-build/tests/smiles.rs +38 -0
  90. xtalforge-0.0.1/crates/xtalforge-build/tests/substitute.rs +27 -0
  91. xtalforge-0.0.1/crates/xtalforge-build/tests/ztc.rs +68 -0
  92. xtalforge-0.0.1/crates/xtalforge-commands/Cargo.toml +22 -0
  93. xtalforge-0.0.1/crates/xtalforge-commands/src/atoms.rs +319 -0
  94. xtalforge-0.0.1/crates/xtalforge-commands/src/bonds.rs +208 -0
  95. xtalforge-0.0.1/crates/xtalforge-commands/src/cell.rs +189 -0
  96. xtalforge-0.0.1/crates/xtalforge-commands/src/clipboard.rs +172 -0
  97. xtalforge-0.0.1/crates/xtalforge-commands/src/command.rs +441 -0
  98. xtalforge-0.0.1/crates/xtalforge-commands/src/document.rs +225 -0
  99. xtalforge-0.0.1/crates/xtalforge-commands/src/edit.rs +184 -0
  100. xtalforge-0.0.1/crates/xtalforge-commands/src/groups.rs +403 -0
  101. xtalforge-0.0.1/crates/xtalforge-commands/src/later.rs +154 -0
  102. xtalforge-0.0.1/crates/xtalforge-commands/src/lib.rs +27 -0
  103. xtalforge-0.0.1/crates/xtalforge-commands/src/symmetry.rs +178 -0
  104. xtalforge-0.0.1/crates/xtalforge-commands/tests/atoms.rs +143 -0
  105. xtalforge-0.0.1/crates/xtalforge-commands/tests/bonds.rs +127 -0
  106. xtalforge-0.0.1/crates/xtalforge-commands/tests/cell.rs +153 -0
  107. xtalforge-0.0.1/crates/xtalforge-commands/tests/clipboard.rs +100 -0
  108. xtalforge-0.0.1/crates/xtalforge-commands/tests/groups.rs +197 -0
  109. xtalforge-0.0.1/crates/xtalforge-commands/tests/later.rs +55 -0
  110. xtalforge-0.0.1/crates/xtalforge-commands/tests/stack.rs +286 -0
  111. xtalforge-0.0.1/crates/xtalforge-commands/tests/symmetry.rs +137 -0
  112. xtalforge-0.0.1/crates/xtalforge-core/Cargo.toml +27 -0
  113. xtalforge-0.0.1/crates/xtalforge-core/data/README.md +17 -0
  114. xtalforge-0.0.1/crates/xtalforge-core/data/elements.json.gz +0 -0
  115. xtalforge-0.0.1/crates/xtalforge-core/src/bonding.rs +255 -0
  116. xtalforge-0.0.1/crates/xtalforge-core/src/cell.rs +59 -0
  117. xtalforge-0.0.1/crates/xtalforge-core/src/data.rs +216 -0
  118. xtalforge-0.0.1/crates/xtalforge-core/src/describe.rs +41 -0
  119. xtalforge-0.0.1/crates/xtalforge-core/src/elements.rs +301 -0
  120. xtalforge-0.0.1/crates/xtalforge-core/src/groups.rs +144 -0
  121. xtalforge-0.0.1/crates/xtalforge-core/src/lattice/functions.rs +37 -0
  122. xtalforge-0.0.1/crates/xtalforge-core/src/lattice/math.rs +92 -0
  123. xtalforge-0.0.1/crates/xtalforge-core/src/lattice.rs +476 -0
  124. xtalforge-0.0.1/crates/xtalforge-core/src/lib.rs +127 -0
  125. xtalforge-0.0.1/crates/xtalforge-core/src/limits.rs +451 -0
  126. xtalforge-0.0.1/crates/xtalforge-core/src/measure.rs +180 -0
  127. xtalforge-0.0.1/crates/xtalforge-core/src/neighbors.rs +115 -0
  128. xtalforge-0.0.1/crates/xtalforge-core/src/p1.rs +134 -0
  129. xtalforge-0.0.1/crates/xtalforge-core/src/param_presets.rs +178 -0
  130. xtalforge-0.0.1/crates/xtalforge-core/src/params.rs +291 -0
  131. xtalforge-0.0.1/crates/xtalforge-core/src/rings.rs +176 -0
  132. xtalforge-0.0.1/crates/xtalforge-core/src/scalars.rs +49 -0
  133. xtalforge-0.0.1/crates/xtalforge-core/src/selection.rs +146 -0
  134. xtalforge-0.0.1/crates/xtalforge-core/src/site.rs +209 -0
  135. xtalforge-0.0.1/crates/xtalforge-core/src/slab.rs +289 -0
  136. xtalforge-0.0.1/crates/xtalforge-core/src/structure.rs +475 -0
  137. xtalforge-0.0.1/crates/xtalforge-core/src/supercell.rs +158 -0
  138. xtalforge-0.0.1/crates/xtalforge-core/src/symop.rs +389 -0
  139. xtalforge-0.0.1/crates/xtalforge-core/src/transforms.rs +432 -0
  140. xtalforge-0.0.1/crates/xtalforge-core/tests/bonding.rs +109 -0
  141. xtalforge-0.0.1/crates/xtalforge-core/tests/cell.rs +96 -0
  142. xtalforge-0.0.1/crates/xtalforge-core/tests/data.rs +137 -0
  143. xtalforge-0.0.1/crates/xtalforge-core/tests/elements.rs +172 -0
  144. xtalforge-0.0.1/crates/xtalforge-core/tests/error.rs +44 -0
  145. xtalforge-0.0.1/crates/xtalforge-core/tests/explicit_bonds.rs +62 -0
  146. xtalforge-0.0.1/crates/xtalforge-core/tests/fixtures/greeting.json.gz +0 -0
  147. xtalforge-0.0.1/crates/xtalforge-core/tests/golden.rs +71 -0
  148. xtalforge-0.0.1/crates/xtalforge-core/tests/groups.rs +72 -0
  149. xtalforge-0.0.1/crates/xtalforge-core/tests/lattice.rs +259 -0
  150. xtalforge-0.0.1/crates/xtalforge-core/tests/limits.rs +112 -0
  151. xtalforge-0.0.1/crates/xtalforge-core/tests/measure.rs +57 -0
  152. xtalforge-0.0.1/crates/xtalforge-core/tests/neighbors.rs +83 -0
  153. xtalforge-0.0.1/crates/xtalforge-core/tests/p1.rs +100 -0
  154. xtalforge-0.0.1/crates/xtalforge-core/tests/param_presets.rs +38 -0
  155. xtalforge-0.0.1/crates/xtalforge-core/tests/params.rs +107 -0
  156. xtalforge-0.0.1/crates/xtalforge-core/tests/rings.rs +64 -0
  157. xtalforge-0.0.1/crates/xtalforge-core/tests/scalars.rs +47 -0
  158. xtalforge-0.0.1/crates/xtalforge-core/tests/schema.rs +47 -0
  159. xtalforge-0.0.1/crates/xtalforge-core/tests/selection.rs +47 -0
  160. xtalforge-0.0.1/crates/xtalforge-core/tests/slab.rs +98 -0
  161. xtalforge-0.0.1/crates/xtalforge-core/tests/structure.rs +155 -0
  162. xtalforge-0.0.1/crates/xtalforge-core/tests/supercell.rs +72 -0
  163. xtalforge-0.0.1/crates/xtalforge-core/tests/transforms.rs +77 -0
  164. xtalforge-0.0.1/crates/xtalforge-core/tests/version.rs +14 -0
  165. xtalforge-0.0.1/crates/xtalforge-ff/Cargo.toml +29 -0
  166. xtalforge-0.0.1/crates/xtalforge-ff/data/uff.json +4808 -0
  167. xtalforge-0.0.1/crates/xtalforge-ff/src/calculator.rs +391 -0
  168. xtalforge-0.0.1/crates/xtalforge-ff/src/charges/data.rs +375 -0
  169. xtalforge-0.0.1/crates/xtalforge-ff/src/charges/eeq.rs +189 -0
  170. xtalforge-0.0.1/crates/xtalforge-ff/src/charges/eqeq.rs +181 -0
  171. xtalforge-0.0.1/crates/xtalforge-ff/src/charges/ewald.rs +420 -0
  172. xtalforge-0.0.1/crates/xtalforge-ff/src/charges/mod.rs +319 -0
  173. xtalforge-0.0.1/crates/xtalforge-ff/src/charges/periodic.rs +33 -0
  174. xtalforge-0.0.1/crates/xtalforge-ff/src/charges/qeq.rs +193 -0
  175. xtalforge-0.0.1/crates/xtalforge-ff/src/external/dftb.rs +214 -0
  176. xtalforge-0.0.1/crates/xtalforge-ff/src/external/orca.rs +219 -0
  177. xtalforge-0.0.1/crates/xtalforge-ff/src/external/probe.rs +117 -0
  178. xtalforge-0.0.1/crates/xtalforge-ff/src/external/text.rs +105 -0
  179. xtalforge-0.0.1/crates/xtalforge-ff/src/external/xtb.rs +139 -0
  180. xtalforge-0.0.1/crates/xtalforge-ff/src/external.rs +112 -0
  181. xtalforge-0.0.1/crates/xtalforge-ff/src/lib.rs +122 -0
  182. xtalforge-0.0.1/crates/xtalforge-ff/src/math.rs +346 -0
  183. xtalforge-0.0.1/crates/xtalforge-ff/src/optimize/dof.rs +478 -0
  184. xtalforge-0.0.1/crates/xtalforge-ff/src/optimize/eos.rs +304 -0
  185. xtalforge-0.0.1/crates/xtalforge-ff/src/optimize/fire.rs +92 -0
  186. xtalforge-0.0.1/crates/xtalforge-ff/src/optimize/lbfgs.rs +174 -0
  187. xtalforge-0.0.1/crates/xtalforge-ff/src/optimize/mod.rs +403 -0
  188. xtalforge-0.0.1/crates/xtalforge-ff/src/optimize/tensor.rs +51 -0
  189. xtalforge-0.0.1/crates/xtalforge-ff/src/prepare.rs +305 -0
  190. xtalforge-0.0.1/crates/xtalforge-ff/src/quantum.rs +103 -0
  191. xtalforge-0.0.1/crates/xtalforge-ff/src/registry.rs +50 -0
  192. xtalforge-0.0.1/crates/xtalforge-ff/src/scan/constraints.rs +130 -0
  193. xtalforge-0.0.1/crates/xtalforge-ff/src/scan/coordinates.rs +375 -0
  194. xtalforge-0.0.1/crates/xtalforge-ff/src/scan/driver.rs +292 -0
  195. xtalforge-0.0.1/crates/xtalforge-ff/src/scan.rs +17 -0
  196. xtalforge-0.0.1/crates/xtalforge-ff/src/structure_util.rs +59 -0
  197. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/calculator.rs +82 -0
  198. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/coordination.rs +141 -0
  199. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/geometry.rs +297 -0
  200. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/inversion.rs +242 -0
  201. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/math.rs +140 -0
  202. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/mod.rs +42 -0
  203. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/model.rs +261 -0
  204. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/params.rs +342 -0
  205. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/perception.rs +231 -0
  206. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/rules.rs +466 -0
  207. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/terms.rs +383 -0
  208. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/topology.rs +330 -0
  209. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/torsion.rs +294 -0
  210. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/typer.rs +220 -0
  211. xtalforge-0.0.1/crates/xtalforge-ff/src/uff/vdw.rs +107 -0
  212. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/constants.rs +41 -0
  213. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/hessian.rs +325 -0
  214. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/ir.rs +294 -0
  215. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/mod.rs +46 -0
  216. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/modes.rs +320 -0
  217. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/phonons.rs +131 -0
  218. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/qha.rs +165 -0
  219. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/rigid.rs +143 -0
  220. xtalforge-0.0.1/crates/xtalforge-ff/src/vibrations/thermo.rs +339 -0
  221. xtalforge-0.0.1/crates/xtalforge-ff/tests/charges.rs +318 -0
  222. xtalforge-0.0.1/crates/xtalforge-ff/tests/external.rs +235 -0
  223. xtalforge-0.0.1/crates/xtalforge-ff/tests/optimize.rs +240 -0
  224. xtalforge-0.0.1/crates/xtalforge-ff/tests/prepare.rs +137 -0
  225. xtalforge-0.0.1/crates/xtalforge-ff/tests/quantum.rs +62 -0
  226. xtalforge-0.0.1/crates/xtalforge-ff/tests/scan.rs +172 -0
  227. xtalforge-0.0.1/crates/xtalforge-ff/tests/thermo.rs +230 -0
  228. xtalforge-0.0.1/crates/xtalforge-ff/tests/uff.rs +357 -0
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