gfn1-rs-python 0.5.0__tar.gz → 0.7.2__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 (453) hide show
  1. gfn1_rs_python-0.7.2/CHANGELOG.md +164 -0
  2. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/Cargo.lock +137 -3
  3. gfn1_rs_python-0.7.2/Cargo.toml +473 -0
  4. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/PKG-INFO +56 -62
  5. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/README.md +45 -58
  6. gfn1_rs_python-0.7.2/THIRD_PARTY_NOTICES.md +256 -0
  7. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/CONTRIBUTING.md +1 -1
  8. gfn1_rs_python-0.7.2/docs/README.md +48 -0
  9. gfn1_rs_python-0.7.2/docs/api-overview.md +252 -0
  10. gfn1_rs_python-0.7.2/docs/cp-settings.md +106 -0
  11. gfn1_rs_python-0.7.2/docs/crystal-cli.md +250 -0
  12. gfn1_rs_python-0.7.2/docs/crystal-dfpt-results.md +155 -0
  13. gfn1_rs_python-0.7.2/docs/crystal-properties-results.md +234 -0
  14. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/derivatives.md +331 -15
  15. gfn1_rs_python-0.7.2/docs/electromechanical.md +237 -0
  16. gfn1_rs_python-0.7.2/docs/ethylene-excited-optimization.md +156 -0
  17. gfn1_rs_python-0.7.2/docs/excited-hessians.md +175 -0
  18. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/finite-temperature.md +60 -15
  19. gfn1_rs_python-0.7.2/docs/fragments.md +247 -0
  20. gfn1_rs_python-0.7.2/docs/images/stda-seam-angular-response.svg +2146 -0
  21. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/limitations.md +177 -167
  22. gfn1_rs_python-0.7.2/docs/mechanical-properties.md +343 -0
  23. gfn1_rs_python-0.7.2/docs/ml-property-training.md +309 -0
  24. gfn1_rs_python-0.7.2/docs/ml-training.md +275 -0
  25. gfn1_rs_python-0.7.2/docs/parameters.md +304 -0
  26. gfn1_rs_python-0.7.2/docs/pbc-scc.md +152 -0
  27. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/pbc.md +328 -279
  28. gfn1_rs_python-0.7.2/docs/phonon-band-properties.md +287 -0
  29. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/python-api.md +150 -49
  30. gfn1_rs_python-0.7.2/docs/real-crystal-property-survey.md +219 -0
  31. gfn1_rs_python-0.7.2/docs/resources.md +108 -0
  32. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/rust-api.md +90 -60
  33. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/scope.md +77 -20
  34. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/sigma_hole_preset.md +2 -2
  35. gfn1_rs_python-0.7.2/docs/soc-dfpt.md +271 -0
  36. gfn1_rs_python-0.7.2/docs/stda-pes-local-topology.md +161 -0
  37. gfn1_rs_python-0.7.2/docs/stda-pes.md +171 -0
  38. gfn1_rs_python-0.7.2/docs/stda-xtb.md +239 -0
  39. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/docs/td.md +205 -34
  40. gfn1_rs_python-0.7.2/docs/tda-stda-comparison.md +124 -0
  41. gfn1_rs_python-0.7.2/examples/README.md +5 -0
  42. gfn1_rs_python-0.7.2/examples/crystal-phonon-request.json +40 -0
  43. gfn1_rs_python-0.7.2/examples/crystal-response-request.json +39 -0
  44. gfn1_rs_python-0.7.2/examples/crystal-sic-cod9008856-relaxed-request.json +97 -0
  45. gfn1_rs_python-0.7.2/models/h2-fci-reference.json +465 -0
  46. gfn1_rs_python-0.7.2/models/h2-fci-trained-report.json +2053 -0
  47. gfn1_rs_python-0.7.2/models/h2-fci-trained.model +13 -0
  48. gfn1_rs_python-0.7.2/models/h2-radial-demo.model +13 -0
  49. gfn1_rs_python-0.7.2/models/water-clusters-reference.json +1835 -0
  50. gfn1_rs_python-0.7.2/models/water-clusters-trained-report.json +2467 -0
  51. gfn1_rs_python-0.7.2/models/water-clusters-trained.model +17 -0
  52. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/pyproject.toml +13 -5
  53. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/python/gfn1_rs/__init__.py +3 -0
  54. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/python/gfn1_rs/ase.py +527 -36
  55. gfn1_rs_python-0.7.2/python/gfn1_rs/cli.py +12 -0
  56. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/python/gfn1_rs/native.py +78 -1
  57. gfn1_rs_python-0.7.2/python/gfn1_rs/training.py +36 -0
  58. gfn1_rs_python-0.7.2/references.bib +198 -0
  59. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/scripts/gen_secondary_basis.py +45 -14
  60. gfn1_rs_python-0.7.2/scripts/generate_h2_fci.py +86 -0
  61. gfn1_rs_python-0.7.2/scripts/generate_water_clusters.py +159 -0
  62. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/basis.rs +5 -1
  63. gfn1_rs_python-0.7.2/src/bin/gfn1_rs.rs +7 -0
  64. gfn1_rs_python-0.7.2/src/bin/gfn1_rs_train.rs +4 -0
  65. gfn1_rs_python-0.7.2/src/citations.rs +84 -0
  66. gfn1_rs_python-0.7.2/src/cli/calculation.rs +2707 -0
  67. gfn1_rs_python-0.7.2/src/cli/mod.rs +106 -0
  68. gfn1_rs_python-0.7.2/src/cli/observables.rs +347 -0
  69. gfn1_rs_python-0.7.2/src/cli/properties.rs +1191 -0
  70. gfn1_rs_python-0.7.2/src/cli/train_support.rs +407 -0
  71. gfn1_rs_python-0.7.2/src/cli/training.rs +587 -0
  72. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/constants.rs +4 -0
  73. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/data_tables.rs +260 -88
  74. gfn1_rs_python-0.7.2/src/derivative_assembly.rs +415 -0
  75. gfn1_rs_python-0.7.2/src/derivative_files.rs +0 -0
  76. gfn1_rs_python-0.7.2/src/dispersion/reduced_hessian.rs +181 -0
  77. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/dispersion.rs +107 -24
  78. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/electronic.rs +944 -488
  79. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/exchange.rs +24 -24
  80. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/fourth_derivative/assemble.rs +644 -148
  81. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/fourth_derivative/directional.rs +48 -59
  82. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/fourth_derivative/mod.rs +42 -7
  83. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/fourth_derivative/response_stage.rs +122 -168
  84. gfn1_rs_python-0.7.2/src/fragment/cluster.rs +588 -0
  85. gfn1_rs_python-0.7.2/src/fragment/dc.rs +389 -0
  86. gfn1_rs_python-0.7.2/src/fragment/geometry.rs +564 -0
  87. gfn1_rs_python-0.7.2/src/fragment/mod.rs +592 -0
  88. gfn1_rs_python-0.7.2/src/fragment/spectral.rs +230 -0
  89. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/gradient.rs +77 -10
  90. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/halogen.rs +77 -29
  91. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/hessian/mod.rs +210 -91
  92. gfn1_rs_python-0.7.2/src/hessian/tests.rs +1421 -0
  93. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/integrals.rs +72 -4
  94. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/integrals_fourth_derivatives.rs +4 -16
  95. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/lattice.rs +87 -9
  96. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/lib.rs +59 -19
  97. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/linalg.rs +191 -37
  98. gfn1_rs_python-0.7.2/src/logging.rs +258 -0
  99. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/magnetic.rs +200 -25
  100. gfn1_rs_python-0.7.2/src/ml.rs +1424 -0
  101. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/multipole.rs +35 -14
  102. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/param_deriv.rs +2 -2
  103. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/params.rs +4 -1
  104. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/complex.rs +169 -4
  105. gfn1_rs_python-0.7.2/src/pbc/elastic_response.rs +992 -0
  106. gfn1_rs_python-0.7.2/src/pbc/electromechanical.rs +743 -0
  107. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/gamma_response.rs +328 -214
  108. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/gamma_third.rs +250 -116
  109. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/gradient.rs +27 -2
  110. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/hessian.rs +435 -89
  111. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/kpoint_third.rs +260 -173
  112. gfn1_rs_python-0.7.2/src/pbc/mechanical.rs +1144 -0
  113. gfn1_rs_python-0.7.2/src/pbc/ml.rs +239 -0
  114. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/mod.rs +27 -3
  115. gfn1_rs_python-0.7.2/src/pbc/phonon.rs +296 -0
  116. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/polarization.rs +24 -2
  117. gfn1_rs_python-0.7.2/src/pbc/polarization_response.rs +632 -0
  118. gfn1_rs_python-0.7.2/src/pbc/scc_solver.rs +355 -0
  119. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/scf.rs +294 -26
  120. gfn1_rs_python-0.7.2/src/pbc/soc.rs +439 -0
  121. gfn1_rs_python-0.7.2/src/pbc/soc_response.rs +422 -0
  122. gfn1_rs_python-0.7.2/src/pbc/spectra.rs +872 -0
  123. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/stress.rs +54 -5
  124. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/plus_u.rs +77 -16
  125. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/plus_u_dudr.rs +287 -75
  126. gfn1_rs_python-0.7.2/src/property_training.rs +1377 -0
  127. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/python.rs +2395 -282
  128. gfn1_rs_python-0.7.2/src/python_resources.rs +62 -0
  129. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/repulsion.rs +116 -2
  130. gfn1_rs_python-0.7.2/src/resources.rs +469 -0
  131. gfn1_rs_python-0.7.2/src/response/charge_space/dk_third.rs +322 -0
  132. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/response/charge_space.rs +394 -289
  133. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/response/cpxtb.rs +142 -59
  134. gfn1_rs_python-0.7.2/src/scalar_dual.rs +161 -0
  135. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/secondary_bases/gfn1-xtb-cc-pv5z.txt +7 -3
  136. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/secondary_bases/gfn1-xtb-cc-pvdz.txt +7 -3
  137. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/secondary_bases/gfn1-xtb-cc-pvqz.txt +7 -3
  138. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/secondary_bases/gfn1-xtb-cc-pvtz.txt +7 -3
  139. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/secondary_basis.rs +2 -2
  140. gfn1_rs_python-0.7.2/src/smoothness.rs +123 -0
  141. gfn1_rs_python-0.7.2/src/soc.rs +618 -0
  142. gfn1_rs_python-0.7.2/src/solvation.rs +875 -0
  143. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/spin.rs +668 -208
  144. gfn1_rs_python-0.7.2/src/stda_xtb/dual.rs +2 -0
  145. gfn1_rs_python-0.7.2/src/stda_xtb/gradient.rs +824 -0
  146. gfn1_rs_python-0.7.2/src/stda_xtb/ground/differential.rs +611 -0
  147. gfn1_rs_python-0.7.2/src/stda_xtb/ground.rs +835 -0
  148. gfn1_rs_python-0.7.2/src/stda_xtb/native.rs +448 -0
  149. gfn1_rs_python-0.7.2/src/stda_xtb/thermal.rs +563 -0
  150. gfn1_rs_python-0.7.2/src/stda_xtb.rs +33 -0
  151. gfn1_rs_python-0.7.2/src/td/hessian.rs +1214 -0
  152. gfn1_rs_python-0.7.2/src/td/periodic.rs +292 -0
  153. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/td.rs +1043 -318
  154. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/terms.rs +176 -0
  155. gfn1_rs_python-0.7.2/src/third_derivative/contracted.rs +1078 -0
  156. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/third_derivative/finite_t.rs +456 -340
  157. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/third_derivative/mod.rs +184 -30
  158. gfn1_rs_python-0.7.2/src/third_derivative/tests.rs +8211 -0
  159. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/trah.rs +57 -1
  160. gfn1_rs_python-0.7.2/src/training.rs +643 -0
  161. gfn1_rs_python-0.7.2/src/variational_derivatives.rs +185 -0
  162. gfn1_rs_python-0.7.2/src/vibrational.rs +391 -0
  163. gfn1_rs_python-0.7.2/src/vpt2.rs +703 -0
  164. gfn1_rs_python-0.7.2/tests/README.md +44 -0
  165. gfn1_rs_python-0.7.2/tests/backend_linalg.rs +75 -0
  166. gfn1_rs_python-0.7.2/tests/cotton_mouton.rs +164 -0
  167. gfn1_rs_python-0.7.2/tests/crystal_cli.rs +358 -0
  168. gfn1_rs_python-0.7.2/tests/data/backend-update-audit.json +29475 -0
  169. gfn1_rs_python-0.7.2/tests/data/cotton-mouton-audit.json +790 -0
  170. gfn1_rs_python-0.7.2/tests/data/crystal-dfpt-results.json +3678 -0
  171. gfn1_rs_python-0.7.2/tests/data/crystal-electromechanical-properties.json +46355 -0
  172. gfn1_rs_python-0.7.2/tests/data/crystal-mechanical-properties.json +15306 -0
  173. gfn1_rs_python-0.7.2/tests/data/ethylene-excited-optimization.json +24469 -0
  174. gfn1_rs_python-0.7.2/tests/data/ethylene-stda-crossing-seed.json +47 -0
  175. gfn1_rs_python-0.7.2/tests/data/ethylene-stda-original-stationary.json +1860 -0
  176. gfn1_rs_python-0.7.2/tests/data/h2-reference-reproduction.json +48 -0
  177. gfn1_rs_python-0.7.2/tests/data/ml-periodic-property-training.json +838 -0
  178. gfn1_rs_python-0.7.2/tests/data/multipole-rank4-ph3-diagnostic.json +180 -0
  179. gfn1_rs_python-0.7.2/tests/data/nuclear-derivatives-raw.json.gz +0 -0
  180. gfn1_rs_python-0.7.2/tests/data/nuclear-derivatives-report.json +3072 -0
  181. gfn1_rs_python-0.7.2/tests/data/pbc-scc-results.json +5362 -0
  182. gfn1_rs_python-0.7.2/tests/data/periodic-response-optimization.json +36 -0
  183. gfn1_rs_python-0.7.2/tests/data/real-crystal-cli-validation.json +78 -0
  184. gfn1_rs_python-0.7.2/tests/data/real-crystal-phonons-report-v051.json +2131 -0
  185. gfn1_rs_python-0.7.2/tests/data/real-crystal-phonons-report.json +7479 -0
  186. gfn1_rs_python-0.7.2/tests/data/real-crystal-property-survey.json +66002 -0
  187. gfn1_rs_python-0.7.2/tests/data/real-crystal-survey-inputs.json +550 -0
  188. gfn1_rs_python-0.7.2/tests/data/real_crystals.json +600 -0
  189. gfn1_rs_python-0.7.2/tests/data/release-v070-validation.json +218 -0
  190. gfn1_rs_python-0.7.2/tests/data/secondary-basis-provenance.json +220 -0
  191. gfn1_rs_python-0.7.2/tests/data/stda-ci-instability.json +46 -0
  192. gfn1_rs_python-0.7.2/tests/data/stda-dipole-reference.json +1088 -0
  193. gfn1_rs_python-0.7.2/tests/data/stda-ground-reference.json +4533 -0
  194. gfn1_rs_python-0.7.2/tests/data/stda-pes-degeneracy.json +31328 -0
  195. gfn1_rs_python-0.7.2/tests/data/stda-pes-optimization.json +5013 -0
  196. gfn1_rs_python-0.7.2/tests/data/stda-pes-release-reproduction.json +23453 -0
  197. gfn1_rs_python-0.7.2/tests/data/stda-seam-angular-response.json +834 -0
  198. gfn1_rs_python-0.7.2/tests/data/stda-spectrum-reference.json +644 -0
  199. gfn1_rs_python-0.7.2/tests/data/stda-trust-region-results.json +13578 -0
  200. gfn1_rs_python-0.7.2/tests/data/strain-skeleton-performance.json +75 -0
  201. gfn1_rs_python-0.7.2/tests/data/tda-stda-native-comparison.json +1877 -0
  202. gfn1_rs_python-0.7.2/tests/data/v070-crystal-scc-ml-validation.json +166 -0
  203. gfn1_rs_python-0.7.2/tests/data/v070-properties-survey-validation.json +209 -0
  204. gfn1_rs_python-0.7.2/tests/data/vpt2-molecular-audit.json +574 -0
  205. gfn1_rs_python-0.7.2/tests/data/water-reference-reproduction.json +81 -0
  206. gfn1_rs_python-0.7.2/tests/data/xtb-validation-report.json +1446 -0
  207. gfn1_rs_python-0.7.2/tests/excited_hessian.rs +395 -0
  208. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/fourth_derivative.rs +55 -4
  209. gfn1_rs_python-0.7.2/tests/fragment.rs +340 -0
  210. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/gruneisen_second_order_delta.rs +6 -7
  211. gfn1_rs_python-0.7.2/tests/logging.rs +171 -0
  212. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/magnetic.rs +83 -20
  213. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/magnetizability_frame_invariance.rs +25 -11
  214. gfn1_rs_python-0.7.2/tests/ml.rs +137 -0
  215. gfn1_rs_python-0.7.2/tests/ml_derivatives.rs +160 -0
  216. gfn1_rs_python-0.7.2/tests/nuclear_derivative_audit.rs +625 -0
  217. gfn1_rs_python-0.7.2/tests/oracle_regressions.rs +42 -0
  218. gfn1_rs_python-0.7.2/tests/pbc_electromechanical.rs +494 -0
  219. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/pbc_gamma_third_analytic.rs +162 -19
  220. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/pbc_kpoint_third_analytic.rs +268 -20
  221. gfn1_rs_python-0.7.2/tests/pbc_mechanical.rs +587 -0
  222. gfn1_rs_python-0.7.2/tests/pbc_ml.rs +416 -0
  223. gfn1_rs_python-0.7.2/tests/pbc_scc_solver.rs +158 -0
  224. gfn1_rs_python-0.7.2/tests/pbc_soc.rs +381 -0
  225. gfn1_rs_python-0.7.2/tests/pbc_spectra.rs +359 -0
  226. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/pbc_third_derivative.rs +117 -61
  227. gfn1_rs_python-0.7.2/tests/periodic_cli.rs +116 -0
  228. gfn1_rs_python-0.7.2/tests/ph3_rank4.rs +53 -0
  229. gfn1_rs_python-0.7.2/tests/phonon.rs +102 -0
  230. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/physical_consistency.rs +134 -58
  231. gfn1_rs_python-0.7.2/tests/profiling/profile_contracted_fc3.rs +113 -0
  232. {gfn1_rs_python-0.5.0/examples → gfn1_rs_python-0.7.2/tests/profiling}/profile_fc4.rs +9 -15
  233. {gfn1_rs_python-0.5.0/examples → gfn1_rs_python-0.7.2/tests/profiling}/profile_magnetic.rs +2 -1
  234. {gfn1_rs_python-0.5.0/examples → gfn1_rs_python-0.7.2/tests/profiling}/profile_pbc.rs +2 -1
  235. {gfn1_rs_python-0.5.0/examples → gfn1_rs_python-0.7.2/tests/profiling}/profile_phase7.rs +3 -2
  236. gfn1_rs_python-0.7.2/tests/profiling/strain_skeleton.rs +67 -0
  237. gfn1_rs_python-0.7.2/tests/property_training.rs +457 -0
  238. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/python/test_ase_units.py +6 -3
  239. gfn1_rs_python-0.7.2/tests/python/test_cli_and_thermal.py +47 -0
  240. gfn1_rs_python-0.7.2/tests/python/test_cp_settings.py +51 -0
  241. gfn1_rs_python-0.7.2/tests/python/test_crystal_cli.py +142 -0
  242. gfn1_rs_python-0.7.2/tests/python/test_crystal_dfpt_api.py +30 -0
  243. gfn1_rs_python-0.7.2/tests/python/test_crystal_properties.py +285 -0
  244. gfn1_rs_python-0.7.2/tests/python/test_excited_hessian.py +52 -0
  245. gfn1_rs_python-0.7.2/tests/python/test_fragment_api.py +33 -0
  246. gfn1_rs_python-0.7.2/tests/python/test_magnetic_review.py +93 -0
  247. gfn1_rs_python-0.7.2/tests/python/test_ml_logging.py +93 -0
  248. gfn1_rs_python-0.7.2/tests/python/test_periodic_soc.py +44 -0
  249. gfn1_rs_python-0.7.2/tests/python/test_ph3_rank4.py +29 -0
  250. gfn1_rs_python-0.7.2/tests/python/test_resources.py +79 -0
  251. gfn1_rs_python-0.7.2/tests/python/test_stda_native.py +189 -0
  252. gfn1_rs_python-0.7.2/tests/python/test_user_ml_training.py +53 -0
  253. gfn1_rs_python-0.7.2/tests/real_crystal_phonons.rs +342 -0
  254. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/smearing.rs +42 -65
  255. gfn1_rs_python-0.7.2/tests/smoothness.rs +29 -0
  256. gfn1_rs_python-0.7.2/tests/soc.rs +186 -0
  257. gfn1_rs_python-0.7.2/tests/solvation.rs +283 -0
  258. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/tblite_parity.rs +70 -43
  259. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/td.rs +311 -26
  260. gfn1_rs_python-0.7.2/tests/third_derivative_contracted.rs +577 -0
  261. gfn1_rs_python-0.7.2/tests/training_cli.rs +163 -0
  262. gfn1_rs_python-0.7.2/tests/training_observables.rs +210 -0
  263. gfn1_rs_python-0.7.2/tests/validation/audit_assets.py +63 -0
  264. gfn1_rs_python-0.7.2/tests/validation/collect_derivative_audits.py +132 -0
  265. gfn1_rs_python-0.7.2/tests/validation/compare_backend_audits.py +163 -0
  266. {gfn1_rs_python-0.5.0/scripts → gfn1_rs_python-0.7.2/tests/validation}/compare_optimizations.py +2 -2
  267. gfn1_rs_python-0.7.2/tests/validation/crystal_dfpt_validation.rs +221 -0
  268. gfn1_rs_python-0.7.2/tests/validation/crystal_electromechanical_validation.rs +334 -0
  269. gfn1_rs_python-0.7.2/tests/validation/crystal_force_noise.rs +100 -0
  270. gfn1_rs_python-0.7.2/tests/validation/crystal_mechanical_validation.rs +334 -0
  271. gfn1_rs_python-0.7.2/tests/validation/ethylene_excited_optimization.py +223 -0
  272. gfn1_rs_python-0.7.2/tests/validation/ethylene_geometry.py +48 -0
  273. gfn1_rs_python-0.7.2/tests/validation/ethylene_negative_mode_restart.py +74 -0
  274. {gfn1_rs_python-0.5.0/examples → gfn1_rs_python-0.7.2/tests/validation}/lao_kinetic_grid_check.rs +1 -0
  275. {gfn1_rs_python-0.5.0/examples → gfn1_rs_python-0.7.2/tests/validation}/mag_cpscc_check.rs +1 -0
  276. {gfn1_rs_python-0.5.0/examples → gfn1_rs_python-0.7.2/tests/validation}/magnetizability_validation.rs +2 -1
  277. gfn1_rs_python-0.7.2/tests/validation/minimize_stda_trust_region.py +148 -0
  278. gfn1_rs_python-0.7.2/tests/validation/optimize_stda_crossing.py +98 -0
  279. gfn1_rs_python-0.7.2/tests/validation/pbc_scc_validation.rs +130 -0
  280. gfn1_rs_python-0.7.2/tests/validation/periodic_overlap_spectrum.rs +39 -0
  281. gfn1_rs_python-0.7.2/tests/validation/probe_stda_pes_degeneracy.py +86 -0
  282. gfn1_rs_python-0.7.2/tests/validation/real_crystal_cutoff_convergence.py +56 -0
  283. gfn1_rs_python-0.7.2/tests/validation/real_crystal_properties.py +189 -0
  284. gfn1_rs_python-0.7.2/tests/validation/real_crystal_relaxed_qha.py +112 -0
  285. gfn1_rs_python-0.7.2/tests/validation/search_stda_stationary.py +116 -0
  286. gfn1_rs_python-0.7.2/tests/validation/stda_pes_orbital_probe.rs +67 -0
  287. gfn1_rs_python-0.7.2/tests/validation/stda_seam_angular_response.py +125 -0
  288. gfn1_rs_python-0.7.2/tests/validation/td_ethylene_gradient_audit.py +69 -0
  289. gfn1_rs_python-0.7.2/tests/validation/tda_stda_analysis.rs +120 -0
  290. {gfn1_rs_python-0.5.0/examples → gfn1_rs_python-0.7.2/tests/validation}/third_deriv_diag.rs +11 -9
  291. gfn1_rs_python-0.7.2/tests/validation/validate_backend.rs +250 -0
  292. gfn1_rs_python-0.7.2/tests/validation/validate_stda_crossing.py +119 -0
  293. gfn1_rs_python-0.7.2/tests/validation/validate_stda_stationary.py +79 -0
  294. gfn1_rs_python-0.7.2/tests/validation/validate_vpt2.rs +184 -0
  295. gfn1_rs_python-0.7.2/tests/validation/verify_ethylene_optimized_points.py +76 -0
  296. gfn1_rs_python-0.7.2/tests/validation/verify_upstream_assets.py +84 -0
  297. gfn1_rs_python-0.7.2/tests/vpt2_molecules.rs +138 -0
  298. gfn1_rs_python-0.7.2/tests/water_cluster_model.rs +152 -0
  299. gfn1_rs_python-0.7.2/tests/xtb_gradient_audit.rs +232 -0
  300. gfn1_rs_python-0.7.2/tests/xtb_parity.rs +273 -0
  301. gfn1_rs_python-0.7.2/third_party/assets.json +844 -0
  302. gfn1_rs_python-0.7.2/third_party/basis_set_exchange/LICENSE +29 -0
  303. gfn1_rs_python-0.7.2/third_party/cod/LICENSE.txt +24 -0
  304. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/PROVENANCE.md +0 -2
  305. gfn1_rs_python-0.7.2/third_party/stda_xtb/.param_stda1.xtb +427 -0
  306. gfn1_rs_python-0.7.2/third_party/stda_xtb/.param_stda2.xtb +355 -0
  307. gfn1_rs_python-0.7.2/third_party/stda_xtb/README.md +17 -0
  308. gfn1_rs_python-0.7.2/third_party/stda_xtb/tables.json +1254 -0
  309. gfn1_rs_python-0.7.2/third_party/tblite/COPYING +674 -0
  310. gfn1_rs_python-0.7.2/third_party/tblite/COPYING.LESSER +165 -0
  311. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/tblite/PROVENANCE.md +5 -2
  312. gfn1_rs_python-0.7.2/third_party/upstream-byte-review.json +230 -0
  313. gfn1_rs_python-0.7.2/third_party/xtb/COPYING +674 -0
  314. gfn1_rs_python-0.7.2/third_party/xtb/COPYING.LESSER +165 -0
  315. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/xtb/PROVENANCE.md +1 -1
  316. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_acetone.fh +198 -0
  317. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_acetonitrile.fh +198 -0
  318. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_aniline.fh +198 -0
  319. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_benzaldehyde.fh +198 -0
  320. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_benzene.fh +198 -0
  321. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_ch2cl2.fh +198 -0
  322. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_chcl3.fh +198 -0
  323. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_cs2.fh +198 -0
  324. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_dioxane.fh +198 -0
  325. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_dmf.fh +198 -0
  326. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_dmso.fh +198 -0
  327. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_ethanol.fh +199 -0
  328. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_ether.fh +198 -0
  329. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_ethylacetate.fh +198 -0
  330. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_furane.fh +198 -0
  331. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_hexadecane.fh +198 -0
  332. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_hexane.fh +198 -0
  333. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_methanol.fh +198 -0
  334. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_nitromethane.fh +198 -0
  335. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_octanol.fh +199 -0
  336. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_phenol.fh +198 -0
  337. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_thf.fh +198 -0
  338. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_toluene.fh +198 -0
  339. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_water.fh +198 -0
  340. gfn1_rs_python-0.7.2/third_party/xtb/include/param_alpb_woctanol.fh +198 -0
  341. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_acetone.fh +132 -0
  342. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_acetonitrile.fh +132 -0
  343. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_benzene.fh +132 -0
  344. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_ch2cl2.fh +132 -0
  345. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_chcl3.fh +132 -0
  346. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_cs2.fh +132 -0
  347. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_dmf.fh +66 -0
  348. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_dmso.fh +132 -0
  349. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_ether.fh +132 -0
  350. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_h2o.fh +132 -0
  351. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_methanol.fh +132 -0
  352. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_nhexan.fh +66 -0
  353. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_thf.fh +132 -0
  354. gfn1_rs_python-0.7.2/third_party/xtb/include/param_gbsa_toluene.fh +132 -0
  355. gfn1_rs_python-0.7.2/third_party/xtb/src/mctc/convert.f90 +115 -0
  356. gfn1_rs_python-0.7.2/third_party/xtb/src/param/vdwradd3.f90 +99 -0
  357. gfn1_rs_python-0.7.2/third_party/xtb/src/solv/born.f90 +380 -0
  358. gfn1_rs_python-0.7.2/third_party/xtb/src/solv/cm5.f90 +133 -0
  359. gfn1_rs_python-0.7.2/third_party/xtb/src/solv/gbsa.f90 +1156 -0
  360. gfn1_rs_python-0.7.2/third_party/xtb/src/solv/kernel.f90 +763 -0
  361. gfn1_rs_python-0.7.2/third_party/xtb/src/solv/lebedev.f90 +5080 -0
  362. gfn1_rs_python-0.7.2/third_party/xtb/src/solv/model.f90 +740 -0
  363. gfn1_rs_python-0.7.2/third_party/xtb/src/solv/sasa.f90 +195 -0
  364. gfn1_rs_python-0.7.2/third_party/xtb/src/solv/state.f90 +88 -0
  365. gfn1_rs_python-0.5.0/Cargo.toml +0 -74
  366. gfn1_rs_python-0.5.0/THIRD_PARTY_NOTICES.md +0 -95
  367. gfn1_rs_python-0.5.0/docs/README.md +0 -22
  368. gfn1_rs_python-0.5.0/docs/parameters.md +0 -145
  369. gfn1_rs_python-0.5.0/src/bin/gfn1_rs.rs +0 -1377
  370. gfn1_rs_python-0.5.0/src/hessian/tests.rs +0 -1419
  371. gfn1_rs_python-0.5.0/src/hessian.rs +0 -3255
  372. gfn1_rs_python-0.5.0/src/third_derivative/tests.rs +0 -6961
  373. gfn1_rs_python-0.5.0/src/third_derivative.rs +0 -8662
  374. gfn1_rs_python-0.5.0/src/vibrational.rs +0 -129
  375. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/LICENSE +0 -0
  376. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/ammonia.xyz +0 -0
  377. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/bromoethanol.xyz +0 -0
  378. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/diamond.xyz +0 -0
  379. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/diamond222.xyz +0 -0
  380. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/dppf_pdcl2.xyz +0 -0
  381. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/h2.engrad +0 -0
  382. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/h2.xyz +0 -0
  383. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/methane.xyz +0 -0
  384. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/ni_co4.xyz +0 -0
  385. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/water.xyz +0 -0
  386. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/water100.xyz +0 -0
  387. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/water48.xyz +0 -0
  388. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/examples/water_opt.xyz +0 -0
  389. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/python/gfn1_rs/torch_interop.py +0 -0
  390. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/scripts/optimize.py +0 -0
  391. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/scripts/run_mgo_kpoint_md.py +0 -0
  392. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/coordination.rs +0 -0
  393. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/coulomb.rs +0 -0
  394. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/cphf.rs +0 -0
  395. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/d4_reference.rs +0 -0
  396. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/error.rs +0 -0
  397. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/field.rs +0 -0
  398. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/hamiltonian.rs +0 -0
  399. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/integrals_second_derivatives.rs +0 -0
  400. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/integrals_third_derivatives.rs +0 -0
  401. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/jets.rs +0 -0
  402. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/math.rs +0 -0
  403. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/model.rs +0 -0
  404. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/nmr.rs +0 -0
  405. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/optimizer.rs +0 -0
  406. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pairlist.rs +0 -0
  407. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/bloch.rs +0 -0
  408. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/ewald.rs +0 -0
  409. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/ewald_multipole.rs +0 -0
  410. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/gruneisen.rs +0 -0
  411. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/kpoints.rs +0 -0
  412. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/pbc/third_derivative.rs +0 -0
  413. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/profile.rs +0 -0
  414. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/properties.rs +0 -0
  415. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/response/mod.rs +0 -0
  416. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/secondary_bases.rs +0 -0
  417. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/sto.rs +0 -0
  418. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/src/system.rs +0 -0
  419. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/d4.rs +0 -0
  420. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/field.rs +0 -0
  421. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/fourth_derivative_nocap.rs +0 -0
  422. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/gradient_fd_probe.rs +0 -0
  423. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/hessian.rs +0 -0
  424. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/kpoint_hessian_repro.rs +0 -0
  425. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/nonpbc_smoke.rs +0 -0
  426. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/optimizer.rs +0 -0
  427. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/param_deriv.rs +0 -0
  428. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/pbc_finite_t.rs +0 -0
  429. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/pbc_integration.rs +0 -0
  430. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/pbc_polarization.rs +0 -0
  431. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/properties.rs +0 -0
  432. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/python/test_v050_derivatives.py +0 -0
  433. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/scf_accelerators.rs +0 -0
  434. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/tests/third_derivative.rs +0 -0
  435. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/CITATION.bib +0 -0
  436. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/COPYING +0 -0
  437. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/COPYING.LESSER +0 -0
  438. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/assets/parameters.toml +0 -0
  439. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/src/dftd4/data/hardness.f90 +0 -0
  440. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/src/dftd4/data/r4r2.f90 +0 -0
  441. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/src/dftd4/data/wfpair.f90 +0 -0
  442. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/src/dftd4/data/zeff.f90 +0 -0
  443. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/src/dftd4/reference.f90 +0 -0
  444. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/dftd4/src/dftd4/reference.inc +0 -0
  445. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/simple-dftd3/COPYING +0 -0
  446. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/simple-dftd3/COPYING.LESSER +0 -0
  447. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/simple-dftd3/src/dftd3/data/r4r2.f90 +0 -0
  448. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/simple-dftd3/src/dftd3/reference.f90 +0 -0
  449. {gfn1_rs_python-0.5.0/third_party/xtb → gfn1_rs_python-0.7.2/third_party/stda_xtb}/COPYING +0 -0
  450. {gfn1_rs_python-0.5.0/third_party/xtb → gfn1_rs_python-0.7.2/third_party/stda_xtb}/COPYING.LESSER +0 -0
  451. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/tblite/spin.f90 +0 -0
  452. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/xtb/param_gfn1-si-xtb.txt +0 -0
  453. {gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/third_party/xtb/param_gfn1-xtb.txt +0 -0
gfn1_rs_python-0.7.2/CHANGELOG.md ADDED
@@ -0,0 +1,164 @@
1
+ # Changelog
2
+
3
+ ## v0.7.2
4
+
5
+ - Differentiate molecular TDA and RPA with fractional occupations and degenerate
6
+ orbitals using block Fock and canonical occupation matrices.
7
+ - Add RPA manifold derivatives and a rotation-invariant finite-temperature sTDA
8
+ ensemble model with analytic gradients and Hessians.
9
+ - Apply directional TD derivatives directly to selected eigenvectors and
10
+ bound parallel Hessian work by the calculation's workspace budget.
11
+ - Transport near-degenerate orbitals together in thermal TDA/RPA gradients and
12
+ Hessians to reduce cancellation in their nuclear response.
13
+ - Use stationary variational molecular FC3/FC4 and bounded packed Cartesian
14
+ polarization where applicable. Stream CLI tensor components from packed storage.
15
+ - Add optional file-backed FC3 and FC4 output in CLI, Rust, Python native and
16
+ ASE. File-backed FC4 supports Cartesian sizes beyond the expanded-output cap.
17
+
18
+ ## v0.7.1
19
+
20
+ - Default to analytic TDA gradients across the CLI, Rust selector, Python
21
+ native and ASE. Report degenerate roots in all interfaces and provide separately
22
+ selected gradients and Hessians of the mean TDA surface.
23
+ - Add fractional-occupation molecular and Γ-point TDA, molecular full-TD RPA
24
+ spectra and analytic nuclear derivatives through second order, and optical
25
+ periodic TD-DFPT excitation energies with optional explicit SOC.
26
+ - Add analytic ALPB/GBSA Hessians, FC3 and FC4 for molecular canonical free
27
+ energies, including solvated PES-only VPT2.
28
+ - Print cubic and quartic tensor components directly. Expose the periodic DFPT
29
+ Hessian, molecular excited Hessians, magnetic tensors, chiroptical,
30
+ electromechanical, vibrational and fragment properties in the shared CLI.
31
+ - List embedded ML-xTB weights, including the water-cluster model and its
32
+ canonical identifier.
33
+
34
+ ## v0.7.0
35
+
36
+ - Organize the Rust/native/ASE/CLI API entry map, units, compatibility spellings
37
+ and supported domains. Exclude one-off recording/report/capture helpers from
38
+ source packages while retaining reusable physical audits and measured data.
39
+ - Wire 21 crystal calculation/postprocessing operations to the shared Rust/pip
40
+ `gfn1-rs properties` CLI, with strict units/conditions, result references,
41
+ user-weight identity and nonzero exits for failed/nonconverged tasks. Add a
42
+ Rust/native/ASE/CLI coverage table and executed request examples.
43
+ - Execute twenty property families on attributed diamond, ZnS, SiC and NaCl
44
+ CIF descendants. Retain source/model geometry changes, metallic-Berry and
45
+ overlap-cutoff failures, and both sparse and full 2x2x2 diamond QHA records.
46
+ - Extend original-surface sTDA diagnostics with 48 branching-plane samples,
47
+ angular derivative checks and six unconstrained exact-Hessian trust-region
48
+ searches. Preserve their nonconvergence and the measured direction-dependent
49
+ projector limit; no unvalidated smoothing model replaces original sTDA.
50
+
51
+ - Add adaptive periodic SCC with canonical finite-temperature analytic charge
52
+ Newton steps, residual backtracking, actual-work diagnostics and working
53
+ explicit Broyden/CDIIS/linear/Newton selections. Resolve cold LiF convergence
54
+ without changing its temperature, Hamiltonian or convergence thresholds.
55
+ - Improve periodic atomic/cell relaxation with accepted-state SCC guesses,
56
+ replication-scaled strain coordinates, origin-independent atomic step limits
57
+ and bounded geometry caches. Add EOS and analytic material elasticity,
58
+ internal-strain response, compliance, moduli and sound speeds.
59
+ - Add analytic structural-ML Born charges, proper piezoelectricity, electronic
60
+ dielectric response and coupled relaxed-ion properties, with explicit
61
+ stationarity/stability guards, IR oscillator strengths and LO–TO corrections.
62
+ - Add commensurate phonon mesh/DOS and harmonic thermodynamics, volume-sampled
63
+ QHA, electronic bands/DOS, and full Rust/native/ASE guides and crystal results.
64
+ - Add user-model property-objective fine-tuning with explicit physical
65
+ conditions, weighted component masks/scales, held-out validation and saved
66
+ model identity. General objectives use explicitly named parameter differences
67
+ around analytic physical backends; existing molecular E/F objectives reuse
68
+ analytic model-parameter gradients when admitted.
69
+ - Find and independently audit unconstrained force-zero stationary points on
70
+ the original signed sTDA composite surface. Classify their negative internal
71
+ Hessian modes as saddles; subsequent downhill searches still approach the
72
+ frontier-degeneracy model singularity rather than a verified smooth minimum.
73
+
74
+ - Support smearing through all standard molecular FC3/FC4 and periodic Γ/k-mesh
75
+ FC3 APIs, including exact fractional degeneracy. Preserve canonical analytic
76
+ free-energy response and correct omitted periodic CN/SCC reference chains.
77
+ - Add scoped CPU worker counts and checked workspace budgets through Rust,
78
+ both CLIs, Python native and ASE, with configuration logging.
79
+ - Add scoped absolute/relative CP residual tolerances and iterative limits
80
+ through all interfaces, with explicit direct/iterative residual checks.
81
+ - Pass local parallelism directly to Faer eigensolvers and LU solves, fixing
82
+ recursive worker-pool entry and the resulting higher-derivative stack overflow.
83
+ - Explicitly include upstream hidden sTDA parameter files in Cargo source
84
+ packages, exclude generated Python bytecode from wheels, and verify a build
85
+ from the extracted Cargo archive.
86
+ - Mix complete spin densities for +U/CAMM feedback, conserving the requested
87
+ electronic temperature and resolving the combined CAMM/linear-response-U
88
+ convergence failure. Check the analytic gradient against all Cartesian
89
+ components of reconverged finite differences at 300 K.
90
+ - Add analytic molecular TD-GFN1/sTDA excited-state Hessians through Rust,
91
+ native Python and ASE, including complete CI eigenvector response. Follow
92
+ signed nondegenerate sTDA CI branches across zero without silently relabelling
93
+ filtered roots, and report reference-instability diagnostics explicitly.
94
+ - Diagnose the native sTDA frontier-degeneracy PES limit. Retain the unresolved
95
+ ordinary signed-sheet minimum explicitly and add a separately defined
96
+ uncoupled upper-envelope crossing optimization with all-component audits.
97
+ - Use the supplied prototype ZIP as the development base, preserving its edits.
98
+ - Share the Rust calculation and training drivers with Python console scripts.
99
+ Command names are `gfn1-rs` and `gfn1-rs-train` for both Cargo and pip installs.
100
+ - Route positive-temperature Python FC3/FC4 calls to analytic free-energy
101
+ response. Add a quadratic-cost finite-temperature cubic vector contraction and
102
+ a molecular `--fourth-derivative` CLI option.
103
+ - Support exactly degenerate fractional occupations in the third density
104
+ response used by finite-temperature analytic molecular FC4.
105
+ - Implement independent native Rust sTDA-xTB with its dedicated VTB/xTB
106
+ orbitals, sourced parameters, configuration selection and dipole integrals.
107
+ Add analytic excitation gradients and an explicitly named composite
108
+ GFN1-free-energy plus sTDA-excitation total gradient.
109
+ - Remove the official-program driver API and executable-path options from
110
+ Rust, Python and the CLI. Official sources are cited and used only for
111
+ independent offline validation fixtures.
112
+ - Preserve legacy TD-GFN1 TDA calls and add an optional AO length-gauge
113
+ transition dipole. Document actual native TDA/sTDA spectra with identical
114
+ geometries, charge, spin and 300 K electronic temperature.
115
+ - Repair TDA fractional-occupation admission: molecular, Gamma and k-point
116
+ paths reject unsupported thermal fillings before generic CP pair building
117
+ can introduce unweighted intravalence transitions. Keep gapped 300 K spectra
118
+ and analytic gradients unchanged; add whole-energy derivative regressions.
119
+ - Add embedded FMO2/FMO3, covalent hybrid-orbital-projection boundaries and
120
+ overlapping density-matrix divide-and-conquer, with molecular/periodic
121
+ analytic forces and Gamma-periodic analytic stress. Bound local allocation
122
+ and reuse the embedding response factorization.
123
+ - Review magnetic SCC stationarity and input validation; cache the unchanged
124
+ overlap orthogonalization per SCC solve. Verify magnetic forces, all tensor
125
+ components and mixed-energy Cotton–Mouton differences. Clarify the static
126
+ MCD and common-gauge-origin NMR model boundaries.
127
+ - Add complete Rust, native Python and ASE guides for SOC/DFPT, FMO/DC and
128
+ user ML training, weight loading and explicit source/hash logging.
129
+ - Report 300 K DFPT results for C, Si, SiC, LiF, NaCl and MgO with all 432
130
+ Hessian entries checked, actual imaginary modes and convergence conditions.
131
+ Add a compatible explicit Gamma-centred Python/ASE Hessian sampling option.
132
+ - Reconstruct and verify the inherited secondary-basis subsets against BSE
133
+ and the original GFN1 hydrogen construction; preserve their numerical bodies
134
+ and correct the provenance/license descriptions.
135
+ - Move developer diagnostics, numerical validation and profiling drivers out
136
+ of `examples/` into `tests/validation/` and `tests/profiling/`, with explicit
137
+ Cargo test targets and updated reproduction commands.
138
+
139
+ ## v0.6.0
140
+
141
+ - Add molecular GFN1 ALPB/GBSA, explicit-parameter physical-spinor SOC, periodic
142
+ SOC/ML response, commensurate-supercell phonons and PES-only VPT2.
143
+ - Add independent embedded H2/water reference models, a separate training CLI,
144
+ observable training and JSONL operational logs.
145
+ - Repair high-rank PH3 convergence at unchanged zero electronic temperature.
146
+ - Validate implemented nuclear derivatives with exhaustive Cartesian component
147
+ differences, and real molecular VPT2 and static Cotton–Mouton energy checks.
148
+ - Update `private-gemm-x86` to a non-yanked version and resolve the validated
149
+ Python dependency/fixture warnings.
150
+
151
+ ## v0.5.1 inherited baseline
152
+
153
+ The supplied project originated from this version. It already contained the
154
+ molecular/periodic GFN1 engine, analytic derivative infrastructure, spectroscopy,
155
+ magnetic M0/M1 models, optimization and Python/ASE interfaces. No separate
156
+ v0.5.1 commit history was supplied, so patch-level changes are not reconstructed.
157
+
158
+ ## v0.5.0 (documented source milestones)
159
+
160
+ - Add analytic molecular quartic force constants and remove the directional
161
+ quartic degree-of-freedom cap.
162
+ - Add periodic analytic cubic response at Gamma and k meshes.
163
+ - Deduplicate polarization directions and share reference data when expanding
164
+ symmetric higher-derivative tensors.
{gfn1_rs_python-0.5.0 → gfn1_rs_python-0.7.2}/Cargo.lock RENAMED
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33
33
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34
34
  checksum = "b4388bee8683e3d04af747c73422af53102d2bd24d9eadb6cbc100baef4b43f8"
35
35
 
36
+ [[package]]
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+ dependencies = [
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+ "generic-array",
43
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44
+
36
45
  [[package]]
37
46
  name = "bytemuck"
38
47
  version = "1.25.0"
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84
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85
  checksum = "9330f8b2ff13f34540b44e946ef35111825727b38d33286ef986142615121801"
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86
 
87
+ [[package]]
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+ name = "cpufeatures"
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+ version = "0.2.17"
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+ source = "registry+https://github.com/rust-lang/crates.io-index"
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+ dependencies = [
93
+ "libc",
94
+ ]
95
+
78
96
  [[package]]
79
97
  name = "crossbeam"
80
98
  version = "0.8.4"
@@ -137,12 +155,32 @@ version = "0.2.4"
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155
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156
  checksum = "460fbee9c2c2f33933d720630a6a0bac33ba7053db5344fac858d4b8952d77d5"
139
157
 
158
+ [[package]]
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+ name = "crypto-common"
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+ source = "registry+https://github.com/rust-lang/crates.io-index"
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164
+ "generic-array",
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166
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167
+
140
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  [[package]]
141
169
  name = "defer"
142
170
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171
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144
172
  checksum = "930c7171c8df9fb1782bdf9b918ed9ed2d33d1d22300abb754f9085bc48bf8e8"
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173
 
174
+ [[package]]
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+ dependencies = [
180
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181
+ "crypto-common",
182
+ ]
183
+
146
184
  [[package]]
147
185
  name = "dyn-stack"
148
186
  version = "0.13.2"
@@ -418,14 +456,27 @@ dependencies = [
418
456
  "windows-result",
419
457
  ]
420
458
 
459
+ [[package]]
460
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461
+ version = "0.14.7"
462
+ source = "registry+https://github.com/rust-lang/crates.io-index"
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+ dependencies = [
465
+ "typenum",
466
+ "version_check",
467
+ ]
468
+
421
469
  [[package]]
422
470
  name = "gfn1-rs"
423
- version = "0.5.0"
471
+ version = "0.7.2"
424
472
  dependencies = [
425
473
  "faer",
426
474
  "libm",
427
475
  "pyo3",
428
476
  "rayon",
477
+ "serde",
478
+ "serde_json",
479
+ "sha2",
429
480
  ]
430
481
 
431
482
  [[package]]
@@ -473,6 +524,12 @@ dependencies = [
473
524
  "syn 1.0.109",
474
525
  ]
475
526
 
527
+ [[package]]
528
+ name = "itoa"
529
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530
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532
+
476
533
  [[package]]
477
534
  name = "lazy_static"
478
535
  version = "1.5.0"
@@ -669,9 +726,9 @@ checksum = "c33a9471896f1c69cecef8d20cbe2f7accd12527ce60845ff44c153bb2a21b49"
669
726
 
670
727
  [[package]]
671
728
  name = "private-gemm-x86"
672
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729
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673
730
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675
732
  dependencies = [
676
733
  "crossbeam",
677
734
  "defer",
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878
935
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936
  checksum = "1bc711410fbe7399f390ca1c3b60ad0f53f80e95c5eb935e52268a0e2cd49acc"
880
937
 
938
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939
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943
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944
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945
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946
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947
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948
+ [[package]]
949
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950
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954
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955
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956
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957
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963
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964
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966
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968
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970
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974
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975
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976
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977
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979
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980
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981
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982
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983
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987
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988
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989
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990
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991
+
881
992
  [[package]]
882
993
  name = "sharded-slab"
883
994
  version = "0.1.7"
@@ -934,6 +1045,17 @@ dependencies = [
934
1045
  "unicode-ident",
935
1046
  ]
936
1047
 
1048
+ [[package]]
1049
+ name = "syn"
1050
+ version = "3.0.9"
1051
+ source = "registry+https://github.com/rust-lang/crates.io-index"
1052
+ checksum = "d78c8dee4c7bf0e14673097256fed6142ce9d3b85a408189d07482442145823b"
1053
+ dependencies = [
1054
+ "proc-macro2",
1055
+ "quote",
1056
+ "unicode-ident",
1057
+ ]
1058
+
937
1059
  [[package]]
938
1060
  name = "sysctl"
939
1061
  version = "0.6.0"
@@ -1032,6 +1154,12 @@ dependencies = [
1032
1154
  "tracing-log",
1033
1155
  ]
1034
1156
 
1157
+ [[package]]
1158
+ name = "typenum"
1159
+ version = "1.20.1"
1160
+ source = "registry+https://github.com/rust-lang/crates.io-index"
1161
+ checksum = "b6f5e870be6c3b371b77fe0ee0bafb859fa4964b4404c27de1d380043c4dda20"
1162
+
1035
1163
  [[package]]
1036
1164
  name = "unicode-ident"
1037
1165
  version = "1.0.24"
@@ -1175,3 +1303,9 @@ dependencies = [
1175
1303
  "quote",
1176
1304
  "syn 2.0.118",
1177
1305
  ]
1306
+
1307
+ [[package]]
1308
+ name = "zmij"
1309
+ version = "1.0.23"
1310
+ source = "registry+https://github.com/rust-lang/crates.io-index"
1311
+ checksum = "29666d0abbfad1e3dc4dcf6144730dd3a3ab225bbbdac83319345b1b44ccfc1b"