mlmm-toolkit 0.2.2.dev0__py3-none-any.whl

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Files changed (372) hide show
  1. hessian_ff/__init__.py +50 -0
  2. hessian_ff/analytical_hessian.py +609 -0
  3. hessian_ff/constants.py +46 -0
  4. hessian_ff/forcefield.py +339 -0
  5. hessian_ff/loaders.py +608 -0
  6. hessian_ff/native/Makefile +8 -0
  7. hessian_ff/native/__init__.py +28 -0
  8. hessian_ff/native/analytical_hessian.py +88 -0
  9. hessian_ff/native/analytical_hessian_ext.cpp +258 -0
  10. hessian_ff/native/bonded.py +82 -0
  11. hessian_ff/native/bonded_ext.cpp +640 -0
  12. hessian_ff/native/loader.py +349 -0
  13. hessian_ff/native/nonbonded.py +118 -0
  14. hessian_ff/native/nonbonded_ext.cpp +1150 -0
  15. hessian_ff/prmtop_parmed.py +23 -0
  16. hessian_ff/system.py +107 -0
  17. hessian_ff/terms/__init__.py +14 -0
  18. hessian_ff/terms/angle.py +73 -0
  19. hessian_ff/terms/bond.py +44 -0
  20. hessian_ff/terms/cmap.py +406 -0
  21. hessian_ff/terms/dihedral.py +141 -0
  22. hessian_ff/terms/nonbonded.py +209 -0
  23. hessian_ff/tests/__init__.py +0 -0
  24. hessian_ff/tests/conftest.py +75 -0
  25. hessian_ff/tests/data/small/complex.parm7 +1346 -0
  26. hessian_ff/tests/data/small/complex.pdb +125 -0
  27. hessian_ff/tests/data/small/complex.rst7 +63 -0
  28. hessian_ff/tests/test_coords_input.py +44 -0
  29. hessian_ff/tests/test_energy_force.py +49 -0
  30. hessian_ff/tests/test_hessian.py +137 -0
  31. hessian_ff/tests/test_smoke.py +18 -0
  32. hessian_ff/tests/test_validation.py +40 -0
  33. hessian_ff/workflows.py +889 -0
  34. mlmm/__init__.py +36 -0
  35. mlmm/__main__.py +7 -0
  36. mlmm/_version.py +34 -0
  37. mlmm/add_elem_info.py +374 -0
  38. mlmm/advanced_help.py +91 -0
  39. mlmm/align_freeze_atoms.py +601 -0
  40. mlmm/all.py +3535 -0
  41. mlmm/bond_changes.py +231 -0
  42. mlmm/bool_compat.py +223 -0
  43. mlmm/cli.py +574 -0
  44. mlmm/cli_utils.py +166 -0
  45. mlmm/default_group.py +337 -0
  46. mlmm/defaults.py +467 -0
  47. mlmm/define_layer.py +526 -0
  48. mlmm/dft.py +1041 -0
  49. mlmm/energy_diagram.py +253 -0
  50. mlmm/extract.py +2213 -0
  51. mlmm/fix_altloc.py +464 -0
  52. mlmm/freq.py +1406 -0
  53. mlmm/harmonic_constraints.py +140 -0
  54. mlmm/hessian_cache.py +44 -0
  55. mlmm/hessian_calc.py +174 -0
  56. mlmm/irc.py +638 -0
  57. mlmm/mlmm_calc.py +2262 -0
  58. mlmm/mm_parm.py +945 -0
  59. mlmm/oniom_export.py +1983 -0
  60. mlmm/oniom_import.py +457 -0
  61. mlmm/opt.py +1742 -0
  62. mlmm/path_opt.py +1353 -0
  63. mlmm/path_search.py +2299 -0
  64. mlmm/preflight.py +88 -0
  65. mlmm/py.typed +1 -0
  66. mlmm/pysis_runner.py +45 -0
  67. mlmm/scan.py +1047 -0
  68. mlmm/scan2d.py +1226 -0
  69. mlmm/scan3d.py +1265 -0
  70. mlmm/scan_common.py +184 -0
  71. mlmm/summary_log.py +736 -0
  72. mlmm/trj2fig.py +448 -0
  73. mlmm/tsopt.py +2871 -0
  74. mlmm/utils.py +2309 -0
  75. mlmm/xtb_embedcharge_correction.py +475 -0
  76. mlmm_toolkit-0.2.2.dev0.dist-info/METADATA +1159 -0
  77. mlmm_toolkit-0.2.2.dev0.dist-info/RECORD +372 -0
  78. mlmm_toolkit-0.2.2.dev0.dist-info/WHEEL +5 -0
  79. mlmm_toolkit-0.2.2.dev0.dist-info/entry_points.txt +2 -0
  80. mlmm_toolkit-0.2.2.dev0.dist-info/licenses/LICENSE +674 -0
  81. mlmm_toolkit-0.2.2.dev0.dist-info/top_level.txt +4 -0
  82. pysisyphus/Geometry.py +1667 -0
  83. pysisyphus/LICENSE +674 -0
  84. pysisyphus/TableFormatter.py +63 -0
  85. pysisyphus/TablePrinter.py +74 -0
  86. pysisyphus/__init__.py +12 -0
  87. pysisyphus/calculators/AFIR.py +452 -0
  88. pysisyphus/calculators/AnaPot.py +20 -0
  89. pysisyphus/calculators/AnaPot2.py +48 -0
  90. pysisyphus/calculators/AnaPot3.py +12 -0
  91. pysisyphus/calculators/AnaPot4.py +20 -0
  92. pysisyphus/calculators/AnaPotBase.py +337 -0
  93. pysisyphus/calculators/AnaPotCBM.py +25 -0
  94. pysisyphus/calculators/AtomAtomTransTorque.py +154 -0
  95. pysisyphus/calculators/CFOUR.py +250 -0
  96. pysisyphus/calculators/Calculator.py +844 -0
  97. pysisyphus/calculators/CerjanMiller.py +24 -0
  98. pysisyphus/calculators/Composite.py +123 -0
  99. pysisyphus/calculators/ConicalIntersection.py +171 -0
  100. pysisyphus/calculators/DFTBp.py +430 -0
  101. pysisyphus/calculators/DFTD3.py +66 -0
  102. pysisyphus/calculators/DFTD4.py +84 -0
  103. pysisyphus/calculators/Dalton.py +61 -0
  104. pysisyphus/calculators/Dimer.py +681 -0
  105. pysisyphus/calculators/Dummy.py +20 -0
  106. pysisyphus/calculators/EGO.py +76 -0
  107. pysisyphus/calculators/EnergyMin.py +224 -0
  108. pysisyphus/calculators/ExternalPotential.py +264 -0
  109. pysisyphus/calculators/FakeASE.py +35 -0
  110. pysisyphus/calculators/FourWellAnaPot.py +28 -0
  111. pysisyphus/calculators/FreeEndNEBPot.py +39 -0
  112. pysisyphus/calculators/Gaussian09.py +18 -0
  113. pysisyphus/calculators/Gaussian16.py +726 -0
  114. pysisyphus/calculators/HardSphere.py +159 -0
  115. pysisyphus/calculators/IDPPCalculator.py +49 -0
  116. pysisyphus/calculators/IPIClient.py +133 -0
  117. pysisyphus/calculators/IPIServer.py +234 -0
  118. pysisyphus/calculators/LEPSBase.py +24 -0
  119. pysisyphus/calculators/LEPSExpr.py +139 -0
  120. pysisyphus/calculators/LennardJones.py +80 -0
  121. pysisyphus/calculators/MOPAC.py +219 -0
  122. pysisyphus/calculators/MullerBrownSympyPot.py +51 -0
  123. pysisyphus/calculators/MultiCalc.py +85 -0
  124. pysisyphus/calculators/NFK.py +45 -0
  125. pysisyphus/calculators/OBabel.py +87 -0
  126. pysisyphus/calculators/ONIOMv2.py +1129 -0
  127. pysisyphus/calculators/ORCA.py +893 -0
  128. pysisyphus/calculators/ORCA5.py +6 -0
  129. pysisyphus/calculators/OpenMM.py +88 -0
  130. pysisyphus/calculators/OpenMolcas.py +281 -0
  131. pysisyphus/calculators/OverlapCalculator.py +908 -0
  132. pysisyphus/calculators/Psi4.py +218 -0
  133. pysisyphus/calculators/PyPsi4.py +37 -0
  134. pysisyphus/calculators/PySCF.py +341 -0
  135. pysisyphus/calculators/PyXTB.py +73 -0
  136. pysisyphus/calculators/QCEngine.py +106 -0
  137. pysisyphus/calculators/Rastrigin.py +22 -0
  138. pysisyphus/calculators/Remote.py +76 -0
  139. pysisyphus/calculators/Rosenbrock.py +15 -0
  140. pysisyphus/calculators/SocketCalc.py +97 -0
  141. pysisyphus/calculators/TIP3P.py +111 -0
  142. pysisyphus/calculators/TransTorque.py +161 -0
  143. pysisyphus/calculators/Turbomole.py +965 -0
  144. pysisyphus/calculators/VRIPot.py +37 -0
  145. pysisyphus/calculators/WFOWrapper.py +333 -0
  146. pysisyphus/calculators/WFOWrapper2.py +341 -0
  147. pysisyphus/calculators/XTB.py +418 -0
  148. pysisyphus/calculators/__init__.py +81 -0
  149. pysisyphus/calculators/cosmo_data.py +139 -0
  150. pysisyphus/calculators/parser.py +150 -0
  151. pysisyphus/color.py +19 -0
  152. pysisyphus/config.py +133 -0
  153. pysisyphus/constants.py +65 -0
  154. pysisyphus/cos/AdaptiveNEB.py +230 -0
  155. pysisyphus/cos/ChainOfStates.py +725 -0
  156. pysisyphus/cos/FreeEndNEB.py +25 -0
  157. pysisyphus/cos/FreezingString.py +103 -0
  158. pysisyphus/cos/GrowingChainOfStates.py +71 -0
  159. pysisyphus/cos/GrowingNT.py +309 -0
  160. pysisyphus/cos/GrowingString.py +508 -0
  161. pysisyphus/cos/NEB.py +189 -0
  162. pysisyphus/cos/SimpleZTS.py +64 -0
  163. pysisyphus/cos/__init__.py +22 -0
  164. pysisyphus/cos/stiffness.py +199 -0
  165. pysisyphus/drivers/__init__.py +17 -0
  166. pysisyphus/drivers/afir.py +855 -0
  167. pysisyphus/drivers/barriers.py +271 -0
  168. pysisyphus/drivers/birkholz.py +138 -0
  169. pysisyphus/drivers/cluster.py +318 -0
  170. pysisyphus/drivers/diabatization.py +133 -0
  171. pysisyphus/drivers/merge.py +368 -0
  172. pysisyphus/drivers/merge_mol2.py +322 -0
  173. pysisyphus/drivers/opt.py +375 -0
  174. pysisyphus/drivers/perf.py +91 -0
  175. pysisyphus/drivers/pka.py +52 -0
  176. pysisyphus/drivers/precon_pos_rot.py +669 -0
  177. pysisyphus/drivers/rates.py +480 -0
  178. pysisyphus/drivers/replace.py +219 -0
  179. pysisyphus/drivers/scan.py +212 -0
  180. pysisyphus/drivers/spectrum.py +166 -0
  181. pysisyphus/drivers/thermo.py +31 -0
  182. pysisyphus/dynamics/Gaussian.py +103 -0
  183. pysisyphus/dynamics/__init__.py +20 -0
  184. pysisyphus/dynamics/colvars.py +136 -0
  185. pysisyphus/dynamics/driver.py +297 -0
  186. pysisyphus/dynamics/helpers.py +256 -0
  187. pysisyphus/dynamics/lincs.py +105 -0
  188. pysisyphus/dynamics/mdp.py +364 -0
  189. pysisyphus/dynamics/rattle.py +121 -0
  190. pysisyphus/dynamics/thermostats.py +128 -0
  191. pysisyphus/dynamics/wigner.py +266 -0
  192. pysisyphus/elem_data.py +3473 -0
  193. pysisyphus/exceptions.py +2 -0
  194. pysisyphus/filtertrj.py +69 -0
  195. pysisyphus/helpers.py +623 -0
  196. pysisyphus/helpers_pure.py +649 -0
  197. pysisyphus/init_logging.py +50 -0
  198. pysisyphus/intcoords/Bend.py +69 -0
  199. pysisyphus/intcoords/Bend2.py +25 -0
  200. pysisyphus/intcoords/BondedFragment.py +32 -0
  201. pysisyphus/intcoords/Cartesian.py +41 -0
  202. pysisyphus/intcoords/CartesianCoords.py +140 -0
  203. pysisyphus/intcoords/Coords.py +56 -0
  204. pysisyphus/intcoords/DLC.py +197 -0
  205. pysisyphus/intcoords/DistanceFunction.py +34 -0
  206. pysisyphus/intcoords/DummyImproper.py +70 -0
  207. pysisyphus/intcoords/DummyTorsion.py +72 -0
  208. pysisyphus/intcoords/LinearBend.py +105 -0
  209. pysisyphus/intcoords/LinearDisplacement.py +80 -0
  210. pysisyphus/intcoords/OutOfPlane.py +59 -0
  211. pysisyphus/intcoords/PrimTypes.py +286 -0
  212. pysisyphus/intcoords/Primitive.py +137 -0
  213. pysisyphus/intcoords/RedundantCoords.py +659 -0
  214. pysisyphus/intcoords/RobustTorsion.py +59 -0
  215. pysisyphus/intcoords/Rotation.py +147 -0
  216. pysisyphus/intcoords/Stretch.py +31 -0
  217. pysisyphus/intcoords/Torsion.py +101 -0
  218. pysisyphus/intcoords/Torsion2.py +25 -0
  219. pysisyphus/intcoords/Translation.py +45 -0
  220. pysisyphus/intcoords/__init__.py +61 -0
  221. pysisyphus/intcoords/augment_bonds.py +126 -0
  222. pysisyphus/intcoords/derivatives.py +10512 -0
  223. pysisyphus/intcoords/eval.py +80 -0
  224. pysisyphus/intcoords/exceptions.py +37 -0
  225. pysisyphus/intcoords/findiffs.py +48 -0
  226. pysisyphus/intcoords/generate_derivatives.py +414 -0
  227. pysisyphus/intcoords/helpers.py +235 -0
  228. pysisyphus/intcoords/logging_conf.py +10 -0
  229. pysisyphus/intcoords/mp_derivatives.py +10836 -0
  230. pysisyphus/intcoords/setup.py +962 -0
  231. pysisyphus/intcoords/setup_fast.py +176 -0
  232. pysisyphus/intcoords/update.py +272 -0
  233. pysisyphus/intcoords/valid.py +89 -0
  234. pysisyphus/interpolate/Geodesic.py +93 -0
  235. pysisyphus/interpolate/IDPP.py +55 -0
  236. pysisyphus/interpolate/Interpolator.py +116 -0
  237. pysisyphus/interpolate/LST.py +70 -0
  238. pysisyphus/interpolate/Redund.py +152 -0
  239. pysisyphus/interpolate/__init__.py +9 -0
  240. pysisyphus/interpolate/helpers.py +34 -0
  241. pysisyphus/io/__init__.py +22 -0
  242. pysisyphus/io/aomix.py +178 -0
  243. pysisyphus/io/cjson.py +24 -0
  244. pysisyphus/io/crd.py +101 -0
  245. pysisyphus/io/cube.py +220 -0
  246. pysisyphus/io/fchk.py +184 -0
  247. pysisyphus/io/hdf5.py +49 -0
  248. pysisyphus/io/hessian.py +72 -0
  249. pysisyphus/io/mol2.py +146 -0
  250. pysisyphus/io/molden.py +293 -0
  251. pysisyphus/io/orca.py +189 -0
  252. pysisyphus/io/pdb.py +269 -0
  253. pysisyphus/io/psf.py +79 -0
  254. pysisyphus/io/pubchem.py +31 -0
  255. pysisyphus/io/qcschema.py +34 -0
  256. pysisyphus/io/sdf.py +29 -0
  257. pysisyphus/io/xyz.py +61 -0
  258. pysisyphus/io/zmat.py +175 -0
  259. pysisyphus/irc/DWI.py +108 -0
  260. pysisyphus/irc/DampedVelocityVerlet.py +134 -0
  261. pysisyphus/irc/Euler.py +22 -0
  262. pysisyphus/irc/EulerPC.py +345 -0
  263. pysisyphus/irc/GonzalezSchlegel.py +187 -0
  264. pysisyphus/irc/IMKMod.py +164 -0
  265. pysisyphus/irc/IRC.py +878 -0
  266. pysisyphus/irc/IRCDummy.py +10 -0
  267. pysisyphus/irc/Instanton.py +307 -0
  268. pysisyphus/irc/LQA.py +53 -0
  269. pysisyphus/irc/ModeKill.py +136 -0
  270. pysisyphus/irc/ParamPlot.py +53 -0
  271. pysisyphus/irc/RK4.py +36 -0
  272. pysisyphus/irc/__init__.py +31 -0
  273. pysisyphus/irc/initial_displ.py +219 -0
  274. pysisyphus/linalg.py +411 -0
  275. pysisyphus/line_searches/Backtracking.py +88 -0
  276. pysisyphus/line_searches/HagerZhang.py +184 -0
  277. pysisyphus/line_searches/LineSearch.py +232 -0
  278. pysisyphus/line_searches/StrongWolfe.py +108 -0
  279. pysisyphus/line_searches/__init__.py +9 -0
  280. pysisyphus/line_searches/interpol.py +15 -0
  281. pysisyphus/modefollow/NormalMode.py +40 -0
  282. pysisyphus/modefollow/__init__.py +10 -0
  283. pysisyphus/modefollow/davidson.py +199 -0
  284. pysisyphus/modefollow/lanczos.py +95 -0
  285. pysisyphus/optimizers/BFGS.py +99 -0
  286. pysisyphus/optimizers/BacktrackingOptimizer.py +113 -0
  287. pysisyphus/optimizers/ConjugateGradient.py +98 -0
  288. pysisyphus/optimizers/CubicNewton.py +75 -0
  289. pysisyphus/optimizers/FIRE.py +113 -0
  290. pysisyphus/optimizers/HessianOptimizer.py +1176 -0
  291. pysisyphus/optimizers/LBFGS.py +228 -0
  292. pysisyphus/optimizers/LayerOpt.py +411 -0
  293. pysisyphus/optimizers/MicroOptimizer.py +169 -0
  294. pysisyphus/optimizers/NCOptimizer.py +90 -0
  295. pysisyphus/optimizers/Optimizer.py +1084 -0
  296. pysisyphus/optimizers/PreconLBFGS.py +260 -0
  297. pysisyphus/optimizers/PreconSteepestDescent.py +7 -0
  298. pysisyphus/optimizers/QuickMin.py +74 -0
  299. pysisyphus/optimizers/RFOptimizer.py +181 -0
  300. pysisyphus/optimizers/RSA.py +99 -0
  301. pysisyphus/optimizers/StabilizedQNMethod.py +248 -0
  302. pysisyphus/optimizers/SteepestDescent.py +23 -0
  303. pysisyphus/optimizers/StringOptimizer.py +173 -0
  304. pysisyphus/optimizers/__init__.py +41 -0
  305. pysisyphus/optimizers/closures.py +301 -0
  306. pysisyphus/optimizers/cls_map.py +58 -0
  307. pysisyphus/optimizers/exceptions.py +6 -0
  308. pysisyphus/optimizers/gdiis.py +280 -0
  309. pysisyphus/optimizers/guess_hessians.py +311 -0
  310. pysisyphus/optimizers/hessian_updates.py +355 -0
  311. pysisyphus/optimizers/poly_fit.py +285 -0
  312. pysisyphus/optimizers/precon.py +153 -0
  313. pysisyphus/optimizers/restrict_step.py +24 -0
  314. pysisyphus/pack.py +172 -0
  315. pysisyphus/peakdetect.py +948 -0
  316. pysisyphus/plot.py +1031 -0
  317. pysisyphus/run.py +2106 -0
  318. pysisyphus/socket_helper.py +74 -0
  319. pysisyphus/stocastic/FragmentKick.py +132 -0
  320. pysisyphus/stocastic/Kick.py +81 -0
  321. pysisyphus/stocastic/Pipeline.py +303 -0
  322. pysisyphus/stocastic/__init__.py +21 -0
  323. pysisyphus/stocastic/align.py +127 -0
  324. pysisyphus/testing.py +96 -0
  325. pysisyphus/thermo.py +156 -0
  326. pysisyphus/trj.py +824 -0
  327. pysisyphus/tsoptimizers/RSIRFOptimizer.py +56 -0
  328. pysisyphus/tsoptimizers/RSPRFOptimizer.py +182 -0
  329. pysisyphus/tsoptimizers/TRIM.py +59 -0
  330. pysisyphus/tsoptimizers/TSHessianOptimizer.py +463 -0
  331. pysisyphus/tsoptimizers/__init__.py +23 -0
  332. pysisyphus/wavefunction/Basis.py +239 -0
  333. pysisyphus/wavefunction/DIIS.py +76 -0
  334. pysisyphus/wavefunction/__init__.py +25 -0
  335. pysisyphus/wavefunction/build_ext.py +42 -0
  336. pysisyphus/wavefunction/cart2sph.py +190 -0
  337. pysisyphus/wavefunction/diabatization.py +304 -0
  338. pysisyphus/wavefunction/excited_states.py +435 -0
  339. pysisyphus/wavefunction/gen_ints.py +1811 -0
  340. pysisyphus/wavefunction/helpers.py +104 -0
  341. pysisyphus/wavefunction/ints/__init__.py +0 -0
  342. pysisyphus/wavefunction/ints/boys.py +193 -0
  343. pysisyphus/wavefunction/ints/boys_table_N_64_xasym_27.1_step_0.01.npy +0 -0
  344. pysisyphus/wavefunction/ints/cart_gto3d.py +176 -0
  345. pysisyphus/wavefunction/ints/coulomb3d.py +25928 -0
  346. pysisyphus/wavefunction/ints/diag_quadrupole3d.py +10036 -0
  347. pysisyphus/wavefunction/ints/dipole3d.py +8762 -0
  348. pysisyphus/wavefunction/ints/int2c2e3d.py +7198 -0
  349. pysisyphus/wavefunction/ints/int3c2e3d_sph.py +65040 -0
  350. pysisyphus/wavefunction/ints/kinetic3d.py +8240 -0
  351. pysisyphus/wavefunction/ints/ovlp3d.py +3777 -0
  352. pysisyphus/wavefunction/ints/quadrupole3d.py +15054 -0
  353. pysisyphus/wavefunction/ints/self_ovlp3d.py +198 -0
  354. pysisyphus/wavefunction/localization.py +458 -0
  355. pysisyphus/wavefunction/multipole.py +159 -0
  356. pysisyphus/wavefunction/normalization.py +36 -0
  357. pysisyphus/wavefunction/pop_analysis.py +134 -0
  358. pysisyphus/wavefunction/shells.py +1171 -0
  359. pysisyphus/wavefunction/wavefunction.py +504 -0
  360. pysisyphus/wrapper/__init__.py +11 -0
  361. pysisyphus/wrapper/exceptions.py +2 -0
  362. pysisyphus/wrapper/jmol.py +120 -0
  363. pysisyphus/wrapper/mwfn.py +169 -0
  364. pysisyphus/wrapper/packmol.py +71 -0
  365. pysisyphus/xyzloader.py +168 -0
  366. pysisyphus/yaml_mods.py +45 -0
  367. thermoanalysis/LICENSE +674 -0
  368. thermoanalysis/QCData.py +244 -0
  369. thermoanalysis/__init__.py +0 -0
  370. thermoanalysis/config.py +3 -0
  371. thermoanalysis/constants.py +20 -0
  372. thermoanalysis/thermo.py +1011 -0

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