hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

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Files changed (468) hide show
  1. hillclimber/__init__.py +41 -0
  2. hillclimber/actions.py +53 -0
  3. hillclimber/analysis.py +590 -0
  4. hillclimber/biases.py +293 -0
  5. hillclimber/calc.py +22 -0
  6. hillclimber/cvs.py +1070 -0
  7. hillclimber/interfaces.py +133 -0
  8. hillclimber/metadynamics.py +416 -0
  9. hillclimber/nodes.py +6 -0
  10. hillclimber/opes.py +359 -0
  11. hillclimber/pycv.py +362 -0
  12. hillclimber/selectors.py +230 -0
  13. hillclimber/virtual_atoms.py +341 -0
  14. hillclimber-0.1.6.dist-info/METADATA +325 -0
  15. hillclimber-0.1.6.dist-info/RECORD +468 -0
  16. hillclimber-0.1.6.dist-info/WHEEL +6 -0
  17. hillclimber-0.1.6.dist-info/entry_points.txt +8 -0
  18. hillclimber-0.1.6.dist-info/licenses/LICENSE +165 -0
  19. plumed/__init__.py +104 -0
  20. plumed/_lib/bin/plumed +0 -0
  21. plumed/_lib/bin/plumed-config +9 -0
  22. plumed/_lib/bin/plumed-patch +9 -0
  23. plumed/_lib/include/plumed/adjmat/AdjacencyMatrixBase.h +659 -0
  24. plumed/_lib/include/plumed/adjmat/ContactMatrix.h +59 -0
  25. plumed/_lib/include/plumed/asmjit/arch.h +228 -0
  26. plumed/_lib/include/plumed/asmjit/arm.h +43 -0
  27. plumed/_lib/include/plumed/asmjit/asmjit.h +69 -0
  28. plumed/_lib/include/plumed/asmjit/asmjit_apibegin.h +143 -0
  29. plumed/_lib/include/plumed/asmjit/asmjit_apiend.h +93 -0
  30. plumed/_lib/include/plumed/asmjit/asmjit_build.h +971 -0
  31. plumed/_lib/include/plumed/asmjit/assembler.h +183 -0
  32. plumed/_lib/include/plumed/asmjit/base.h +56 -0
  33. plumed/_lib/include/plumed/asmjit/codebuilder.h +944 -0
  34. plumed/_lib/include/plumed/asmjit/codecompiler.h +767 -0
  35. plumed/_lib/include/plumed/asmjit/codeemitter.h +528 -0
  36. plumed/_lib/include/plumed/asmjit/codeholder.h +777 -0
  37. plumed/_lib/include/plumed/asmjit/constpool.h +286 -0
  38. plumed/_lib/include/plumed/asmjit/cpuinfo.h +402 -0
  39. plumed/_lib/include/plumed/asmjit/func.h +1327 -0
  40. plumed/_lib/include/plumed/asmjit/globals.h +370 -0
  41. plumed/_lib/include/plumed/asmjit/inst.h +137 -0
  42. plumed/_lib/include/plumed/asmjit/logging.h +317 -0
  43. plumed/_lib/include/plumed/asmjit/misc_p.h +103 -0
  44. plumed/_lib/include/plumed/asmjit/moved_string.h +318 -0
  45. plumed/_lib/include/plumed/asmjit/operand.h +1599 -0
  46. plumed/_lib/include/plumed/asmjit/osutils.h +207 -0
  47. plumed/_lib/include/plumed/asmjit/regalloc_p.h +597 -0
  48. plumed/_lib/include/plumed/asmjit/runtime.h +227 -0
  49. plumed/_lib/include/plumed/asmjit/simdtypes.h +1104 -0
  50. plumed/_lib/include/plumed/asmjit/utils.h +1387 -0
  51. plumed/_lib/include/plumed/asmjit/vmem.h +183 -0
  52. plumed/_lib/include/plumed/asmjit/x86.h +45 -0
  53. plumed/_lib/include/plumed/asmjit/x86assembler.h +125 -0
  54. plumed/_lib/include/plumed/asmjit/x86builder.h +117 -0
  55. plumed/_lib/include/plumed/asmjit/x86compiler.h +322 -0
  56. plumed/_lib/include/plumed/asmjit/x86emitter.h +5149 -0
  57. plumed/_lib/include/plumed/asmjit/x86globals.h +535 -0
  58. plumed/_lib/include/plumed/asmjit/x86inst.h +2547 -0
  59. plumed/_lib/include/plumed/asmjit/x86instimpl_p.h +74 -0
  60. plumed/_lib/include/plumed/asmjit/x86internal_p.h +108 -0
  61. plumed/_lib/include/plumed/asmjit/x86logging_p.h +92 -0
  62. plumed/_lib/include/plumed/asmjit/x86misc.h +417 -0
  63. plumed/_lib/include/plumed/asmjit/x86operand.h +1133 -0
  64. plumed/_lib/include/plumed/asmjit/x86regalloc_p.h +734 -0
  65. plumed/_lib/include/plumed/asmjit/zone.h +1157 -0
  66. plumed/_lib/include/plumed/bias/Bias.h +82 -0
  67. plumed/_lib/include/plumed/bias/ReweightBase.h +58 -0
  68. plumed/_lib/include/plumed/blas/blas.h +253 -0
  69. plumed/_lib/include/plumed/blas/def_external.h +61 -0
  70. plumed/_lib/include/plumed/blas/def_internal.h +97 -0
  71. plumed/_lib/include/plumed/blas/real.h +49 -0
  72. plumed/_lib/include/plumed/cltools/CLTool.h +32 -0
  73. plumed/_lib/include/plumed/clusters/ClusteringBase.h +70 -0
  74. plumed/_lib/include/plumed/colvar/Colvar.h +32 -0
  75. plumed/_lib/include/plumed/colvar/ColvarInput.h +68 -0
  76. plumed/_lib/include/plumed/colvar/ColvarShortcut.h +81 -0
  77. plumed/_lib/include/plumed/colvar/CoordinationBase.h +52 -0
  78. plumed/_lib/include/plumed/colvar/MultiColvarTemplate.h +333 -0
  79. plumed/_lib/include/plumed/colvar/PathMSDBase.h +101 -0
  80. plumed/_lib/include/plumed/colvar/RMSDVector.h +78 -0
  81. plumed/_lib/include/plumed/config/Config.h +118 -0
  82. plumed/_lib/include/plumed/config/version.h +9 -0
  83. plumed/_lib/include/plumed/contour/ContourFindingObject.h +87 -0
  84. plumed/_lib/include/plumed/contour/DistanceFromContourBase.h +82 -0
  85. plumed/_lib/include/plumed/contour/FindContour.h +67 -0
  86. plumed/_lib/include/plumed/core/Action.h +540 -0
  87. plumed/_lib/include/plumed/core/ActionAnyorder.h +48 -0
  88. plumed/_lib/include/plumed/core/ActionAtomistic.h +343 -0
  89. plumed/_lib/include/plumed/core/ActionForInterface.h +99 -0
  90. plumed/_lib/include/plumed/core/ActionPilot.h +57 -0
  91. plumed/_lib/include/plumed/core/ActionRegister.h +124 -0
  92. plumed/_lib/include/plumed/core/ActionSet.h +163 -0
  93. plumed/_lib/include/plumed/core/ActionSetup.h +48 -0
  94. plumed/_lib/include/plumed/core/ActionShortcut.h +73 -0
  95. plumed/_lib/include/plumed/core/ActionToGetData.h +59 -0
  96. plumed/_lib/include/plumed/core/ActionToPutData.h +101 -0
  97. plumed/_lib/include/plumed/core/ActionWithArguments.h +140 -0
  98. plumed/_lib/include/plumed/core/ActionWithMatrix.h +87 -0
  99. plumed/_lib/include/plumed/core/ActionWithValue.h +258 -0
  100. plumed/_lib/include/plumed/core/ActionWithVector.h +94 -0
  101. plumed/_lib/include/plumed/core/ActionWithVirtualAtom.h +123 -0
  102. plumed/_lib/include/plumed/core/CLTool.h +177 -0
  103. plumed/_lib/include/plumed/core/CLToolMain.h +102 -0
  104. plumed/_lib/include/plumed/core/CLToolRegister.h +108 -0
  105. plumed/_lib/include/plumed/core/Colvar.h +115 -0
  106. plumed/_lib/include/plumed/core/DataPassingObject.h +94 -0
  107. plumed/_lib/include/plumed/core/DataPassingTools.h +54 -0
  108. plumed/_lib/include/plumed/core/DomainDecomposition.h +120 -0
  109. plumed/_lib/include/plumed/core/ExchangePatterns.h +47 -0
  110. plumed/_lib/include/plumed/core/FlexibleBin.h +63 -0
  111. plumed/_lib/include/plumed/core/GREX.h +61 -0
  112. plumed/_lib/include/plumed/core/GenericMolInfo.h +89 -0
  113. plumed/_lib/include/plumed/core/Group.h +41 -0
  114. plumed/_lib/include/plumed/core/ModuleMap.h +30 -0
  115. plumed/_lib/include/plumed/core/ParallelTaskManager.h +1023 -0
  116. plumed/_lib/include/plumed/core/PbcAction.h +61 -0
  117. plumed/_lib/include/plumed/core/PlumedMain.h +632 -0
  118. plumed/_lib/include/plumed/core/PlumedMainInitializer.h +118 -0
  119. plumed/_lib/include/plumed/core/RegisterBase.h +340 -0
  120. plumed/_lib/include/plumed/core/TargetDist.h +48 -0
  121. plumed/_lib/include/plumed/core/Value.h +547 -0
  122. plumed/_lib/include/plumed/core/WithCmd.h +93 -0
  123. plumed/_lib/include/plumed/dimred/SMACOF.h +55 -0
  124. plumed/_lib/include/plumed/drr/DRR.h +383 -0
  125. plumed/_lib/include/plumed/drr/colvar_UIestimator.h +777 -0
  126. plumed/_lib/include/plumed/fisst/legendre_rule_fast.h +44 -0
  127. plumed/_lib/include/plumed/function/Custom.h +54 -0
  128. plumed/_lib/include/plumed/function/Function.h +85 -0
  129. plumed/_lib/include/plumed/function/FunctionOfMatrix.h +368 -0
  130. plumed/_lib/include/plumed/function/FunctionOfScalar.h +135 -0
  131. plumed/_lib/include/plumed/function/FunctionOfVector.h +296 -0
  132. plumed/_lib/include/plumed/function/FunctionSetup.h +180 -0
  133. plumed/_lib/include/plumed/function/FunctionShortcut.h +130 -0
  134. plumed/_lib/include/plumed/function/FunctionWithSingleArgument.h +165 -0
  135. plumed/_lib/include/plumed/gridtools/ActionWithGrid.h +43 -0
  136. plumed/_lib/include/plumed/gridtools/EvaluateGridFunction.h +99 -0
  137. plumed/_lib/include/plumed/gridtools/FunctionOfGrid.h +295 -0
  138. plumed/_lib/include/plumed/gridtools/GridCoordinatesObject.h +179 -0
  139. plumed/_lib/include/plumed/gridtools/GridSearch.h +135 -0
  140. plumed/_lib/include/plumed/gridtools/Interpolator.h +45 -0
  141. plumed/_lib/include/plumed/gridtools/KDE.h +455 -0
  142. plumed/_lib/include/plumed/gridtools/RDF.h +40 -0
  143. plumed/_lib/include/plumed/gridtools/SumOfKernels.h +219 -0
  144. plumed/_lib/include/plumed/isdb/MetainferenceBase.h +398 -0
  145. plumed/_lib/include/plumed/lapack/def_external.h +207 -0
  146. plumed/_lib/include/plumed/lapack/def_internal.h +388 -0
  147. plumed/_lib/include/plumed/lapack/lapack.h +899 -0
  148. plumed/_lib/include/plumed/lapack/lapack_limits.h +79 -0
  149. plumed/_lib/include/plumed/lapack/real.h +50 -0
  150. plumed/_lib/include/plumed/lepton/CompiledExpression.h +164 -0
  151. plumed/_lib/include/plumed/lepton/CustomFunction.h +143 -0
  152. plumed/_lib/include/plumed/lepton/Exception.h +93 -0
  153. plumed/_lib/include/plumed/lepton/ExpressionProgram.h +137 -0
  154. plumed/_lib/include/plumed/lepton/ExpressionTreeNode.h +145 -0
  155. plumed/_lib/include/plumed/lepton/Lepton.h +85 -0
  156. plumed/_lib/include/plumed/lepton/MSVC_erfc.h +123 -0
  157. plumed/_lib/include/plumed/lepton/Operation.h +1302 -0
  158. plumed/_lib/include/plumed/lepton/ParsedExpression.h +165 -0
  159. plumed/_lib/include/plumed/lepton/Parser.h +111 -0
  160. plumed/_lib/include/plumed/lepton/windowsIncludes.h +73 -0
  161. plumed/_lib/include/plumed/mapping/Path.h +44 -0
  162. plumed/_lib/include/plumed/mapping/PathProjectionCalculator.h +57 -0
  163. plumed/_lib/include/plumed/matrixtools/MatrixOperationBase.h +54 -0
  164. plumed/_lib/include/plumed/matrixtools/MatrixTimesMatrix.h +309 -0
  165. plumed/_lib/include/plumed/matrixtools/MatrixTimesVectorBase.h +365 -0
  166. plumed/_lib/include/plumed/matrixtools/OuterProduct.h +238 -0
  167. plumed/_lib/include/plumed/maze/Core.h +65 -0
  168. plumed/_lib/include/plumed/maze/Loss.h +86 -0
  169. plumed/_lib/include/plumed/maze/Member.h +66 -0
  170. plumed/_lib/include/plumed/maze/Memetic.h +799 -0
  171. plumed/_lib/include/plumed/maze/Optimizer.h +357 -0
  172. plumed/_lib/include/plumed/maze/Random_MT.h +156 -0
  173. plumed/_lib/include/plumed/maze/Tools.h +183 -0
  174. plumed/_lib/include/plumed/metatomic/vesin.h +188 -0
  175. plumed/_lib/include/plumed/molfile/Gromacs.h +2013 -0
  176. plumed/_lib/include/plumed/molfile/endianswap.h +217 -0
  177. plumed/_lib/include/plumed/molfile/fastio.h +683 -0
  178. plumed/_lib/include/plumed/molfile/largefiles.h +78 -0
  179. plumed/_lib/include/plumed/molfile/libmolfile_plugin.h +77 -0
  180. plumed/_lib/include/plumed/molfile/molfile_plugin.h +1034 -0
  181. plumed/_lib/include/plumed/molfile/periodic_table.h +248 -0
  182. plumed/_lib/include/plumed/molfile/readpdb.h +447 -0
  183. plumed/_lib/include/plumed/molfile/vmdplugin.h +236 -0
  184. plumed/_lib/include/plumed/multicolvar/MultiColvarShortcuts.h +45 -0
  185. plumed/_lib/include/plumed/opes/ExpansionCVs.h +79 -0
  186. plumed/_lib/include/plumed/sasa/Sasa.h +32 -0
  187. plumed/_lib/include/plumed/secondarystructure/SecondaryStructureBase.h +372 -0
  188. plumed/_lib/include/plumed/setup/ActionSetup.h +25 -0
  189. plumed/_lib/include/plumed/small_vector/small_vector.h +6114 -0
  190. plumed/_lib/include/plumed/symfunc/CoordinationNumbers.h +41 -0
  191. plumed/_lib/include/plumed/tools/Angle.h +52 -0
  192. plumed/_lib/include/plumed/tools/AtomDistribution.h +138 -0
  193. plumed/_lib/include/plumed/tools/AtomNumber.h +152 -0
  194. plumed/_lib/include/plumed/tools/BiasRepresentation.h +106 -0
  195. plumed/_lib/include/plumed/tools/BitmaskEnum.h +167 -0
  196. plumed/_lib/include/plumed/tools/Brent1DRootSearch.h +159 -0
  197. plumed/_lib/include/plumed/tools/CheckInRange.h +44 -0
  198. plumed/_lib/include/plumed/tools/Citations.h +74 -0
  199. plumed/_lib/include/plumed/tools/ColvarOutput.h +118 -0
  200. plumed/_lib/include/plumed/tools/Communicator.h +316 -0
  201. plumed/_lib/include/plumed/tools/ConjugateGradient.h +80 -0
  202. plumed/_lib/include/plumed/tools/DLLoader.h +79 -0
  203. plumed/_lib/include/plumed/tools/ERMSD.h +73 -0
  204. plumed/_lib/include/plumed/tools/Exception.h +406 -0
  205. plumed/_lib/include/plumed/tools/File.h +28 -0
  206. plumed/_lib/include/plumed/tools/FileBase.h +153 -0
  207. plumed/_lib/include/plumed/tools/FileTools.h +37 -0
  208. plumed/_lib/include/plumed/tools/ForwardDecl.h +54 -0
  209. plumed/_lib/include/plumed/tools/Grid.h +638 -0
  210. plumed/_lib/include/plumed/tools/HistogramBead.h +136 -0
  211. plumed/_lib/include/plumed/tools/IFile.h +117 -0
  212. plumed/_lib/include/plumed/tools/KernelFunctions.h +113 -0
  213. plumed/_lib/include/plumed/tools/Keywords.h +380 -0
  214. plumed/_lib/include/plumed/tools/LatticeReduction.h +66 -0
  215. plumed/_lib/include/plumed/tools/LeptonCall.h +64 -0
  216. plumed/_lib/include/plumed/tools/LinkCells.h +126 -0
  217. plumed/_lib/include/plumed/tools/Log.h +41 -0
  218. plumed/_lib/include/plumed/tools/LoopUnroller.h +163 -0
  219. plumed/_lib/include/plumed/tools/Matrix.h +721 -0
  220. plumed/_lib/include/plumed/tools/MatrixSquareBracketsAccess.h +138 -0
  221. plumed/_lib/include/plumed/tools/MergeVectorTools.h +153 -0
  222. plumed/_lib/include/plumed/tools/Minimise1DBrent.h +244 -0
  223. plumed/_lib/include/plumed/tools/MinimiseBase.h +120 -0
  224. plumed/_lib/include/plumed/tools/MolDataClass.h +51 -0
  225. plumed/_lib/include/plumed/tools/NeighborList.h +112 -0
  226. plumed/_lib/include/plumed/tools/OFile.h +286 -0
  227. plumed/_lib/include/plumed/tools/OpenACC.h +180 -0
  228. plumed/_lib/include/plumed/tools/OpenMP.h +75 -0
  229. plumed/_lib/include/plumed/tools/PDB.h +154 -0
  230. plumed/_lib/include/plumed/tools/Pbc.h +139 -0
  231. plumed/_lib/include/plumed/tools/PlumedHandle.h +105 -0
  232. plumed/_lib/include/plumed/tools/RMSD.h +493 -0
  233. plumed/_lib/include/plumed/tools/Random.h +80 -0
  234. plumed/_lib/include/plumed/tools/RootFindingBase.h +79 -0
  235. plumed/_lib/include/plumed/tools/Stopwatch.h +475 -0
  236. plumed/_lib/include/plumed/tools/Subprocess.h +142 -0
  237. plumed/_lib/include/plumed/tools/SwitchingFunction.h +208 -0
  238. plumed/_lib/include/plumed/tools/Tensor.h +724 -0
  239. plumed/_lib/include/plumed/tools/TokenizedLine.h +123 -0
  240. plumed/_lib/include/plumed/tools/Tools.h +638 -0
  241. plumed/_lib/include/plumed/tools/Torsion.h +55 -0
  242. plumed/_lib/include/plumed/tools/TrajectoryParser.h +118 -0
  243. plumed/_lib/include/plumed/tools/Tree.h +61 -0
  244. plumed/_lib/include/plumed/tools/TypesafePtr.h +463 -0
  245. plumed/_lib/include/plumed/tools/Units.h +167 -0
  246. plumed/_lib/include/plumed/tools/Vector.h +433 -0
  247. plumed/_lib/include/plumed/tools/View.h +296 -0
  248. plumed/_lib/include/plumed/tools/View2D.h +100 -0
  249. plumed/_lib/include/plumed/tools/h36.h +39 -0
  250. plumed/_lib/include/plumed/vatom/ActionWithVirtualAtom.h +32 -0
  251. plumed/_lib/include/plumed/ves/BasisFunctions.h +380 -0
  252. plumed/_lib/include/plumed/ves/CoeffsBase.h +310 -0
  253. plumed/_lib/include/plumed/ves/CoeffsMatrix.h +220 -0
  254. plumed/_lib/include/plumed/ves/CoeffsVector.h +251 -0
  255. plumed/_lib/include/plumed/ves/FermiSwitchingFunction.h +74 -0
  256. plumed/_lib/include/plumed/ves/GridIntegrationWeights.h +50 -0
  257. plumed/_lib/include/plumed/ves/GridLinearInterpolation.h +81 -0
  258. plumed/_lib/include/plumed/ves/GridProjWeights.h +61 -0
  259. plumed/_lib/include/plumed/ves/LinearBasisSetExpansion.h +303 -0
  260. plumed/_lib/include/plumed/ves/Optimizer.h +444 -0
  261. plumed/_lib/include/plumed/ves/TargetDistModifer.h +53 -0
  262. plumed/_lib/include/plumed/ves/TargetDistribution.h +266 -0
  263. plumed/_lib/include/plumed/ves/VesBias.h +545 -0
  264. plumed/_lib/include/plumed/ves/VesTools.h +142 -0
  265. plumed/_lib/include/plumed/ves/WaveletGrid.h +75 -0
  266. plumed/_lib/include/plumed/volumes/ActionVolume.h +268 -0
  267. plumed/_lib/include/plumed/volumes/VolumeShortcut.h +147 -0
  268. plumed/_lib/include/plumed/wrapper/Plumed.h +5025 -0
  269. plumed/_lib/include/plumed/xdrfile/xdrfile.h +663 -0
  270. plumed/_lib/include/plumed/xdrfile/xdrfile_trr.h +89 -0
  271. plumed/_lib/include/plumed/xdrfile/xdrfile_xtc.h +90 -0
  272. plumed/_lib/lib/PythonCVInterface.dylib +0 -0
  273. plumed/_lib/lib/libplumed.dylib +0 -0
  274. plumed/_lib/lib/libplumedKernel.dylib +0 -0
  275. plumed/_lib/lib/libplumedWrapper.a +0 -0
  276. plumed/_lib/lib/pkgconfig/plumed.pc +13 -0
  277. plumed/_lib/lib/pkgconfig/plumedInternals.pc +13 -0
  278. plumed/_lib/lib/pkgconfig/plumedWrapper.pc +13 -0
  279. plumed/_lib/lib/plumed/fortran/plumed.f90 +879 -0
  280. plumed/_lib/lib/plumed/fortran/plumed_f08.f90 +2625 -0
  281. plumed/_lib/lib/plumed/modulefile +69 -0
  282. plumed/_lib/lib/plumed/patches/gromacs-2022.5.config +43 -0
  283. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt +543 -0
  284. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt.preplumed +540 -0
  285. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.cpp +1628 -0
  286. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.cpp.preplumed +1590 -0
  287. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h +103 -0
  288. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h.preplumed +99 -0
  289. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/sim_util.cpp +2527 -0
  290. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/sim_util.cpp.preplumed +2513 -0
  291. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp +208 -0
  292. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed +175 -0
  293. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.h +408 -0
  294. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed +394 -0
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