hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

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Files changed (469) hide show
  1. hillclimber/__init__.py +39 -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 +1065 -0
  7. hillclimber/interfaces.py +133 -0
  8. hillclimber/metadynamics.py +325 -0
  9. hillclimber/nodes.py +6 -0
  10. hillclimber/opes.py +359 -0
  11. hillclimber/selectors.py +230 -0
  12. hillclimber/virtual_atoms.py +341 -0
  13. hillclimber-0.1.5a8.dist-info/METADATA +209 -0
  14. hillclimber-0.1.5a8.dist-info/RECORD +469 -0
  15. hillclimber-0.1.5a8.dist-info/WHEEL +6 -0
  16. hillclimber-0.1.5a8.dist-info/entry_points.txt +8 -0
  17. hillclimber-0.1.5a8.dist-info/licenses/LICENSE +165 -0
  18. plumed/__init__.py +104 -0
  19. plumed/_lib/bin/plumed +0 -0
  20. plumed/_lib/bin/plumed-config +9 -0
  21. plumed/_lib/bin/plumed-patch +9 -0
  22. plumed/_lib/include/plumed/adjmat/AdjacencyMatrixBase.h +659 -0
  23. plumed/_lib/include/plumed/adjmat/ContactMatrix.h +59 -0
  24. plumed/_lib/include/plumed/asmjit/arch.h +228 -0
  25. plumed/_lib/include/plumed/asmjit/arm.h +43 -0
  26. plumed/_lib/include/plumed/asmjit/asmjit.h +69 -0
  27. plumed/_lib/include/plumed/asmjit/asmjit_apibegin.h +143 -0
  28. plumed/_lib/include/plumed/asmjit/asmjit_apiend.h +93 -0
  29. plumed/_lib/include/plumed/asmjit/asmjit_build.h +971 -0
  30. plumed/_lib/include/plumed/asmjit/assembler.h +183 -0
  31. plumed/_lib/include/plumed/asmjit/base.h +56 -0
  32. plumed/_lib/include/plumed/asmjit/codebuilder.h +944 -0
  33. plumed/_lib/include/plumed/asmjit/codecompiler.h +767 -0
  34. plumed/_lib/include/plumed/asmjit/codeemitter.h +528 -0
  35. plumed/_lib/include/plumed/asmjit/codeholder.h +777 -0
  36. plumed/_lib/include/plumed/asmjit/constpool.h +286 -0
  37. plumed/_lib/include/plumed/asmjit/cpuinfo.h +402 -0
  38. plumed/_lib/include/plumed/asmjit/func.h +1327 -0
  39. plumed/_lib/include/plumed/asmjit/globals.h +370 -0
  40. plumed/_lib/include/plumed/asmjit/inst.h +137 -0
  41. plumed/_lib/include/plumed/asmjit/logging.h +317 -0
  42. plumed/_lib/include/plumed/asmjit/misc_p.h +103 -0
  43. plumed/_lib/include/plumed/asmjit/moved_string.h +318 -0
  44. plumed/_lib/include/plumed/asmjit/operand.h +1599 -0
  45. plumed/_lib/include/plumed/asmjit/osutils.h +207 -0
  46. plumed/_lib/include/plumed/asmjit/regalloc_p.h +597 -0
  47. plumed/_lib/include/plumed/asmjit/runtime.h +227 -0
  48. plumed/_lib/include/plumed/asmjit/simdtypes.h +1104 -0
  49. plumed/_lib/include/plumed/asmjit/utils.h +1387 -0
  50. plumed/_lib/include/plumed/asmjit/vmem.h +183 -0
  51. plumed/_lib/include/plumed/asmjit/x86.h +45 -0
  52. plumed/_lib/include/plumed/asmjit/x86assembler.h +125 -0
  53. plumed/_lib/include/plumed/asmjit/x86builder.h +117 -0
  54. plumed/_lib/include/plumed/asmjit/x86compiler.h +322 -0
  55. plumed/_lib/include/plumed/asmjit/x86emitter.h +5149 -0
  56. plumed/_lib/include/plumed/asmjit/x86globals.h +535 -0
  57. plumed/_lib/include/plumed/asmjit/x86inst.h +2547 -0
  58. plumed/_lib/include/plumed/asmjit/x86instimpl_p.h +74 -0
  59. plumed/_lib/include/plumed/asmjit/x86internal_p.h +108 -0
  60. plumed/_lib/include/plumed/asmjit/x86logging_p.h +92 -0
  61. plumed/_lib/include/plumed/asmjit/x86misc.h +417 -0
  62. plumed/_lib/include/plumed/asmjit/x86operand.h +1133 -0
  63. plumed/_lib/include/plumed/asmjit/x86regalloc_p.h +734 -0
  64. plumed/_lib/include/plumed/asmjit/zone.h +1157 -0
  65. plumed/_lib/include/plumed/bias/Bias.h +82 -0
  66. plumed/_lib/include/plumed/bias/ReweightBase.h +58 -0
  67. plumed/_lib/include/plumed/blas/blas.h +253 -0
  68. plumed/_lib/include/plumed/blas/def_external.h +61 -0
  69. plumed/_lib/include/plumed/blas/def_internal.h +97 -0
  70. plumed/_lib/include/plumed/blas/real.h +49 -0
  71. plumed/_lib/include/plumed/cltools/CLTool.h +32 -0
  72. plumed/_lib/include/plumed/clusters/ClusteringBase.h +70 -0
  73. plumed/_lib/include/plumed/colvar/Colvar.h +32 -0
  74. plumed/_lib/include/plumed/colvar/ColvarInput.h +68 -0
  75. plumed/_lib/include/plumed/colvar/ColvarShortcut.h +81 -0
  76. plumed/_lib/include/plumed/colvar/CoordinationBase.h +52 -0
  77. plumed/_lib/include/plumed/colvar/MultiColvarTemplate.h +333 -0
  78. plumed/_lib/include/plumed/colvar/PathMSDBase.h +101 -0
  79. plumed/_lib/include/plumed/colvar/RMSDVector.h +78 -0
  80. plumed/_lib/include/plumed/config/Config.h +118 -0
  81. plumed/_lib/include/plumed/config/version.h +9 -0
  82. plumed/_lib/include/plumed/contour/ContourFindingObject.h +87 -0
  83. plumed/_lib/include/plumed/contour/DistanceFromContourBase.h +82 -0
  84. plumed/_lib/include/plumed/contour/FindContour.h +67 -0
  85. plumed/_lib/include/plumed/core/Action.h +540 -0
  86. plumed/_lib/include/plumed/core/ActionAnyorder.h +48 -0
  87. plumed/_lib/include/plumed/core/ActionAtomistic.h +343 -0
  88. plumed/_lib/include/plumed/core/ActionForInterface.h +99 -0
  89. plumed/_lib/include/plumed/core/ActionPilot.h +57 -0
  90. plumed/_lib/include/plumed/core/ActionRegister.h +124 -0
  91. plumed/_lib/include/plumed/core/ActionSet.h +163 -0
  92. plumed/_lib/include/plumed/core/ActionSetup.h +48 -0
  93. plumed/_lib/include/plumed/core/ActionShortcut.h +73 -0
  94. plumed/_lib/include/plumed/core/ActionToGetData.h +59 -0
  95. plumed/_lib/include/plumed/core/ActionToPutData.h +101 -0
  96. plumed/_lib/include/plumed/core/ActionWithArguments.h +140 -0
  97. plumed/_lib/include/plumed/core/ActionWithMatrix.h +87 -0
  98. plumed/_lib/include/plumed/core/ActionWithValue.h +258 -0
  99. plumed/_lib/include/plumed/core/ActionWithVector.h +94 -0
  100. plumed/_lib/include/plumed/core/ActionWithVirtualAtom.h +123 -0
  101. plumed/_lib/include/plumed/core/CLTool.h +177 -0
  102. plumed/_lib/include/plumed/core/CLToolMain.h +102 -0
  103. plumed/_lib/include/plumed/core/CLToolRegister.h +108 -0
  104. plumed/_lib/include/plumed/core/Colvar.h +115 -0
  105. plumed/_lib/include/plumed/core/DataPassingObject.h +94 -0
  106. plumed/_lib/include/plumed/core/DataPassingTools.h +54 -0
  107. plumed/_lib/include/plumed/core/DomainDecomposition.h +120 -0
  108. plumed/_lib/include/plumed/core/ExchangePatterns.h +47 -0
  109. plumed/_lib/include/plumed/core/FlexibleBin.h +63 -0
  110. plumed/_lib/include/plumed/core/GREX.h +61 -0
  111. plumed/_lib/include/plumed/core/GenericMolInfo.h +89 -0
  112. plumed/_lib/include/plumed/core/Group.h +41 -0
  113. plumed/_lib/include/plumed/core/ModuleMap.h +30 -0
  114. plumed/_lib/include/plumed/core/ParallelTaskManager.h +1023 -0
  115. plumed/_lib/include/plumed/core/PbcAction.h +61 -0
  116. plumed/_lib/include/plumed/core/PlumedMain.h +632 -0
  117. plumed/_lib/include/plumed/core/PlumedMainInitializer.h +118 -0
  118. plumed/_lib/include/plumed/core/RegisterBase.h +340 -0
  119. plumed/_lib/include/plumed/core/TargetDist.h +48 -0
  120. plumed/_lib/include/plumed/core/Value.h +547 -0
  121. plumed/_lib/include/plumed/core/WithCmd.h +93 -0
  122. plumed/_lib/include/plumed/dimred/SMACOF.h +55 -0
  123. plumed/_lib/include/plumed/drr/DRR.h +383 -0
  124. plumed/_lib/include/plumed/drr/colvar_UIestimator.h +777 -0
  125. plumed/_lib/include/plumed/fisst/legendre_rule_fast.h +44 -0
  126. plumed/_lib/include/plumed/function/Custom.h +54 -0
  127. plumed/_lib/include/plumed/function/Function.h +85 -0
  128. plumed/_lib/include/plumed/function/FunctionOfMatrix.h +368 -0
  129. plumed/_lib/include/plumed/function/FunctionOfScalar.h +135 -0
  130. plumed/_lib/include/plumed/function/FunctionOfVector.h +296 -0
  131. plumed/_lib/include/plumed/function/FunctionSetup.h +180 -0
  132. plumed/_lib/include/plumed/function/FunctionShortcut.h +130 -0
  133. plumed/_lib/include/plumed/function/FunctionWithSingleArgument.h +165 -0
  134. plumed/_lib/include/plumed/gridtools/ActionWithGrid.h +43 -0
  135. plumed/_lib/include/plumed/gridtools/EvaluateGridFunction.h +99 -0
  136. plumed/_lib/include/plumed/gridtools/FunctionOfGrid.h +295 -0
  137. plumed/_lib/include/plumed/gridtools/GridCoordinatesObject.h +179 -0
  138. plumed/_lib/include/plumed/gridtools/GridSearch.h +135 -0
  139. plumed/_lib/include/plumed/gridtools/Interpolator.h +45 -0
  140. plumed/_lib/include/plumed/gridtools/KDE.h +455 -0
  141. plumed/_lib/include/plumed/gridtools/RDF.h +40 -0
  142. plumed/_lib/include/plumed/gridtools/SumOfKernels.h +219 -0
  143. plumed/_lib/include/plumed/isdb/MetainferenceBase.h +398 -0
  144. plumed/_lib/include/plumed/lapack/def_external.h +207 -0
  145. plumed/_lib/include/plumed/lapack/def_internal.h +388 -0
  146. plumed/_lib/include/plumed/lapack/lapack.h +899 -0
  147. plumed/_lib/include/plumed/lapack/lapack_limits.h +79 -0
  148. plumed/_lib/include/plumed/lapack/real.h +50 -0
  149. plumed/_lib/include/plumed/lepton/CompiledExpression.h +164 -0
  150. plumed/_lib/include/plumed/lepton/CustomFunction.h +143 -0
  151. plumed/_lib/include/plumed/lepton/Exception.h +93 -0
  152. plumed/_lib/include/plumed/lepton/ExpressionProgram.h +137 -0
  153. plumed/_lib/include/plumed/lepton/ExpressionTreeNode.h +145 -0
  154. plumed/_lib/include/plumed/lepton/Lepton.h +85 -0
  155. plumed/_lib/include/plumed/lepton/MSVC_erfc.h +123 -0
  156. plumed/_lib/include/plumed/lepton/Operation.h +1302 -0
  157. plumed/_lib/include/plumed/lepton/ParsedExpression.h +165 -0
  158. plumed/_lib/include/plumed/lepton/Parser.h +111 -0
  159. plumed/_lib/include/plumed/lepton/windowsIncludes.h +73 -0
  160. plumed/_lib/include/plumed/mapping/Path.h +44 -0
  161. plumed/_lib/include/plumed/mapping/PathProjectionCalculator.h +57 -0
  162. plumed/_lib/include/plumed/matrixtools/MatrixOperationBase.h +54 -0
  163. plumed/_lib/include/plumed/matrixtools/MatrixTimesMatrix.h +309 -0
  164. plumed/_lib/include/plumed/matrixtools/MatrixTimesVectorBase.h +365 -0
  165. plumed/_lib/include/plumed/matrixtools/OuterProduct.h +238 -0
  166. plumed/_lib/include/plumed/maze/Core.h +65 -0
  167. plumed/_lib/include/plumed/maze/Loss.h +86 -0
  168. plumed/_lib/include/plumed/maze/Member.h +66 -0
  169. plumed/_lib/include/plumed/maze/Memetic.h +799 -0
  170. plumed/_lib/include/plumed/maze/Optimizer.h +357 -0
  171. plumed/_lib/include/plumed/maze/Random_MT.h +156 -0
  172. plumed/_lib/include/plumed/maze/Tools.h +183 -0
  173. plumed/_lib/include/plumed/metatomic/vesin.h +188 -0
  174. plumed/_lib/include/plumed/molfile/Gromacs.h +2013 -0
  175. plumed/_lib/include/plumed/molfile/endianswap.h +217 -0
  176. plumed/_lib/include/plumed/molfile/fastio.h +683 -0
  177. plumed/_lib/include/plumed/molfile/largefiles.h +78 -0
  178. plumed/_lib/include/plumed/molfile/libmolfile_plugin.h +77 -0
  179. plumed/_lib/include/plumed/molfile/molfile_plugin.h +1034 -0
  180. plumed/_lib/include/plumed/molfile/periodic_table.h +248 -0
  181. plumed/_lib/include/plumed/molfile/readpdb.h +447 -0
  182. plumed/_lib/include/plumed/molfile/vmdplugin.h +236 -0
  183. plumed/_lib/include/plumed/multicolvar/MultiColvarShortcuts.h +45 -0
  184. plumed/_lib/include/plumed/opes/ExpansionCVs.h +79 -0
  185. plumed/_lib/include/plumed/sasa/Sasa.h +32 -0
  186. plumed/_lib/include/plumed/secondarystructure/SecondaryStructureBase.h +372 -0
  187. plumed/_lib/include/plumed/setup/ActionSetup.h +25 -0
  188. plumed/_lib/include/plumed/small_vector/small_vector.h +6114 -0
  189. plumed/_lib/include/plumed/symfunc/CoordinationNumbers.h +41 -0
  190. plumed/_lib/include/plumed/tools/Angle.h +52 -0
  191. plumed/_lib/include/plumed/tools/AtomDistribution.h +138 -0
  192. plumed/_lib/include/plumed/tools/AtomNumber.h +152 -0
  193. plumed/_lib/include/plumed/tools/BiasRepresentation.h +106 -0
  194. plumed/_lib/include/plumed/tools/BitmaskEnum.h +167 -0
  195. plumed/_lib/include/plumed/tools/Brent1DRootSearch.h +159 -0
  196. plumed/_lib/include/plumed/tools/CheckInRange.h +44 -0
  197. plumed/_lib/include/plumed/tools/Citations.h +74 -0
  198. plumed/_lib/include/plumed/tools/ColvarOutput.h +118 -0
  199. plumed/_lib/include/plumed/tools/Communicator.h +316 -0
  200. plumed/_lib/include/plumed/tools/ConjugateGradient.h +80 -0
  201. plumed/_lib/include/plumed/tools/DLLoader.h +79 -0
  202. plumed/_lib/include/plumed/tools/ERMSD.h +73 -0
  203. plumed/_lib/include/plumed/tools/Exception.h +406 -0
  204. plumed/_lib/include/plumed/tools/File.h +28 -0
  205. plumed/_lib/include/plumed/tools/FileBase.h +153 -0
  206. plumed/_lib/include/plumed/tools/FileTools.h +37 -0
  207. plumed/_lib/include/plumed/tools/ForwardDecl.h +54 -0
  208. plumed/_lib/include/plumed/tools/Grid.h +638 -0
  209. plumed/_lib/include/plumed/tools/HistogramBead.h +136 -0
  210. plumed/_lib/include/plumed/tools/IFile.h +117 -0
  211. plumed/_lib/include/plumed/tools/KernelFunctions.h +113 -0
  212. plumed/_lib/include/plumed/tools/Keywords.h +380 -0
  213. plumed/_lib/include/plumed/tools/LatticeReduction.h +66 -0
  214. plumed/_lib/include/plumed/tools/LeptonCall.h +64 -0
  215. plumed/_lib/include/plumed/tools/LinkCells.h +126 -0
  216. plumed/_lib/include/plumed/tools/Log.h +41 -0
  217. plumed/_lib/include/plumed/tools/LoopUnroller.h +163 -0
  218. plumed/_lib/include/plumed/tools/Matrix.h +721 -0
  219. plumed/_lib/include/plumed/tools/MatrixSquareBracketsAccess.h +138 -0
  220. plumed/_lib/include/plumed/tools/MergeVectorTools.h +153 -0
  221. plumed/_lib/include/plumed/tools/Minimise1DBrent.h +244 -0
  222. plumed/_lib/include/plumed/tools/MinimiseBase.h +120 -0
  223. plumed/_lib/include/plumed/tools/MolDataClass.h +51 -0
  224. plumed/_lib/include/plumed/tools/NeighborList.h +112 -0
  225. plumed/_lib/include/plumed/tools/OFile.h +286 -0
  226. plumed/_lib/include/plumed/tools/OpenACC.h +180 -0
  227. plumed/_lib/include/plumed/tools/OpenMP.h +75 -0
  228. plumed/_lib/include/plumed/tools/PDB.h +154 -0
  229. plumed/_lib/include/plumed/tools/Pbc.h +139 -0
  230. plumed/_lib/include/plumed/tools/PlumedHandle.h +105 -0
  231. plumed/_lib/include/plumed/tools/RMSD.h +493 -0
  232. plumed/_lib/include/plumed/tools/Random.h +80 -0
  233. plumed/_lib/include/plumed/tools/RootFindingBase.h +79 -0
  234. plumed/_lib/include/plumed/tools/Stopwatch.h +475 -0
  235. plumed/_lib/include/plumed/tools/Subprocess.h +142 -0
  236. plumed/_lib/include/plumed/tools/SwitchingFunction.h +208 -0
  237. plumed/_lib/include/plumed/tools/Tensor.h +724 -0
  238. plumed/_lib/include/plumed/tools/TokenizedLine.h +123 -0
  239. plumed/_lib/include/plumed/tools/Tools.h +638 -0
  240. plumed/_lib/include/plumed/tools/Torsion.h +55 -0
  241. plumed/_lib/include/plumed/tools/TrajectoryParser.h +118 -0
  242. plumed/_lib/include/plumed/tools/Tree.h +61 -0
  243. plumed/_lib/include/plumed/tools/TypesafePtr.h +463 -0
  244. plumed/_lib/include/plumed/tools/Units.h +167 -0
  245. plumed/_lib/include/plumed/tools/Vector.h +433 -0
  246. plumed/_lib/include/plumed/tools/View.h +296 -0
  247. plumed/_lib/include/plumed/tools/View2D.h +100 -0
  248. plumed/_lib/include/plumed/tools/h36.h +39 -0
  249. plumed/_lib/include/plumed/vatom/ActionWithVirtualAtom.h +32 -0
  250. plumed/_lib/include/plumed/ves/BasisFunctions.h +380 -0
  251. plumed/_lib/include/plumed/ves/CoeffsBase.h +310 -0
  252. plumed/_lib/include/plumed/ves/CoeffsMatrix.h +220 -0
  253. plumed/_lib/include/plumed/ves/CoeffsVector.h +251 -0
  254. plumed/_lib/include/plumed/ves/FermiSwitchingFunction.h +74 -0
  255. plumed/_lib/include/plumed/ves/GridIntegrationWeights.h +50 -0
  256. plumed/_lib/include/plumed/ves/GridLinearInterpolation.h +81 -0
  257. plumed/_lib/include/plumed/ves/GridProjWeights.h +61 -0
  258. plumed/_lib/include/plumed/ves/LinearBasisSetExpansion.h +303 -0
  259. plumed/_lib/include/plumed/ves/Optimizer.h +444 -0
  260. plumed/_lib/include/plumed/ves/TargetDistModifer.h +53 -0
  261. plumed/_lib/include/plumed/ves/TargetDistribution.h +266 -0
  262. plumed/_lib/include/plumed/ves/VesBias.h +545 -0
  263. plumed/_lib/include/plumed/ves/VesTools.h +142 -0
  264. plumed/_lib/include/plumed/ves/WaveletGrid.h +75 -0
  265. plumed/_lib/include/plumed/volumes/ActionVolume.h +268 -0
  266. plumed/_lib/include/plumed/volumes/VolumeShortcut.h +147 -0
  267. plumed/_lib/include/plumed/wrapper/Plumed.h +5025 -0
  268. plumed/_lib/include/plumed/xdrfile/xdrfile.h +663 -0
  269. plumed/_lib/include/plumed/xdrfile/xdrfile_trr.h +89 -0
  270. plumed/_lib/include/plumed/xdrfile/xdrfile_xtc.h +90 -0
  271. plumed/_lib/lib/PythonCVInterface.dylib +0 -0
  272. plumed/_lib/lib/libplumed.dylib +0 -0
  273. plumed/_lib/lib/libplumedKernel.dylib +0 -0
  274. plumed/_lib/lib/libplumedWrapper.a +0 -0
  275. plumed/_lib/lib/pkgconfig/plumed.pc +13 -0
  276. plumed/_lib/lib/pkgconfig/plumedInternals.pc +13 -0
  277. plumed/_lib/lib/pkgconfig/plumedWrapper.pc +13 -0
  278. plumed/_lib/lib/plumed/fortran/plumed.f90 +879 -0
  279. plumed/_lib/lib/plumed/fortran/plumed_f08.f90 +2625 -0
  280. plumed/_lib/lib/plumed/modulefile +69 -0
  281. plumed/_lib/lib/plumed/patches/gromacs-2022.5.config +43 -0
  282. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt +543 -0
  283. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt.preplumed +540 -0
  284. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.cpp +1628 -0
  285. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.cpp.preplumed +1590 -0
  286. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h +103 -0
  287. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h.preplumed +99 -0
  288. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/sim_util.cpp +2527 -0
  289. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/sim_util.cpp.preplumed +2513 -0
  290. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp +208 -0
  291. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed +175 -0
  292. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.h +408 -0
  293. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed +394 -0
  294. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/md.cpp +2348 -0
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@@ -0,0 +1,183 @@
1
+ /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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+ Copyright (c) 2008-2017, Petr Kobalicek
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+
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+ This software is provided 'as-is', without any express or implied
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+ warranty. In no event will the authors be held liable for any damages
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+ arising from the use of this software.
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+
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+ Permission is granted to anyone to use this software for any purpose,
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+ including commercial applications, and to alter it and redistribute it
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+ freely, subject to the following restrictions:
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+
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+ 1. The origin of this software must not be misrepresented; you must not
13
+ claim that you wrote the original software. If you use this software
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+ in a product, an acknowledgment in the product documentation would be
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+ appreciated but is not required.
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+ 2. Altered source versions must be plainly marked as such, and must not be
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+ misrepresented as being the original software.
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+ 3. This notice may not be removed or altered from any source distribution.
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+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
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+ #ifndef __PLUMED_asmjit_vmem_h
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+ #define __PLUMED_asmjit_vmem_h
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+ #ifdef __PLUMED_HAS_ASMJIT
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+ #pragma GCC diagnostic push
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+ #pragma GCC diagnostic ignored "-Wpedantic"
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+ // [AsmJit]
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+ // Complete x86/x64 JIT and Remote Assembler for C++.
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+ //
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+ // [License]
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+ // Zlib - See LICENSE.md file in the package.
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+
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+ // [Guard]
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+ #ifndef _ASMJIT_BASE_VMEM_H
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+ #define _ASMJIT_BASE_VMEM_H
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+
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+ // [Dependencies]
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+ #include "./globals.h"
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+ #include "./osutils.h"
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+
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+ // [Api-Begin]
40
+ #include "./asmjit_apibegin.h"
41
+
42
+ namespace PLMD {
43
+ namespace asmjit {
44
+
45
+ //! \addtogroup asmjit_base
46
+ //! \{
47
+
48
+ // ============================================================================
49
+ // [asmjit::VMemMgr]
50
+ // ============================================================================
51
+
52
+ //! Reference implementation of memory manager that uses `VMemUtil` to allocate
53
+ //! chunks of virtual memory and bit arrays to manage it.
54
+ class VMemMgr {
55
+ public:
56
+ //! Type of virtual memory allocation, see `VMemMgr::alloc()`.
57
+ ASMJIT_ENUM(AllocType) {
58
+ //! Normal memory allocation, has to be freed by `VMemMgr::release()`.
59
+ kAllocFreeable = 0,
60
+ //! Allocate permanent memory, can't be freed.
61
+ kAllocPermanent = 1
62
+ };
63
+
64
+ // --------------------------------------------------------------------------
65
+ // [Construction / Destruction]
66
+ // --------------------------------------------------------------------------
67
+
68
+ #if !ASMJIT_OS_WINDOWS
69
+ //! Create a `VMemMgr` instance.
70
+ ASMJIT_API VMemMgr() noexcept;
71
+ #else
72
+ //! Create a `VMemMgr` instance.
73
+ //!
74
+ //! NOTE: When running on Windows it's possible to specify a `hProcess` to
75
+ //! be used for memory allocation. Using `hProcess` allows to allocate memory
76
+ //! of a remote process.
77
+ ASMJIT_API VMemMgr(HANDLE hProcess = static_cast<HANDLE>(0)) noexcept;
78
+ #endif // ASMJIT_OS_WINDOWS
79
+
80
+ //! Destroy the `VMemMgr` instance and free all blocks.
81
+ ASMJIT_API ~VMemMgr() noexcept;
82
+
83
+ // --------------------------------------------------------------------------
84
+ // [Reset]
85
+ // --------------------------------------------------------------------------
86
+
87
+ //! Free all allocated memory.
88
+ ASMJIT_API void reset() noexcept;
89
+
90
+ // --------------------------------------------------------------------------
91
+ // [Accessors]
92
+ // --------------------------------------------------------------------------
93
+
94
+ #if ASMJIT_OS_WINDOWS
95
+ //! Get the handle of the process memory manager is bound to.
96
+ ASMJIT_INLINE HANDLE getProcessHandle() const noexcept { return _hProcess; }
97
+ #endif // ASMJIT_OS_WINDOWS
98
+
99
+ //! Get how many bytes are currently allocated.
100
+ ASMJIT_INLINE size_t getAllocatedBytes() const noexcept { return _allocatedBytes; }
101
+ //! Get how many bytes are currently used.
102
+ ASMJIT_INLINE size_t getUsedBytes() const noexcept { return _usedBytes; }
103
+
104
+ //! Get whether to keep allocated memory after the `VMemMgr` is destroyed.
105
+ //!
106
+ //! \sa \ref setKeepVirtualMemory.
107
+ ASMJIT_INLINE bool getKeepVirtualMemory() const noexcept { return _keepVirtualMemory; }
108
+ //! Set whether to keep allocated memory after the memory manager is destroyed.
109
+ //!
110
+ //! This method is usable when patching code of remote process. You need to
111
+ //! allocate process memory, store generated assembler into it and patch the
112
+ //! method you want to redirect (into your code). This method affects only
113
+ //! VMemMgr destructor. After destruction all internal
114
+ //! structures are freed, only the process virtual memory remains.
115
+ //!
116
+ //! NOTE: Memory allocated with kAllocPermanent is always kept.
117
+ //!
118
+ //! \sa \ref getKeepVirtualMemory.
119
+ ASMJIT_INLINE void setKeepVirtualMemory(bool val) noexcept { _keepVirtualMemory = val; }
120
+
121
+ // --------------------------------------------------------------------------
122
+ // [Alloc / Release]
123
+ // --------------------------------------------------------------------------
124
+
125
+ //! Allocate a `size` bytes of virtual memory.
126
+ //!
127
+ //! Note that if you are implementing your own virtual memory manager then you
128
+ //! can quitly ignore type of allocation. This is mainly for AsmJit to memory
129
+ //! manager that allocated memory will be never freed.
130
+ ASMJIT_API void* alloc(size_t size, uint32_t type = kAllocFreeable) noexcept;
131
+ //! Free previously allocated memory at a given `address`.
132
+ ASMJIT_API Error release(void* p) noexcept;
133
+ //! Free extra memory allocated with `p`.
134
+ ASMJIT_API Error shrink(void* p, size_t used) noexcept;
135
+
136
+ // --------------------------------------------------------------------------
137
+ // [Members]
138
+ // --------------------------------------------------------------------------
139
+
140
+ #if ASMJIT_OS_WINDOWS
141
+ HANDLE _hProcess; //!< Process passed to `VirtualAllocEx` and `VirtualFree`.
142
+ #endif // ASMJIT_OS_WINDOWS
143
+ Lock _lock; //!< Lock to enable thread-safe functionality.
144
+
145
+ size_t _blockSize; //!< Default block size.
146
+ size_t _blockDensity; //!< Default block density.
147
+ bool _keepVirtualMemory; //!< Keep virtual memory after destroyed.
148
+
149
+ size_t _allocatedBytes; //!< How many bytes are currently allocated.
150
+ size_t _usedBytes; //!< How many bytes are currently used.
151
+
152
+ //! \internal
153
+ //! \{
154
+
155
+ struct RbNode;
156
+ struct MemNode;
157
+ struct PermanentNode;
158
+
159
+ // Memory nodes root.
160
+ MemNode* _root;
161
+ // Memory nodes list.
162
+ MemNode* _first;
163
+ MemNode* _last;
164
+ MemNode* _optimal;
165
+ // Permanent memory.
166
+ PermanentNode* _permanent;
167
+
168
+ //! \}
169
+ };
170
+
171
+ //! \}
172
+
173
+ } // asmjit namespace
174
+ } // namespace PLMD
175
+
176
+ // [Api-End]
177
+ #include "./asmjit_apiend.h"
178
+
179
+ // [Guard]
180
+ #endif // _ASMJIT_BASE_VMEM_H
181
+ #pragma GCC diagnostic pop
182
+ #endif // __PLUMED_HAS_ASMJIT
183
+ #endif
@@ -0,0 +1,45 @@
1
+ /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2
+ Copyright (c) 2008-2017, Petr Kobalicek
3
+
4
+ This software is provided 'as-is', without any express or implied
5
+ warranty. In no event will the authors be held liable for any damages
6
+ arising from the use of this software.
7
+
8
+ Permission is granted to anyone to use this software for any purpose,
9
+ including commercial applications, and to alter it and redistribute it
10
+ freely, subject to the following restrictions:
11
+
12
+ 1. The origin of this software must not be misrepresented; you must not
13
+ claim that you wrote the original software. If you use this software
14
+ in a product, an acknowledgment in the product documentation would be
15
+ appreciated but is not required.
16
+ 2. Altered source versions must be plainly marked as such, and must not be
17
+ misrepresented as being the original software.
18
+ 3. This notice may not be removed or altered from any source distribution.
19
+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
20
+ #ifndef __PLUMED_asmjit_x86_h
21
+ #define __PLUMED_asmjit_x86_h
22
+ // [AsmJit]
23
+ // Complete x86/x64 JIT and Remote Assembler for C++.
24
+ //
25
+ // [License]
26
+ // Zlib - See LICENSE.md file in the package.
27
+
28
+ // [Guard]
29
+ #ifndef _ASMJIT_X86_H
30
+ #define _ASMJIT_X86_H
31
+
32
+ // [Dependencies]
33
+ #include "./base.h"
34
+
35
+ #include "./x86assembler.h"
36
+ #include "./x86builder.h"
37
+ #include "./x86compiler.h"
38
+ #include "./x86emitter.h"
39
+ #include "./x86inst.h"
40
+ #include "./x86misc.h"
41
+ #include "./x86operand.h"
42
+
43
+ // [Guard]
44
+ #endif // _ASMJIT_X86_H
45
+ #endif
@@ -0,0 +1,125 @@
1
+ /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2
+ Copyright (c) 2008-2017, Petr Kobalicek
3
+
4
+ This software is provided 'as-is', without any express or implied
5
+ warranty. In no event will the authors be held liable for any damages
6
+ arising from the use of this software.
7
+
8
+ Permission is granted to anyone to use this software for any purpose,
9
+ including commercial applications, and to alter it and redistribute it
10
+ freely, subject to the following restrictions:
11
+
12
+ 1. The origin of this software must not be misrepresented; you must not
13
+ claim that you wrote the original software. If you use this software
14
+ in a product, an acknowledgment in the product documentation would be
15
+ appreciated but is not required.
16
+ 2. Altered source versions must be plainly marked as such, and must not be
17
+ misrepresented as being the original software.
18
+ 3. This notice may not be removed or altered from any source distribution.
19
+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
20
+ #ifndef __PLUMED_asmjit_x86assembler_h
21
+ #define __PLUMED_asmjit_x86assembler_h
22
+ #ifdef __PLUMED_HAS_ASMJIT
23
+ #pragma GCC diagnostic push
24
+ #pragma GCC diagnostic ignored "-Wpedantic"
25
+ // [AsmJit]
26
+ // Complete x86/x64 JIT and Remote Assembler for C++.
27
+ //
28
+ // [License]
29
+ // Zlib - See LICENSE.md file in the package.
30
+
31
+ // [Guard]
32
+ #ifndef _ASMJIT_X86_X86ASSEMBLER_H
33
+ #define _ASMJIT_X86_X86ASSEMBLER_H
34
+
35
+ // [Dependencies]
36
+ #include "./assembler.h"
37
+ #include "./utils.h"
38
+ #include "./x86emitter.h"
39
+ #include "./x86operand.h"
40
+
41
+ // [Api-Begin]
42
+ #include "./asmjit_apibegin.h"
43
+
44
+ namespace PLMD {
45
+ namespace asmjit {
46
+
47
+ //! \addtogroup asmjit_x86
48
+ //! \{
49
+
50
+ // ============================================================================
51
+ // [asmjit::X86Assembler]
52
+ // ============================================================================
53
+
54
+ //! X86/X64 assembler.
55
+ //!
56
+ //! X86/X64 assembler emits machine-code into buffers managed by \ref CodeHolder.
57
+ class ASMJIT_VIRTAPI X86Assembler
58
+ : public Assembler,
59
+ public X86EmitterImplicitT<X86Assembler> {
60
+
61
+ public:
62
+ typedef Assembler Base;
63
+
64
+ // --------------------------------------------------------------------------
65
+ // [Construction / Destruction]
66
+ // --------------------------------------------------------------------------
67
+
68
+ ASMJIT_API X86Assembler(CodeHolder* code = nullptr) noexcept;
69
+ ASMJIT_API virtual ~X86Assembler() noexcept;
70
+
71
+ // --------------------------------------------------------------------------
72
+ // [Compatibility]
73
+ // --------------------------------------------------------------------------
74
+
75
+ //! Explicit cast to `X86Emitter`.
76
+ ASMJIT_INLINE X86Emitter* asEmitter() noexcept { return reinterpret_cast<X86Emitter*>(this); }
77
+ //! Explicit cast to `X86Emitter` (const).
78
+ ASMJIT_INLINE const X86Emitter* asEmitter() const noexcept { return reinterpret_cast<const X86Emitter*>(this); }
79
+
80
+ //! Implicit cast to `X86Emitter`.
81
+ ASMJIT_INLINE operator X86Emitter&() noexcept { return *asEmitter(); }
82
+ //! Implicit cast to `X86Emitter` (const).
83
+ ASMJIT_INLINE operator const X86Emitter&() const noexcept { return *asEmitter(); }
84
+
85
+ // --------------------------------------------------------------------------
86
+ // [Accessors]
87
+ // --------------------------------------------------------------------------
88
+
89
+ // NOTE: X86Assembler uses _privateData to store 'address-override' bit that
90
+ // is used to decide whether to emit address-override (67H) prefix based on
91
+ // the memory BASE+INDEX registers. It's either `kX86MemInfo_67H_X86` or
92
+ // `kX86MemInfo_67H_X64`.
93
+ ASMJIT_INLINE uint32_t _getAddressOverrideMask() const noexcept { return _privateData; }
94
+ ASMJIT_INLINE void _setAddressOverrideMask(uint32_t m) noexcept { _privateData = m; }
95
+
96
+ // --------------------------------------------------------------------------
97
+ // [Events]
98
+ // --------------------------------------------------------------------------
99
+
100
+ ASMJIT_API Error onAttach(CodeHolder* code) noexcept override;
101
+ ASMJIT_API Error onDetach(CodeHolder* code) noexcept override;
102
+
103
+ // --------------------------------------------------------------------------
104
+ // [Code-Generation]
105
+ // --------------------------------------------------------------------------
106
+
107
+ using CodeEmitter::_emit;
108
+
109
+ ASMJIT_API Error _emit(uint32_t instId, const Operand_& o0, const Operand_& o1, const Operand_& o2, const Operand_& o3) override;
110
+ ASMJIT_API Error align(uint32_t mode, uint32_t alignment) override;
111
+ };
112
+
113
+ //! \}
114
+
115
+ } // asmjit namespace
116
+ } // namespace PLMD
117
+
118
+ // [Api-End]
119
+ #include "./asmjit_apiend.h"
120
+
121
+ // [Guard]
122
+ #endif // _ASMJIT_X86_X86ASSEMBLER_H
123
+ #pragma GCC diagnostic pop
124
+ #endif // __PLUMED_HAS_ASMJIT
125
+ #endif
@@ -0,0 +1,117 @@
1
+ /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2
+ Copyright (c) 2008-2017, Petr Kobalicek
3
+
4
+ This software is provided 'as-is', without any express or implied
5
+ warranty. In no event will the authors be held liable for any damages
6
+ arising from the use of this software.
7
+
8
+ Permission is granted to anyone to use this software for any purpose,
9
+ including commercial applications, and to alter it and redistribute it
10
+ freely, subject to the following restrictions:
11
+
12
+ 1. The origin of this software must not be misrepresented; you must not
13
+ claim that you wrote the original software. If you use this software
14
+ in a product, an acknowledgment in the product documentation would be
15
+ appreciated but is not required.
16
+ 2. Altered source versions must be plainly marked as such, and must not be
17
+ misrepresented as being the original software.
18
+ 3. This notice may not be removed or altered from any source distribution.
19
+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
20
+ #ifndef __PLUMED_asmjit_x86builder_h
21
+ #define __PLUMED_asmjit_x86builder_h
22
+ #ifdef __PLUMED_HAS_ASMJIT
23
+ #pragma GCC diagnostic push
24
+ #pragma GCC diagnostic ignored "-Wpedantic"
25
+ // [AsmJit]
26
+ // Complete x86/x64 JIT and Remote Assembler for C++.
27
+ //
28
+ // [License]
29
+ // Zlib - See LICENSE.md file in the package.
30
+
31
+ // [Guard]
32
+ #ifndef _ASMJIT_X86_X86BUILDER_H
33
+ #define _ASMJIT_X86_X86BUILDER_H
34
+
35
+ #include "./asmjit_build.h"
36
+ #if !defined(ASMJIT_DISABLE_BUILDER)
37
+
38
+ // [Dependencies]
39
+ #include "./codebuilder.h"
40
+ #include "./simdtypes.h"
41
+ #include "./x86emitter.h"
42
+ #include "./x86misc.h"
43
+
44
+ // [Api-Begin]
45
+ #include "./asmjit_apibegin.h"
46
+
47
+ namespace PLMD {
48
+ namespace asmjit {
49
+
50
+ //! \addtogroup asmjit_x86
51
+ //! \{
52
+
53
+ // ============================================================================
54
+ // [asmjit::CodeBuilder]
55
+ // ============================================================================
56
+
57
+ //! Architecture-dependent \ref CodeBuilder targeting X86 and X64.
58
+ class ASMJIT_VIRTAPI X86Builder
59
+ : public CodeBuilder,
60
+ public X86EmitterImplicitT<X86Builder> {
61
+
62
+ public:
63
+ ASMJIT_NONCOPYABLE(X86Builder)
64
+ typedef CodeBuilder Base;
65
+
66
+ // --------------------------------------------------------------------------
67
+ // [Construction / Destruction]
68
+ // --------------------------------------------------------------------------
69
+
70
+ //! Create a `X86Builder` instance.
71
+ ASMJIT_API X86Builder(CodeHolder* code = nullptr) noexcept;
72
+ //! Destroy the `X86Builder` instance.
73
+ ASMJIT_API ~X86Builder() noexcept;
74
+
75
+ // --------------------------------------------------------------------------
76
+ // [Compatibility]
77
+ // --------------------------------------------------------------------------
78
+
79
+ //! Explicit cast to `X86Emitter`.
80
+ ASMJIT_INLINE X86Emitter* asEmitter() noexcept { return reinterpret_cast<X86Emitter*>(this); }
81
+ //! Explicit cast to `X86Emitter` (const).
82
+ ASMJIT_INLINE const X86Emitter* asEmitter() const noexcept { return reinterpret_cast<const X86Emitter*>(this); }
83
+
84
+ //! Implicit cast to `X86Emitter`.
85
+ ASMJIT_INLINE operator X86Emitter&() noexcept { return *asEmitter(); }
86
+ //! Implicit cast to `X86Emitter` (const).
87
+ ASMJIT_INLINE operator const X86Emitter&() const noexcept { return *asEmitter(); }
88
+
89
+ // --------------------------------------------------------------------------
90
+ // [Events]
91
+ // --------------------------------------------------------------------------
92
+
93
+ ASMJIT_API virtual Error onAttach(CodeHolder* code) noexcept override;
94
+
95
+ // --------------------------------------------------------------------------
96
+ // [Code-Generation]
97
+ // --------------------------------------------------------------------------
98
+
99
+ using CodeBuilder::_emit;
100
+
101
+ ASMJIT_API virtual Error _emit(uint32_t instId, const Operand_& o0, const Operand_& o1, const Operand_& o2, const Operand_& o3) override;
102
+ };
103
+
104
+ //! \}
105
+
106
+ } // asmjit namespace
107
+ } // namespace PLMD
108
+
109
+ // [Api-End]
110
+ #include "./asmjit_apiend.h"
111
+
112
+ // [Guard]
113
+ #endif // !ASMJIT_DISABLE_BUILDER
114
+ #endif // _ASMJIT_X86_X86BUILDER_H
115
+ #pragma GCC diagnostic pop
116
+ #endif // __PLUMED_HAS_ASMJIT
117
+ #endif