hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

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Files changed (475) 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 +475 -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. hillclimber-0.1.6.dist-info/sboms/auditwheel.cdx.json +1 -0
  20. hillclimber.libs/libgomp-a49a47f9.so.1.0.0 +0 -0
  21. plumed/__init__.py +104 -0
  22. plumed/_lib/bin/plumed +0 -0
  23. plumed/_lib/bin/plumed-config +9 -0
  24. plumed/_lib/bin/plumed-patch +9 -0
  25. plumed/_lib/include/plumed/adjmat/AdjacencyMatrixBase.h +659 -0
  26. plumed/_lib/include/plumed/adjmat/ContactMatrix.h +59 -0
  27. plumed/_lib/include/plumed/asmjit/arch.h +228 -0
  28. plumed/_lib/include/plumed/asmjit/arm.h +43 -0
  29. plumed/_lib/include/plumed/asmjit/asmjit.h +69 -0
  30. plumed/_lib/include/plumed/asmjit/asmjit_apibegin.h +143 -0
  31. plumed/_lib/include/plumed/asmjit/asmjit_apiend.h +93 -0
  32. plumed/_lib/include/plumed/asmjit/asmjit_build.h +971 -0
  33. plumed/_lib/include/plumed/asmjit/assembler.h +183 -0
  34. plumed/_lib/include/plumed/asmjit/base.h +56 -0
  35. plumed/_lib/include/plumed/asmjit/codebuilder.h +944 -0
  36. plumed/_lib/include/plumed/asmjit/codecompiler.h +767 -0
  37. plumed/_lib/include/plumed/asmjit/codeemitter.h +528 -0
  38. plumed/_lib/include/plumed/asmjit/codeholder.h +777 -0
  39. plumed/_lib/include/plumed/asmjit/constpool.h +286 -0
  40. plumed/_lib/include/plumed/asmjit/cpuinfo.h +402 -0
  41. plumed/_lib/include/plumed/asmjit/func.h +1327 -0
  42. plumed/_lib/include/plumed/asmjit/globals.h +370 -0
  43. plumed/_lib/include/plumed/asmjit/inst.h +137 -0
  44. plumed/_lib/include/plumed/asmjit/logging.h +317 -0
  45. plumed/_lib/include/plumed/asmjit/misc_p.h +103 -0
  46. plumed/_lib/include/plumed/asmjit/moved_string.h +318 -0
  47. plumed/_lib/include/plumed/asmjit/operand.h +1599 -0
  48. plumed/_lib/include/plumed/asmjit/osutils.h +207 -0
  49. plumed/_lib/include/plumed/asmjit/regalloc_p.h +597 -0
  50. plumed/_lib/include/plumed/asmjit/runtime.h +227 -0
  51. plumed/_lib/include/plumed/asmjit/simdtypes.h +1104 -0
  52. plumed/_lib/include/plumed/asmjit/utils.h +1387 -0
  53. plumed/_lib/include/plumed/asmjit/vmem.h +183 -0
  54. plumed/_lib/include/plumed/asmjit/x86.h +45 -0
  55. plumed/_lib/include/plumed/asmjit/x86assembler.h +125 -0
  56. plumed/_lib/include/plumed/asmjit/x86builder.h +117 -0
  57. plumed/_lib/include/plumed/asmjit/x86compiler.h +322 -0
  58. plumed/_lib/include/plumed/asmjit/x86emitter.h +5149 -0
  59. plumed/_lib/include/plumed/asmjit/x86globals.h +535 -0
  60. plumed/_lib/include/plumed/asmjit/x86inst.h +2547 -0
  61. plumed/_lib/include/plumed/asmjit/x86instimpl_p.h +74 -0
  62. plumed/_lib/include/plumed/asmjit/x86internal_p.h +108 -0
  63. plumed/_lib/include/plumed/asmjit/x86logging_p.h +92 -0
  64. plumed/_lib/include/plumed/asmjit/x86misc.h +417 -0
  65. plumed/_lib/include/plumed/asmjit/x86operand.h +1133 -0
  66. plumed/_lib/include/plumed/asmjit/x86regalloc_p.h +734 -0
  67. plumed/_lib/include/plumed/asmjit/zone.h +1157 -0
  68. plumed/_lib/include/plumed/bias/Bias.h +82 -0
  69. plumed/_lib/include/plumed/bias/ReweightBase.h +58 -0
  70. plumed/_lib/include/plumed/blas/blas.h +253 -0
  71. plumed/_lib/include/plumed/blas/def_external.h +61 -0
  72. plumed/_lib/include/plumed/blas/def_internal.h +97 -0
  73. plumed/_lib/include/plumed/blas/real.h +49 -0
  74. plumed/_lib/include/plumed/cltools/CLTool.h +32 -0
  75. plumed/_lib/include/plumed/clusters/ClusteringBase.h +70 -0
  76. plumed/_lib/include/plumed/colvar/Colvar.h +32 -0
  77. plumed/_lib/include/plumed/colvar/ColvarInput.h +68 -0
  78. plumed/_lib/include/plumed/colvar/ColvarShortcut.h +81 -0
  79. plumed/_lib/include/plumed/colvar/CoordinationBase.h +52 -0
  80. plumed/_lib/include/plumed/colvar/MultiColvarTemplate.h +333 -0
  81. plumed/_lib/include/plumed/colvar/PathMSDBase.h +101 -0
  82. plumed/_lib/include/plumed/colvar/RMSDVector.h +78 -0
  83. plumed/_lib/include/plumed/config/Config.h +118 -0
  84. plumed/_lib/include/plumed/config/version.h +9 -0
  85. plumed/_lib/include/plumed/contour/ContourFindingObject.h +87 -0
  86. plumed/_lib/include/plumed/contour/DistanceFromContourBase.h +82 -0
  87. plumed/_lib/include/plumed/contour/FindContour.h +67 -0
  88. plumed/_lib/include/plumed/core/Action.h +540 -0
  89. plumed/_lib/include/plumed/core/ActionAnyorder.h +48 -0
  90. plumed/_lib/include/plumed/core/ActionAtomistic.h +343 -0
  91. plumed/_lib/include/plumed/core/ActionForInterface.h +99 -0
  92. plumed/_lib/include/plumed/core/ActionPilot.h +57 -0
  93. plumed/_lib/include/plumed/core/ActionRegister.h +124 -0
  94. plumed/_lib/include/plumed/core/ActionSet.h +163 -0
  95. plumed/_lib/include/plumed/core/ActionSetup.h +48 -0
  96. plumed/_lib/include/plumed/core/ActionShortcut.h +73 -0
  97. plumed/_lib/include/plumed/core/ActionToGetData.h +59 -0
  98. plumed/_lib/include/plumed/core/ActionToPutData.h +101 -0
  99. plumed/_lib/include/plumed/core/ActionWithArguments.h +140 -0
  100. plumed/_lib/include/plumed/core/ActionWithMatrix.h +87 -0
  101. plumed/_lib/include/plumed/core/ActionWithValue.h +258 -0
  102. plumed/_lib/include/plumed/core/ActionWithVector.h +94 -0
  103. plumed/_lib/include/plumed/core/ActionWithVirtualAtom.h +123 -0
  104. plumed/_lib/include/plumed/core/CLTool.h +177 -0
  105. plumed/_lib/include/plumed/core/CLToolMain.h +102 -0
  106. plumed/_lib/include/plumed/core/CLToolRegister.h +108 -0
  107. plumed/_lib/include/plumed/core/Colvar.h +115 -0
  108. plumed/_lib/include/plumed/core/DataPassingObject.h +94 -0
  109. plumed/_lib/include/plumed/core/DataPassingTools.h +54 -0
  110. plumed/_lib/include/plumed/core/DomainDecomposition.h +120 -0
  111. plumed/_lib/include/plumed/core/ExchangePatterns.h +47 -0
  112. plumed/_lib/include/plumed/core/FlexibleBin.h +63 -0
  113. plumed/_lib/include/plumed/core/GREX.h +61 -0
  114. plumed/_lib/include/plumed/core/GenericMolInfo.h +89 -0
  115. plumed/_lib/include/plumed/core/Group.h +41 -0
  116. plumed/_lib/include/plumed/core/ModuleMap.h +30 -0
  117. plumed/_lib/include/plumed/core/ParallelTaskManager.h +1023 -0
  118. plumed/_lib/include/plumed/core/PbcAction.h +61 -0
  119. plumed/_lib/include/plumed/core/PlumedMain.h +632 -0
  120. plumed/_lib/include/plumed/core/PlumedMainInitializer.h +118 -0
  121. plumed/_lib/include/plumed/core/RegisterBase.h +340 -0
  122. plumed/_lib/include/plumed/core/TargetDist.h +48 -0
  123. plumed/_lib/include/plumed/core/Value.h +547 -0
  124. plumed/_lib/include/plumed/core/WithCmd.h +93 -0
  125. plumed/_lib/include/plumed/dimred/SMACOF.h +55 -0
  126. plumed/_lib/include/plumed/drr/DRR.h +383 -0
  127. plumed/_lib/include/plumed/drr/colvar_UIestimator.h +777 -0
  128. plumed/_lib/include/plumed/fisst/legendre_rule_fast.h +44 -0
  129. plumed/_lib/include/plumed/function/Custom.h +54 -0
  130. plumed/_lib/include/plumed/function/Function.h +85 -0
  131. plumed/_lib/include/plumed/function/FunctionOfMatrix.h +368 -0
  132. plumed/_lib/include/plumed/function/FunctionOfScalar.h +135 -0
  133. plumed/_lib/include/plumed/function/FunctionOfVector.h +296 -0
  134. plumed/_lib/include/plumed/function/FunctionSetup.h +180 -0
  135. plumed/_lib/include/plumed/function/FunctionShortcut.h +130 -0
  136. plumed/_lib/include/plumed/function/FunctionWithSingleArgument.h +165 -0
  137. plumed/_lib/include/plumed/gridtools/ActionWithGrid.h +43 -0
  138. plumed/_lib/include/plumed/gridtools/EvaluateGridFunction.h +99 -0
  139. plumed/_lib/include/plumed/gridtools/FunctionOfGrid.h +295 -0
  140. plumed/_lib/include/plumed/gridtools/GridCoordinatesObject.h +179 -0
  141. plumed/_lib/include/plumed/gridtools/GridSearch.h +135 -0
  142. plumed/_lib/include/plumed/gridtools/Interpolator.h +45 -0
  143. plumed/_lib/include/plumed/gridtools/KDE.h +455 -0
  144. plumed/_lib/include/plumed/gridtools/RDF.h +40 -0
  145. plumed/_lib/include/plumed/gridtools/SumOfKernels.h +219 -0
  146. plumed/_lib/include/plumed/isdb/MetainferenceBase.h +398 -0
  147. plumed/_lib/include/plumed/lapack/def_external.h +207 -0
  148. plumed/_lib/include/plumed/lapack/def_internal.h +388 -0
  149. plumed/_lib/include/plumed/lapack/lapack.h +899 -0
  150. plumed/_lib/include/plumed/lapack/lapack_limits.h +79 -0
  151. plumed/_lib/include/plumed/lapack/real.h +50 -0
  152. plumed/_lib/include/plumed/lepton/CompiledExpression.h +164 -0
  153. plumed/_lib/include/plumed/lepton/CustomFunction.h +143 -0
  154. plumed/_lib/include/plumed/lepton/Exception.h +93 -0
  155. plumed/_lib/include/plumed/lepton/ExpressionProgram.h +137 -0
  156. plumed/_lib/include/plumed/lepton/ExpressionTreeNode.h +145 -0
  157. plumed/_lib/include/plumed/lepton/Lepton.h +85 -0
  158. plumed/_lib/include/plumed/lepton/MSVC_erfc.h +123 -0
  159. plumed/_lib/include/plumed/lepton/Operation.h +1302 -0
  160. plumed/_lib/include/plumed/lepton/ParsedExpression.h +165 -0
  161. plumed/_lib/include/plumed/lepton/Parser.h +111 -0
  162. plumed/_lib/include/plumed/lepton/windowsIncludes.h +73 -0
  163. plumed/_lib/include/plumed/mapping/Path.h +44 -0
  164. plumed/_lib/include/plumed/mapping/PathProjectionCalculator.h +57 -0
  165. plumed/_lib/include/plumed/matrixtools/MatrixOperationBase.h +54 -0
  166. plumed/_lib/include/plumed/matrixtools/MatrixTimesMatrix.h +309 -0
  167. plumed/_lib/include/plumed/matrixtools/MatrixTimesVectorBase.h +365 -0
  168. plumed/_lib/include/plumed/matrixtools/OuterProduct.h +238 -0
  169. plumed/_lib/include/plumed/maze/Core.h +65 -0
  170. plumed/_lib/include/plumed/maze/Loss.h +86 -0
  171. plumed/_lib/include/plumed/maze/Member.h +66 -0
  172. plumed/_lib/include/plumed/maze/Memetic.h +799 -0
  173. plumed/_lib/include/plumed/maze/Optimizer.h +357 -0
  174. plumed/_lib/include/plumed/maze/Random_MT.h +156 -0
  175. plumed/_lib/include/plumed/maze/Tools.h +183 -0
  176. plumed/_lib/include/plumed/metatomic/vesin.h +188 -0
  177. plumed/_lib/include/plumed/molfile/Gromacs.h +2013 -0
  178. plumed/_lib/include/plumed/molfile/endianswap.h +217 -0
  179. plumed/_lib/include/plumed/molfile/fastio.h +683 -0
  180. plumed/_lib/include/plumed/molfile/largefiles.h +78 -0
  181. plumed/_lib/include/plumed/molfile/libmolfile_plugin.h +77 -0
  182. plumed/_lib/include/plumed/molfile/molfile_plugin.h +1034 -0
  183. plumed/_lib/include/plumed/molfile/periodic_table.h +248 -0
  184. plumed/_lib/include/plumed/molfile/readpdb.h +447 -0
  185. plumed/_lib/include/plumed/molfile/vmdplugin.h +236 -0
  186. plumed/_lib/include/plumed/multicolvar/MultiColvarShortcuts.h +45 -0
  187. plumed/_lib/include/plumed/opes/ExpansionCVs.h +79 -0
  188. plumed/_lib/include/plumed/sasa/Sasa.h +32 -0
  189. plumed/_lib/include/plumed/secondarystructure/SecondaryStructureBase.h +372 -0
  190. plumed/_lib/include/plumed/setup/ActionSetup.h +25 -0
  191. plumed/_lib/include/plumed/small_vector/small_vector.h +6114 -0
  192. plumed/_lib/include/plumed/symfunc/CoordinationNumbers.h +41 -0
  193. plumed/_lib/include/plumed/tools/Angle.h +52 -0
  194. plumed/_lib/include/plumed/tools/AtomDistribution.h +138 -0
  195. plumed/_lib/include/plumed/tools/AtomNumber.h +152 -0
  196. plumed/_lib/include/plumed/tools/BiasRepresentation.h +106 -0
  197. plumed/_lib/include/plumed/tools/BitmaskEnum.h +167 -0
  198. plumed/_lib/include/plumed/tools/Brent1DRootSearch.h +159 -0
  199. plumed/_lib/include/plumed/tools/CheckInRange.h +44 -0
  200. plumed/_lib/include/plumed/tools/Citations.h +74 -0
  201. plumed/_lib/include/plumed/tools/ColvarOutput.h +118 -0
  202. plumed/_lib/include/plumed/tools/Communicator.h +316 -0
  203. plumed/_lib/include/plumed/tools/ConjugateGradient.h +80 -0
  204. plumed/_lib/include/plumed/tools/DLLoader.h +79 -0
  205. plumed/_lib/include/plumed/tools/ERMSD.h +73 -0
  206. plumed/_lib/include/plumed/tools/Exception.h +406 -0
  207. plumed/_lib/include/plumed/tools/File.h +28 -0
  208. plumed/_lib/include/plumed/tools/FileBase.h +153 -0
  209. plumed/_lib/include/plumed/tools/FileTools.h +37 -0
  210. plumed/_lib/include/plumed/tools/ForwardDecl.h +54 -0
  211. plumed/_lib/include/plumed/tools/Grid.h +638 -0
  212. plumed/_lib/include/plumed/tools/HistogramBead.h +136 -0
  213. plumed/_lib/include/plumed/tools/IFile.h +117 -0
  214. plumed/_lib/include/plumed/tools/KernelFunctions.h +113 -0
  215. plumed/_lib/include/plumed/tools/Keywords.h +380 -0
  216. plumed/_lib/include/plumed/tools/LatticeReduction.h +66 -0
  217. plumed/_lib/include/plumed/tools/LeptonCall.h +64 -0
  218. plumed/_lib/include/plumed/tools/LinkCells.h +126 -0
  219. plumed/_lib/include/plumed/tools/Log.h +41 -0
  220. plumed/_lib/include/plumed/tools/LoopUnroller.h +163 -0
  221. plumed/_lib/include/plumed/tools/Matrix.h +721 -0
  222. plumed/_lib/include/plumed/tools/MatrixSquareBracketsAccess.h +138 -0
  223. plumed/_lib/include/plumed/tools/MergeVectorTools.h +153 -0
  224. plumed/_lib/include/plumed/tools/Minimise1DBrent.h +244 -0
  225. plumed/_lib/include/plumed/tools/MinimiseBase.h +120 -0
  226. plumed/_lib/include/plumed/tools/MolDataClass.h +51 -0
  227. plumed/_lib/include/plumed/tools/NeighborList.h +112 -0
  228. plumed/_lib/include/plumed/tools/OFile.h +286 -0
  229. plumed/_lib/include/plumed/tools/OpenACC.h +180 -0
  230. plumed/_lib/include/plumed/tools/OpenMP.h +75 -0
  231. plumed/_lib/include/plumed/tools/PDB.h +154 -0
  232. plumed/_lib/include/plumed/tools/Pbc.h +139 -0
  233. plumed/_lib/include/plumed/tools/PlumedHandle.h +105 -0
  234. plumed/_lib/include/plumed/tools/RMSD.h +493 -0
  235. plumed/_lib/include/plumed/tools/Random.h +80 -0
  236. plumed/_lib/include/plumed/tools/RootFindingBase.h +79 -0
  237. plumed/_lib/include/plumed/tools/Stopwatch.h +475 -0
  238. plumed/_lib/include/plumed/tools/Subprocess.h +142 -0
  239. plumed/_lib/include/plumed/tools/SwitchingFunction.h +208 -0
  240. plumed/_lib/include/plumed/tools/Tensor.h +724 -0
  241. plumed/_lib/include/plumed/tools/TokenizedLine.h +123 -0
  242. plumed/_lib/include/plumed/tools/Tools.h +638 -0
  243. plumed/_lib/include/plumed/tools/Torsion.h +55 -0
  244. plumed/_lib/include/plumed/tools/TrajectoryParser.h +118 -0
  245. plumed/_lib/include/plumed/tools/Tree.h +61 -0
  246. plumed/_lib/include/plumed/tools/TypesafePtr.h +463 -0
  247. plumed/_lib/include/plumed/tools/Units.h +167 -0
  248. plumed/_lib/include/plumed/tools/Vector.h +433 -0
  249. plumed/_lib/include/plumed/tools/View.h +296 -0
  250. plumed/_lib/include/plumed/tools/View2D.h +100 -0
  251. plumed/_lib/include/plumed/tools/h36.h +39 -0
  252. plumed/_lib/include/plumed/vatom/ActionWithVirtualAtom.h +32 -0
  253. plumed/_lib/include/plumed/ves/BasisFunctions.h +380 -0
  254. plumed/_lib/include/plumed/ves/CoeffsBase.h +310 -0
  255. plumed/_lib/include/plumed/ves/CoeffsMatrix.h +220 -0
  256. plumed/_lib/include/plumed/ves/CoeffsVector.h +251 -0
  257. plumed/_lib/include/plumed/ves/FermiSwitchingFunction.h +74 -0
  258. plumed/_lib/include/plumed/ves/GridIntegrationWeights.h +50 -0
  259. plumed/_lib/include/plumed/ves/GridLinearInterpolation.h +81 -0
  260. plumed/_lib/include/plumed/ves/GridProjWeights.h +61 -0
  261. plumed/_lib/include/plumed/ves/LinearBasisSetExpansion.h +303 -0
  262. plumed/_lib/include/plumed/ves/Optimizer.h +444 -0
  263. plumed/_lib/include/plumed/ves/TargetDistModifer.h +53 -0
  264. plumed/_lib/include/plumed/ves/TargetDistribution.h +266 -0
  265. plumed/_lib/include/plumed/ves/VesBias.h +545 -0
  266. plumed/_lib/include/plumed/ves/VesTools.h +142 -0
  267. plumed/_lib/include/plumed/ves/WaveletGrid.h +75 -0
  268. plumed/_lib/include/plumed/volumes/ActionVolume.h +268 -0
  269. plumed/_lib/include/plumed/volumes/VolumeShortcut.h +147 -0
  270. plumed/_lib/include/plumed/wrapper/Plumed.h +5025 -0
  271. plumed/_lib/include/plumed/xdrfile/xdrfile.h +663 -0
  272. plumed/_lib/include/plumed/xdrfile/xdrfile_trr.h +89 -0
  273. plumed/_lib/include/plumed/xdrfile/xdrfile_xtc.h +90 -0
  274. plumed/_lib/lib/PythonCVInterface.so +0 -0
  275. plumed/_lib/lib/libplumed.a +0 -0
  276. plumed/_lib/lib/libplumed.so +0 -0
  277. plumed/_lib/lib/libplumedKernel.so +0 -0
  278. plumed/_lib/lib/libplumedWrapper.a +0 -0
  279. plumed/_lib/lib/pkgconfig/plumed.pc +13 -0
  280. plumed/_lib/lib/pkgconfig/plumedInternals.pc +13 -0
  281. plumed/_lib/lib/pkgconfig/plumedWrapper.pc +13 -0
  282. plumed/_lib/lib/plumed/fortran/plumed.f90 +879 -0
  283. plumed/_lib/lib/plumed/fortran/plumed_f08.f90 +2625 -0
  284. plumed/_lib/lib/plumed/modulefile +69 -0
  285. plumed/_lib/lib/plumed/patches/gromacs-2022.5.config +43 -0
  286. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt +543 -0
  287. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt.preplumed +540 -0
  288. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.cpp +1628 -0
  289. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.cpp.preplumed +1590 -0
  290. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h +103 -0
  291. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h.preplumed +99 -0
  292. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/sim_util.cpp +2527 -0
  293. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/sim_util.cpp.preplumed +2513 -0
  294. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp +208 -0
  295. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed +175 -0
  296. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.h +408 -0
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@@ -0,0 +1,165 @@
1
+ /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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+ Copyright (c) 2011-2023 The plumed team
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+ (see the PEOPLE file at the root of the distribution for a list of names)
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+
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+ See http://www.plumed.org for more information.
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+
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+ This file is part of plumed, version 2.
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+
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+ plumed is free software: you can redistribute it and/or modify
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+ it under the terms of the GNU Lesser General Public License as published by
11
+ the Free Software Foundation, either version 3 of the License, or
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+ (at your option) any later version.
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+
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+ plumed is distributed in the hope that it will be useful,
15
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
16
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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+ GNU Lesser General Public License for more details.
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+
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+ You should have received a copy of the GNU Lesser General Public License
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+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
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+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
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+ #ifndef __PLUMED_function_FunctionWithSingleArgument_h
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+ #define __PLUMED_function_FunctionWithSingleArgument_h
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+
25
+ #include "../core/ActionWithArguments.h"
26
+ #include "../core/ActionWithValue.h"
27
+ #include "../core/ActionRegister.h"
28
+ #include "FunctionSetup.h"
29
+
30
+ namespace PLMD {
31
+ namespace function {
32
+
33
+ template <class T>
34
+ class FunctionWithSingleArgument :
35
+ public ActionWithValue,
36
+ public ActionWithArguments {
37
+ private:
38
+ T f;
39
+ bool ismatrix;
40
+ public:
41
+ static void registerKeywords(Keywords& keys);
42
+ explicit FunctionWithSingleArgument(const ActionOptions&);
43
+ /// Get the label to write in the graph
44
+ std::string writeInGraph() const override {
45
+ std::size_t und = getName().find_last_of("_");
46
+ return getName().substr(0,und);
47
+ }
48
+ unsigned getNumberOfDerivatives() override ;
49
+ void calculate() override ;
50
+ void apply() override ;
51
+ };
52
+
53
+ template <class T>
54
+ void FunctionWithSingleArgument<T>::registerKeywords(Keywords& keys) {
55
+ Action::registerKeywords(keys);
56
+ ActionWithValue::registerKeywords(keys);
57
+ ActionWithArguments::registerKeywords(keys);
58
+ std::string name = keys.getDisplayName();
59
+ std::size_t und=name.find("_ONEARG");
60
+ keys.setDisplayName( name.substr(0,und) );
61
+ keys.addInputKeyword("compulsory","ARG","vector/matrix","the vector/matrix that is being used in input");
62
+ T::registerKeywords( keys );
63
+ }
64
+
65
+ template <class T>
66
+ FunctionWithSingleArgument<T>::FunctionWithSingleArgument(const ActionOptions&ao):
67
+ Action(ao),
68
+ ActionWithValue(ao),
69
+ ActionWithArguments(ao),
70
+ ismatrix(false) {
71
+
72
+ if( getNumberOfArguments()!=1 ) {
73
+ error("should only be one argument in input for this action");
74
+ }
75
+ ismatrix = getPntrToArgument(0)->getRank()==2 && !getPntrToArgument(0)->hasDerivatives();
76
+
77
+ std::vector<std::size_t> shape;
78
+ FunctionData<T>::setup( f, keywords.getOutputComponents(), shape, true, this );
79
+ }
80
+
81
+ template <class T>
82
+ unsigned FunctionWithSingleArgument<T>::getNumberOfDerivatives() {
83
+ return getPntrToArgument(0)->getNumberOfStoredValues();
84
+ }
85
+
86
+ template <class T>
87
+ void FunctionWithSingleArgument<T>::calculate() {
88
+ const Value* myarg = getPntrToArgument(0);
89
+ std::vector<double> args( myarg->getNumberOfStoredValues() );
90
+ if( ismatrix ) {
91
+ unsigned nvals = 0;
92
+ for(unsigned i=0; i<myarg->getShape()[0]; ++i) {
93
+ nvals += myarg->getRowLength(i);
94
+ }
95
+ args.resize( nvals );
96
+ unsigned k=0;
97
+ unsigned ncols = myarg->getNumberOfColumns();
98
+ for(unsigned i=0; i<myarg->getShape()[0]; ++i) {
99
+ for(unsigned j=0; j<myarg->getRowLength(i); ++j) {
100
+ args[k] = myarg->get(i*ncols + j, false);
101
+ ++k;
102
+ }
103
+ }
104
+ } else {
105
+ for(unsigned i=0; i<args.size(); ++i) {
106
+ args[i] = myarg->get( i );
107
+ }
108
+ }
109
+ std::vector<double> vals( getNumberOfComponents() ), deriv( getNumberOfComponents()*args.size() );
110
+ auto funcout = FunctionOutput::create( getNumberOfComponents(),
111
+ vals.data(),
112
+ args.size(),
113
+ deriv.data() );
114
+ T::calc( f,
115
+ doNotCalculateDerivatives(),
116
+ View<const double>(args.data(), args.size()),
117
+ funcout );
118
+ for(unsigned i=0; i<getNumberOfComponents(); ++i) {
119
+ Value* myval=getPntrToComponent(i);
120
+ myval->set( vals[i] );
121
+
122
+ if( doNotCalculateDerivatives() ) {
123
+ continue ;
124
+ }
125
+
126
+ for(unsigned j=0; j<args.size(); ++j) {
127
+ myval->setDerivative( j, funcout.derivs[i][j] );
128
+ }
129
+ }
130
+ }
131
+
132
+ template <class T>
133
+ void FunctionWithSingleArgument<T>::apply() {
134
+ if( !getPntrToComponent(0)->forcesWereAdded() ) {
135
+ return ;
136
+ }
137
+
138
+ Value* myarg = getPntrToArgument(0);
139
+ if( ismatrix ) {
140
+ for(unsigned i=0; i<getNumberOfComponents(); ++i) {
141
+ unsigned k=0;
142
+ const Value* myval = getPntrToComponent(i);
143
+ double force = myval->getForce();
144
+ unsigned ncols = myarg->getNumberOfColumns();
145
+ for(unsigned n=0; n<myarg->getShape()[0]; ++n) {
146
+ for(unsigned j=0; j<myarg->getRowLength(i); ++j) {
147
+ myarg->addForce( n*ncols+j, force*myval->getDerivative(k), false );
148
+ ++k;
149
+ }
150
+ }
151
+ }
152
+ } else {
153
+ for(unsigned i=0; i<getNumberOfComponents(); ++i) {
154
+ const Value* myval = getPntrToComponent(i);
155
+ double force = myval->getForce();
156
+ for(unsigned j=0; j<myarg->getNumberOfStoredValues(); ++j) {
157
+ myarg->addForce( j, force*myval->getDerivative(j) );
158
+ }
159
+ }
160
+ }
161
+ }
162
+
163
+ }
164
+ }
165
+ #endif
@@ -0,0 +1,43 @@
1
+ /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2
+ Copyright (c) 2012-2017 The plumed team
3
+ (see the PEOPLE file at the root of the distribution for a list of names)
4
+
5
+ See http://www.plumed.org for more information.
6
+
7
+ This file is part of plumed, version 2.
8
+
9
+ plumed is free software: you can redistribute it and/or modify
10
+ it under the terms of the GNU Lesser General Public License as published by
11
+ the Free Software Foundation, either version 3 of the License, or
12
+ (at your option) any later version.
13
+
14
+ plumed is distributed in the hope that it will be useful,
15
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
16
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17
+ GNU Lesser General Public License for more details.
18
+
19
+ You should have received a copy of the GNU Lesser General Public License
20
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
21
+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22
+ #ifndef __PLUMED_gridtools_ActionWithGrid_h
23
+ #define __PLUMED_gridtools_ActionWithGrid_h
24
+
25
+ #include "../core/ActionWithVector.h"
26
+ #include "GridCoordinatesObject.h"
27
+
28
+ namespace PLMD {
29
+ namespace gridtools {
30
+
31
+ class ActionWithGrid : public ActionWithVector {
32
+ public:
33
+ static void registerKeywords( Keywords& keys );
34
+ static ActionWithGrid* getInputActionWithGrid( Action* action );
35
+ explicit ActionWithGrid(const ActionOptions&ao);
36
+ void transferStashToValues( const std::vector<unsigned>& partialTaskList, const std::vector<double>& stash ) override ;
37
+ virtual std::vector<std::string> getGridCoordinateNames() const = 0;
38
+ virtual const GridCoordinatesObject& getGridCoordinatesObject() const = 0;
39
+ };
40
+
41
+ }
42
+ }
43
+ #endif
@@ -0,0 +1,99 @@
1
+ /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2
+ Copyright (c) 2015-2023 The plumed team
3
+ (see the PEOPLE file at the root of the distribution for a list of names)
4
+
5
+ See http://www.plumed.org for more information.
6
+
7
+ This file is part of plumed, version 2.
8
+
9
+ plumed is free software: you can redistribute it and/or modify
10
+ it under the terms of the GNU Lesser General Public License as published by
11
+ the Free Software Foundation, either version 3 of the License, or
12
+ (at your option) any later version.
13
+
14
+ plumed is distributed in the hope that it will be useful,
15
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
16
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17
+ GNU Lesser General Public License for more details.
18
+
19
+ You should have received a copy of the GNU Lesser General Public License
20
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
21
+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22
+ #ifndef __PLUMED_gridtools_EvaluateGridFunction_h
23
+ #define __PLUMED_gridtools_EvaluateGridFunction_h
24
+
25
+ #include "../function/FunctionSetup.h"
26
+ #include "ActionWithGrid.h"
27
+ #include "Interpolator.h"
28
+
29
+ namespace PLMD {
30
+ namespace gridtools {
31
+
32
+ class EvaluateGridFunction {
33
+ public:
34
+ /// Hold the function on the grid
35
+ Value* function=NULL;
36
+ /// This is the grid that is used here
37
+ ActionWithGrid* gridact=NULL;
38
+ /// How should we set the value of this function outside the range
39
+ bool set_zero_outside_range;
40
+ /// How are we doing interpolation
41
+ enum {spline,linear,floor,ceiling} interpolation_type;
42
+ /// This does the interpolating
43
+ std::unique_ptr<Interpolator> spline_interpolator;
44
+ /// This is used to setup the input gridobject's bounds with the grid data from values
45
+ static void registerKeywords( Keywords& keys );
46
+ static void read( EvaluateGridFunction& func, ActionWithArguments* action, function::FunctionOptions& options );
47
+ static void calc( const EvaluateGridFunction& func, bool noderiv, View<const double> args, function::FunctionOutput& funcout );
48
+ /// Get the vector containing the minimum value of the grid in each dimension
49
+ std::vector<std::string> getMin() const ;
50
+ /// Get the vector containing the maximum value of the grid in each dimension
51
+ std::vector<std::string> getMax() const ;
52
+ /// Get the periodicity of the grid
53
+ std::vector<bool> getPbc() const ;
54
+ /// Get the number of grid points in each direction
55
+ std::vector<std::size_t> getNbin() const ;
56
+ /// Get the grid spacing
57
+ const std::vector<double>& getGridSpacing() const ;
58
+ /// This gets the grid object
59
+ const GridCoordinatesObject & getGridObject() const ;
60
+ EvaluateGridFunction& operator=( const EvaluateGridFunction& m ) {
61
+ function = m.function;
62
+ gridact = m.gridact;
63
+ set_zero_outside_range = m.set_zero_outside_range;
64
+ interpolation_type = m.interpolation_type;
65
+ if( interpolation_type==spline ) {
66
+ spline_interpolator = Tools::make_unique<Interpolator>( function, gridact->getGridCoordinatesObject() );
67
+ }
68
+ return *this;
69
+ }
70
+ };
71
+
72
+ inline
73
+ std::vector<std::string> EvaluateGridFunction::getMin() const {
74
+ return (gridact->getGridCoordinatesObject()).getMin();
75
+ }
76
+
77
+ inline
78
+ std::vector<std::string> EvaluateGridFunction::getMax() const {
79
+ return (gridact->getGridCoordinatesObject()).getMax();
80
+ }
81
+
82
+ inline
83
+ std::vector<std::size_t> EvaluateGridFunction::getNbin() const {
84
+ return (gridact->getGridCoordinatesObject()).getNbin(false);
85
+ }
86
+
87
+ inline
88
+ const std::vector<double>& EvaluateGridFunction::getGridSpacing() const {
89
+ return (gridact->getGridCoordinatesObject()).getGridSpacing();
90
+ }
91
+
92
+ inline
93
+ const GridCoordinatesObject & EvaluateGridFunction::getGridObject() const {
94
+ return (gridact->getGridCoordinatesObject());
95
+ }
96
+
97
+ }
98
+ }
99
+ #endif
@@ -0,0 +1,295 @@
1
+ /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2
+ Copyright (c) 2011-2020 The plumed team
3
+ (see the PEOPLE file at the root of the distribution for a list of names)
4
+
5
+ See http://www.plumed.org for more information.
6
+
7
+ This file is part of plumed, version 2.
8
+
9
+ plumed is free software: you can redistribute it and/or modify
10
+ it under the terms of the GNU Lesser General Public License as published by
11
+ the Free Software Foundation, either version 3 of the License, or
12
+ (at your option) any later version.
13
+
14
+ plumed is distributed in the hope that it will be useful,
15
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
16
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17
+ GNU Lesser General Public License for more details.
18
+
19
+ You should have received a copy of the GNU Lesser General Public License
20
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
21
+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22
+ #ifndef __PLUMED_gridtools_FunctionOfGrid_h
23
+ #define __PLUMED_gridtools_FunctionOfGrid_h
24
+
25
+ #include "ActionWithGrid.h"
26
+ #include "../core/ParallelTaskManager.h"
27
+ #include "../function/FunctionSetup.h"
28
+ #include "../function/FunctionOfVector.h"
29
+ #include "../function/Custom.h"
30
+ #include "EvaluateGridFunction.h"
31
+
32
+ namespace PLMD {
33
+ namespace gridtools {
34
+
35
+ template <class T>
36
+ class FunctionOfGrid : public ActionWithGrid {
37
+ public:
38
+ using input_type = function::FunctionData<T>;
39
+ using PTM = ParallelTaskManager<FunctionOfGrid<T>>;
40
+ private:
41
+ /// The parallel task manager
42
+ PTM taskmanager;
43
+ //// Ensures we setup on first step
44
+ bool firststep;
45
+ /// The number of scalars that appear in the input for this calculation
46
+ unsigned nscalars;
47
+ /// Set equal to one if we are doing EvaluateGridFunction
48
+ unsigned argstart;
49
+ public:
50
+ static void registerKeywords(Keywords&);
51
+ explicit FunctionOfGrid(const ActionOptions&);
52
+ /// Get the number of derivatives for this action
53
+ unsigned getNumberOfDerivatives() override ;
54
+ /// Get the label to write in the graph
55
+ std::string writeInGraph() const override ;
56
+ /// Get the underlying names
57
+ std::vector<std::string> getGridCoordinateNames() const override ;
58
+ /// Get the underlying grid coordinates object
59
+ const GridCoordinatesObject& getGridCoordinatesObject() const override ;
60
+ /// Get the input data for doing the parallel calculation
61
+ void getInputData( std::vector<double>& inputdata ) const override ;
62
+ /// Do the calculation
63
+ void calculate() override ;
64
+ // Calculate the value of the function at a grid point
65
+ static void performTask( std::size_t task_index,
66
+ const function::FunctionData<T>& actiondata,
67
+ ParallelActionsInput& input,
68
+ ParallelActionsOutput& output );
69
+ /// Add the forces
70
+ // void apply() override;
71
+ void applyNonZeroRankForces( std::vector<double>& outforces ) override ;
72
+ /// This just returns one
73
+ static int getNumberOfValuesPerTask( std::size_t task_index,
74
+ const function::FunctionData<T>& actiondata );
75
+ /// Get the indexes where the forces are added
76
+ static void getForceIndices( std::size_t task_index,
77
+ std::size_t colno,
78
+ std::size_t ntotal_force,
79
+ const function::FunctionData<T>& actiondata,
80
+ const ParallelActionsInput& input,
81
+ ForceIndexHolder force_indices );
82
+ };
83
+
84
+ template <class T>
85
+ void FunctionOfGrid<T>::registerKeywords(Keywords& keys ) {
86
+ ActionWithGrid::registerKeywords(keys);
87
+ std::string name = keys.getDisplayName();
88
+ std::size_t und=name.find("_GRID");
89
+ keys.setDisplayName( name.substr(0,und) );
90
+ keys.reserve("compulsory","PERIODIC","if the output of your function is periodic then you should specify the periodicity of the function. If the output is not periodic you must state this using PERIODIC=NO");
91
+ T tfunc;
92
+ T::registerKeywords( keys );
93
+ if( typeid(tfunc)==typeid(function::Custom()) ) {
94
+ keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log");
95
+ }
96
+ if( keys.outputComponentExists(".#!value") ) {
97
+ keys.setValueDescription("grid","the grid obtained by doing an element-wise application of " + keys.getOutputComponentDescription(".#!value") + " to the input grid");
98
+ keys.addInputKeyword("compulsory","ARG","scalar/grid","the labels of the scalars and functions on a grid that we are using to compute the required function");
99
+ }
100
+ PTM::registerKeywords( keys );
101
+ }
102
+
103
+ template <class T>
104
+ FunctionOfGrid<T>::FunctionOfGrid(const ActionOptions&ao):
105
+ Action(ao),
106
+ ActionWithGrid(ao),
107
+ taskmanager(this),
108
+ firststep(true),
109
+ nscalars(0),
110
+ argstart(0) {
111
+ if( getNumberOfArguments()==0 ) {
112
+ error("found no arguments");
113
+ }
114
+ if( typeid(taskmanager.getActionInput().f)==typeid(EvaluateGridFunction) ) {
115
+ argstart=1;
116
+ }
117
+ // This will require a fix
118
+ if( getPntrToArgument(argstart)->getRank()==0 || !getPntrToArgument(argstart)->hasDerivatives() ) {
119
+ error("first input to this action must be a grid");
120
+ }
121
+ // Get the shape of the input grid
122
+ std::vector<std::size_t> shape( getPntrToArgument(argstart)->getShape() );
123
+ for(unsigned i=argstart+1; i<getNumberOfArguments(); ++i ) {
124
+ if( getPntrToArgument(i)->getRank()==0 ) {
125
+ nscalars++;
126
+ continue;
127
+ } else if( getPntrToArgument(i)->hasDerivatives() ) {
128
+ std::vector<std::size_t> s( getPntrToArgument(i)->getShape() );
129
+ if( s.size()!=shape.size() ) {
130
+ error("mismatch between dimensionalities of input grids");
131
+ } else if( nscalars>0 ) {
132
+ error("scalars should be specified in argument list after all functions on grid");
133
+ }
134
+ } else {
135
+ error("input arguments should be functions on grid or scalars");
136
+ }
137
+ }
138
+ auto & myfunc = taskmanager.getActionInput();
139
+ myfunc.argstart = argstart;
140
+ myfunc.nscalars = nscalars;
141
+ // Create the values for this grid
142
+ function::FunctionData<T>::setup( myfunc.f, keywords.getOutputComponents(), shape, true, this );
143
+ // Setup the task manager
144
+ taskmanager.setupParallelTaskManager( getNumberOfArguments()-argstart, nscalars );
145
+ }
146
+
147
+ template <class T>
148
+ std::string FunctionOfGrid<T>::writeInGraph() const {
149
+ std::size_t und = getName().find_last_of("_");
150
+ return getName().substr(0,und);
151
+ }
152
+
153
+ template <class T>
154
+ const GridCoordinatesObject& FunctionOfGrid<T>::getGridCoordinatesObject() const {
155
+ ActionWithGrid* ag=ActionWithGrid::getInputActionWithGrid( getPntrToArgument(0)->getPntrToAction() );
156
+ plumed_assert( ag );
157
+ return ag->getGridCoordinatesObject();
158
+ }
159
+
160
+ template <class T>
161
+ std::vector<std::string> FunctionOfGrid<T>::getGridCoordinateNames() const {
162
+ ActionWithGrid* ag=ActionWithGrid::getInputActionWithGrid( getPntrToArgument(0)->getPntrToAction() );
163
+ plumed_assert( ag );
164
+ return ag->getGridCoordinateNames();
165
+ }
166
+
167
+ template <class T>
168
+ unsigned FunctionOfGrid<T>::getNumberOfDerivatives() {
169
+ return getGridCoordinatesObject().getDimension();
170
+ }
171
+
172
+ template <class T>
173
+ void FunctionOfGrid<T>::calculate() {
174
+ if( firststep ) {
175
+ const GridCoordinatesObject& mygrid = getGridCoordinatesObject();
176
+ unsigned npoints = getPntrToArgument(0)->getNumberOfValues();
177
+ if( mygrid.getGridType()=="flat" ) {
178
+ std::vector<std::size_t> shape( mygrid.getNbin(true) );
179
+ for(unsigned i=1; i<getNumberOfArguments(); ++i ) {
180
+ if( getPntrToArgument(i)->getRank()==0 ) {
181
+ continue;
182
+ }
183
+ std::vector<std::size_t> s( getPntrToArgument(i)->getShape() );
184
+ for(unsigned j=0; j<shape.size(); ++j) {
185
+ if( shape[j]!=s[j] ) {
186
+ error("mismatch between sizes of input grids");
187
+ }
188
+ }
189
+ }
190
+ for(unsigned i=0; i<getNumberOfComponents(); ++i) {
191
+ if( getPntrToComponent(i)->getRank()>0 ) {
192
+ getPntrToComponent(i)->setShape(shape);
193
+ }
194
+ }
195
+ }
196
+ // This resizes the scalars
197
+ for(unsigned i=0; i<getNumberOfComponents(); ++i) {
198
+ if( getPntrToComponent(i)->getRank()==0 ) {
199
+ getPntrToComponent(i)->resizeDerivatives( npoints );
200
+ }
201
+ }
202
+ taskmanager.setupParallelTaskManager( getNumberOfArguments()-argstart, nscalars );
203
+ firststep=false;
204
+ }
205
+ taskmanager.runAllTasks();
206
+ }
207
+
208
+ template <class T>
209
+ void FunctionOfGrid<T>::getInputData( std::vector<double>& inputdata ) const {
210
+ unsigned nargs = getNumberOfArguments();
211
+
212
+ std::size_t ntasks = 0, ngder = 0;
213
+ for(unsigned i=argstart; i<nargs; ++i) {
214
+ if( getPntrToArgument(i)->getRank()>0 ) {
215
+ ntasks = getPntrToArgument(i)->getNumberOfStoredValues();
216
+ ngder = getPntrToArgument(i)->getNumberOfDerivatives();
217
+ break;
218
+ }
219
+ }
220
+
221
+ std::size_t ndata = static_cast<std::size_t>(nargs-argstart)*ntasks*(1+ngder);
222
+ if( inputdata.size()!=ndata ) {
223
+ inputdata.resize( ndata );
224
+ }
225
+
226
+ for(unsigned j=argstart; j<nargs; ++j) {
227
+ const Value* myarg = getPntrToArgument(j);
228
+ if( myarg->getRank()==0 ) {
229
+ double val = myarg->get();
230
+ for(unsigned i=0; i<ntasks; ++i) {
231
+ inputdata[(nargs-argstart)*(1+ngder)*i + j-argstart] = val;
232
+ }
233
+ } else {
234
+ for(unsigned i=0; i<ntasks; ++i) {
235
+ inputdata[(nargs-argstart)*(1+ngder)*i + j-argstart] = myarg->get(i);
236
+ for(unsigned k=0; k<ngder; ++k) {
237
+ inputdata[(nargs-argstart)*(1+ngder)*i + (nargs-argstart) + (j-argstart)*ngder + k] = myarg->getGridDerivative( i, k );
238
+ }
239
+ }
240
+ }
241
+ }
242
+ }
243
+
244
+ template <class T>
245
+ void FunctionOfGrid<T>::performTask( std::size_t task_index,
246
+ const function::FunctionData<T>& actiondata,
247
+ ParallelActionsInput& input,
248
+ ParallelActionsOutput& output ) {
249
+
250
+ std::size_t rank=input.ranks[actiondata.argstart];
251
+ std::size_t spacing = (input.nargs-actiondata.argstart)*(1+rank);
252
+ auto funcout = function::FunctionOutput::create( input.ncomponents,
253
+ output.values.data(),
254
+ input.nargs-actiondata.argstart,
255
+ output.derivatives.data() );
256
+ T::calc( actiondata.f,
257
+ input.noderiv,
258
+ View<const double>( input.inputdata + task_index*spacing,
259
+ input.nargs-actiondata.argstart ),
260
+ funcout );
261
+
262
+ for(unsigned j=actiondata.argstart; j<input.nargs; ++j) {
263
+ double df = output.derivatives[j-actiondata.argstart];
264
+ View<const double> inders( input.inputdata + task_index*spacing + (input.nargs-actiondata.argstart) + (j-actiondata.argstart)*rank, rank );
265
+ for(unsigned k=0; k<input.ranks[actiondata.argstart]; ++k) {
266
+ output.values[1+k] += df*inders[k];
267
+ }
268
+ }
269
+ }
270
+
271
+ template <class T>
272
+ void FunctionOfGrid<T>::applyNonZeroRankForces( std::vector<double>& outforces ) {
273
+ taskmanager.applyForces( outforces );
274
+ }
275
+
276
+ template <class T>
277
+ int FunctionOfGrid<T>::getNumberOfValuesPerTask( std::size_t task_index,
278
+ const function::FunctionData<T>& actiondata ) {
279
+ return 1;
280
+ }
281
+
282
+ template <class T>
283
+ void FunctionOfGrid<T>::getForceIndices( std::size_t task_index,
284
+ std::size_t colno,
285
+ std::size_t ntotal_force,
286
+ const function::FunctionData<T>& actiondata,
287
+ const ParallelActionsInput& input,
288
+ ForceIndexHolder force_indices ) {
289
+ // The force indices are found in the same way as in FunctionOfVector so we reuse that function here
290
+ function::FunctionOfVector<T>::getForceIndices( task_index, colno, ntotal_force, actiondata, input, force_indices );
291
+ }
292
+
293
+ }
294
+ }
295
+ #endif