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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+ #
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+ # This file is part of the GROMACS molecular simulation package.
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+ # the research papers on the package. Check out https://www.gromacs.org.
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+
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+ if("${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}")
35
+ message(FATAL_ERROR "CMake called with the wrong directory; please use the top GROMACS directory (${CMAKE_CURRENT_SOURCE_DIR}/../../)")
36
+ endif()
37
+
38
+ set(LIBGROMACS_SOURCES)
39
+
40
+ if (GMX_CLANG_CUDA)
41
+ include(gmxClangCudaUtils)
42
+ endif()
43
+
44
+ set_property(GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
45
+ set_property(GLOBAL PROPERTY CUDA_SOURCES)
46
+ set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
47
+ set_property(GLOBAL PROPERTY GMX_AVX_512_SOURCE)
48
+
49
+ set(libgromacs_object_library_dependencies "")
50
+ function (_gmx_add_files_to_property PROPERTY)
51
+ foreach (_file ${ARGN})
52
+ if (IS_ABSOLUTE "${_file}")
53
+ set_property(GLOBAL APPEND PROPERTY ${PROPERTY} ${_file})
54
+ else()
55
+ set_property(GLOBAL APPEND PROPERTY ${PROPERTY}
56
+ ${CMAKE_CURRENT_LIST_DIR}/${_file})
57
+ endif()
58
+ endforeach()
59
+ endfunction ()
60
+
61
+ function (gmx_add_libgromacs_sources)
62
+ _gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
63
+ endfunction ()
64
+
65
+ # Permit the configuration to disable compiling the many nbnxm kernels
66
+ # and others involved in force calculations. Currently only
67
+ # short-ranged and bonded kernels are disabled this way, but in future
68
+ # others may be appropriate. Thus the cmake option is not specific to
69
+ # nbnxm module.
70
+ option(GMX_USE_SIMD_KERNELS "Whether to compile NBNXM and other SIMD kernels" ON)
71
+ mark_as_advanced(GMX_USE_SIMD_KERNELS)
72
+
73
+ # pulling is using the muparser target as well, so detect it early
74
+ gmx_manage_muparser()
75
+
76
+ # Add these contents first because linking their tests can take a lot
77
+ # of time, so we want lots of parallel work still available after
78
+ # linking starts.
79
+ add_subdirectory(utility)
80
+ # Add normal contents
81
+ add_subdirectory(gmxlib)
82
+ add_subdirectory(mdlib)
83
+ add_subdirectory(applied_forces)
84
+ add_subdirectory(listed_forces)
85
+ add_subdirectory(nbnxm)
86
+ add_subdirectory(commandline)
87
+ add_subdirectory(domdec)
88
+ add_subdirectory(ewald)
89
+ add_subdirectory(fft)
90
+ add_subdirectory(gpu_utils)
91
+ add_subdirectory(hardware)
92
+ add_subdirectory(linearalgebra)
93
+ add_subdirectory(math)
94
+ add_subdirectory(mdrun)
95
+ add_subdirectory(mdrunutility)
96
+ add_subdirectory(mdspan)
97
+ add_subdirectory(mdtypes)
98
+ add_subdirectory(onlinehelp)
99
+ add_subdirectory(options)
100
+ add_subdirectory(pbcutil)
101
+ add_subdirectory(random)
102
+ add_subdirectory(restraint)
103
+ add_subdirectory(tables)
104
+ add_subdirectory(taskassignment)
105
+ add_subdirectory(timing)
106
+ add_subdirectory(topology)
107
+ add_subdirectory(trajectory)
108
+ add_subdirectory(swap)
109
+ add_subdirectory(essentialdynamics)
110
+ add_subdirectory(pulling)
111
+ add_subdirectory(simd)
112
+ add_subdirectory(imd)
113
+ add_subdirectory(compat)
114
+ add_subdirectory(mimic)
115
+ add_subdirectory(modularsimulator)
116
+ add_subdirectory(gmxana)
117
+ add_subdirectory(gmxpreprocess)
118
+ add_subdirectory(correlationfunctions)
119
+ add_subdirectory(statistics)
120
+ add_subdirectory(analysisdata)
121
+ add_subdirectory(coordinateio)
122
+ add_subdirectory(trajectoryanalysis)
123
+ add_subdirectory(energyanalysis)
124
+ add_subdirectory(tools)
125
+
126
+ get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
127
+ list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
128
+
129
+ # This would be the standard way to include thread_mpi, but
130
+ # we want libgromacs to link the functions directly
131
+ #if(GMX_THREAD_MPI)
132
+ # add_subdirectory(thread_mpi)
133
+ #endif()
134
+ #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
135
+ tmpi_get_source_list(THREAD_MPI_SOURCES ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/src)
136
+ add_library(thread_mpi OBJECT ${THREAD_MPI_SOURCES})
137
+ target_compile_definitions(thread_mpi PRIVATE HAVE_CONFIG_H)
138
+ target_compile_definitions(thread_mpi PRIVATE TMPI_EXPORTS TMPI_USE_VISIBILITY)
139
+ if(CYGWIN)
140
+ # Needs POSIX-isms for strdup, not just std-isms
141
+ target_compile_definitions(thread_mpi PRIVATE _POSIX_C_SOURCE=200809L)
142
+ endif()
143
+ gmx_target_compile_options(thread_mpi)
144
+ if (WIN32)
145
+ gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
146
+ endif()
147
+ list(APPEND libgromacs_object_library_dependencies thread_mpi)
148
+
149
+ # This code is here instead of utility/CMakeLists.txt, because CMake
150
+ # custom commands and source file properties can only be set in the directory
151
+ # that contains the target that uses them.
152
+ # TODO: Generate a header instead that can be included from baseversion.cpp.
153
+ # That probably simplifies things somewhat.
154
+ set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
155
+ gmx_configure_version_file(
156
+ utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
157
+ REMOTE_HASH
158
+ EXTRA_VARS
159
+ GMX_SOURCE_DOI
160
+ GMX_RELEASE_HASH
161
+ GMX_SOURCE_HASH
162
+ )
163
+ list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
164
+
165
+ # Mark some shared GPU implementation files to compile with CUDA if needed
166
+ if (GMX_GPU_CUDA)
167
+ get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
168
+ set_source_files_properties(${CUDA_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
169
+ endif()
170
+
171
+ if (GMX_GPU_CUDA)
172
+ if(GMX_USE_cuFFTMp)
173
+ # needed as we need to include cufftmp include path before CUDA include path
174
+ cuda_include_directories(${cuFFTMp_INCLUDE_DIR})
175
+ endif()
176
+ # Work around FindCUDA that prevents using target_link_libraries()
177
+ # with keywords otherwise...
178
+ set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
179
+ if (NOT GMX_CLANG_CUDA)
180
+ gmx_cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
181
+ else()
182
+ add_library(libgromacs ${LIBGROMACS_SOURCES})
183
+ endif()
184
+
185
+ #we cannot link with both cufftmp and cufft
186
+ if(GMX_USE_cuFFTMp)
187
+ target_link_libraries(libgromacs PRIVATE ${cuFFTMp_LIBRARY})
188
+ else()
189
+ target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
190
+ endif()
191
+ else()
192
+ add_library(libgromacs ${LIBGROMACS_SOURCES})
193
+ endif()
194
+
195
+ if (TARGET Heffte::Heffte)
196
+ target_link_libraries(libgromacs PRIVATE Heffte::Heffte)
197
+ endif()
198
+
199
+ if(GMX_GPU_FFT_VKFFT)
200
+ target_link_libraries(libgromacs PRIVATE VkFFT)
201
+ endif()
202
+ if(GMX_GPU_FFT_ROCFFT)
203
+ target_link_libraries(libgromacs PRIVATE roc::rocfft)
204
+ endif()
205
+
206
+ target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:common>)
207
+ # As long as the libgromacs target has source files that reference headers from
208
+ # modules that don't provide CMake targets, libgromacs needs to use `src/`
209
+ # amongst its include directories (to support `#include "gromacs/module/header.h"`).
210
+ add_library(legacy_modules INTERFACE)
211
+ target_include_directories(legacy_modules INTERFACE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
212
+ target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:legacy_modules>)
213
+
214
+ # Add these contents first because linking their tests can take a lot
215
+ # of time, so we want lots of parallel work still available after
216
+ # linking starts.
217
+ add_subdirectory(fileio)
218
+ add_subdirectory(selection)
219
+
220
+ # Handle the object libraries that contain the source file
221
+ # dependencies that need special handling because they are generated
222
+ # or external code.
223
+ foreach(object_library ${libgromacs_object_library_dependencies})
224
+ if (BUILD_SHARED_LIBS)
225
+ set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
226
+ endif()
227
+ target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
228
+ target_compile_definitions(${object_library} PRIVATE TMPI_USE_VISIBILITY)
229
+ target_link_libraries(${object_library} PRIVATE common)
230
+
231
+ # Add the sources from the object libraries to the main library.
232
+ target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
233
+ endforeach()
234
+ gmx_target_compile_options(libgromacs)
235
+ target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H
236
+ TMPI_EXPORTS
237
+ PUBLIC TMPI_USE_VISIBILITY)
238
+
239
+ target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
240
+
241
+ if (GMX_GPU_FFT_CLFFT)
242
+ if (NOT GMX_GPU_OPENCL)
243
+ message(FATAL_ERROR "clFFT is only supported in OpenCL builds")
244
+ endif()
245
+ option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
246
+ mark_as_advanced(GMX_EXTERNAL_CLFFT)
247
+
248
+ # Default to using clFFT found on the system
249
+ # switch to quiet at the second run.
250
+ if (DEFINED clFFT_LIBRARY)
251
+ set (clFFT_FIND_QUIETLY TRUE)
252
+ endif()
253
+ find_package(clFFT)
254
+ if (NOT clFFT_FOUND)
255
+ if (GMX_EXTERNAL_CLFFT)
256
+ message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
257
+ endif()
258
+
259
+ if(MSVC)
260
+ message(FATAL_ERROR
261
+ "An OpenCL build was requested with Visual Studio compiler, but GROMACS
262
+ requires clFFT, which was not found on your system. GROMACS does bundle
263
+ clFFT to help with building for OpenCL, but that clFFT has not yet been
264
+ ported to the more recent versions of that compiler that GROMACS itself
265
+ requires. Thus for now, OpenCL is not available with MSVC and the internal
266
+ build of clFFT in GROMACS 2019 and newer. Either change compiler, try
267
+ installing a clFFT package, use VkFFT by setting -DGMX_GPU_FFT_LIBRARY=VkFFT,
268
+ or use GROMACS 2018.8 release (no longer maintained).")
269
+ endif()
270
+
271
+ # Fall back on the internal version
272
+ set (_clFFT_dir ../external/clFFT/src)
273
+ add_subdirectory(${_clFFT_dir} clFFT-build)
274
+ target_sources(libgromacs PRIVATE
275
+ $<TARGET_OBJECTS:clFFT>
276
+ )
277
+ target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
278
+ # Use the magic variable for how to link any library needed for
279
+ # dlopen, etc. which is -ldl where needed, and empty otherwise
280
+ # (e.g. Windows, BSD, Mac).
281
+ target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
282
+ else()
283
+ target_link_libraries(libgromacs PRIVATE clFFT)
284
+ endif()
285
+ endif()
286
+
287
+ # Permit GROMACS code to include externally developed headers, such as
288
+ # the functionality from the nonstd project that we use for
289
+ # gmx::compat::optional. These are included as system headers so that
290
+ # no warnings are issued from them.
291
+ #
292
+ # TODO Perhaps generalize this for all headers from src/external
293
+ target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
294
+
295
+ if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
296
+ # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
297
+ # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
298
+ # with the SIMD_AVX_512_CXX_FLAGS flags.
299
+ set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
300
+ endif()
301
+
302
+ # Do any special handling needed for .cpp files that use
303
+ # CUDA runtime headers
304
+ if (GMX_GPU_CUDA AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
305
+ foreach(_compile_flag ${NVCC_CLANG_SUPPRESSIONS_CXXFLAGS})
306
+ set(GMX_CUDA_CLANG_FLAGS "${GMX_CUDA_CLANG_FLAGS} ${_compile_flag}")
307
+ endforeach()
308
+ if (GMX_CLANG_CUDA)
309
+ foreach (_file ${LIBGROMACS_SOURCES})
310
+ get_filename_component(_ext ${_file} EXT)
311
+ get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
312
+ if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
313
+ gmx_compile_cuda_file_with_clang(${_file})
314
+ endif()
315
+ endforeach()
316
+ else()
317
+ get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
318
+ set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS ${GMX_CUDA_CLANG_FLAGS})
319
+ endif()
320
+ endif()
321
+
322
+ # Only add the -fsycl flag to sources that really need it
323
+ if (GMX_GPU_SYCL)
324
+ get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
325
+ add_sycl_to_target(TARGET libgromacs SOURCES ${SYCL_SOURCES})
326
+ endif()
327
+
328
+ gmx_setup_tng_for_libgromacs()
329
+
330
+ # We apply the SYCL flag explicitly just for libgromacs, since bugs in the beta versions of
331
+ # icpx/dpcpp leads to crashes if we try to link an library without any SYCL code with the
332
+ # -fsycl flag enabled. Once that bug is fixed, we should change it to simply add
333
+ # SYCL_CXX_FLAGS to GMX_SHARED_LINKER_FLAGS.
334
+ target_link_libraries(libgromacs
335
+ PRIVATE
336
+ ${EXTRAE_LIBRARIES}
337
+ ${GMX_EXTRA_LIBRARIES}
338
+ ${GMX_COMMON_LIBRARIES}
339
+ ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
340
+ ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
341
+ ${SYCL_CXX_FLAGS}
342
+ ${OpenCL_LIBRARIES}
343
+ $<$<PLATFORM_ID:SunOS>:socket>
344
+ PUBLIC
345
+ ${GMX_PUBLIC_LIBRARIES}
346
+ )
347
+ target_link_libraries(libgromacs PRIVATE legacy_api)
348
+ # Dependencies from libgromacs to the modules are set up here, but
349
+ # once the add_subdirectory() commands are re-ordered then
350
+ # responsibility for setting this up will move to the respective
351
+ # modules.
352
+ target_link_libraries(libgromacs PRIVATE
353
+ $<BUILD_INTERFACE:analysisdata>
354
+ $<BUILD_INTERFACE:applied_forces>
355
+ $<BUILD_INTERFACE:commandline>
356
+ $<BUILD_INTERFACE:compat>
357
+ $<BUILD_INTERFACE:coordinateio>
358
+ $<BUILD_INTERFACE:correlationfunctions>
359
+ $<BUILD_INTERFACE:domdec>
360
+ # $<BUILD_INTERFACE:energyanalysis>
361
+ $<BUILD_INTERFACE:essentialdynamics>
362
+ $<BUILD_INTERFACE:ewald>
363
+ $<BUILD_INTERFACE:fft>
364
+ $<BUILD_INTERFACE:fileio>
365
+ $<BUILD_INTERFACE:gmxana>
366
+ $<BUILD_INTERFACE:gmxlib>
367
+ $<BUILD_INTERFACE:gmxpreprocess>
368
+ $<BUILD_INTERFACE:gpu_utils>
369
+ $<BUILD_INTERFACE:hardware>
370
+ $<BUILD_INTERFACE:imd>
371
+ $<BUILD_INTERFACE:linearalgebra>
372
+ $<BUILD_INTERFACE:listed_forces>
373
+ $<BUILD_INTERFACE:math>
374
+ $<BUILD_INTERFACE:mdlib>
375
+ $<BUILD_INTERFACE:mdrun>
376
+ $<BUILD_INTERFACE:mdrunutility>
377
+ $<BUILD_INTERFACE:mdspan>
378
+ $<BUILD_INTERFACE:mdtypes>
379
+ $<BUILD_INTERFACE:mimic>
380
+ $<BUILD_INTERFACE:modularsimulator>
381
+ $<BUILD_INTERFACE:nbnxm>
382
+ $<BUILD_INTERFACE:onlinehelp>
383
+ $<BUILD_INTERFACE:options>
384
+ $<BUILD_INTERFACE:pbcutil>
385
+ $<BUILD_INTERFACE:pulling>
386
+ $<BUILD_INTERFACE:random>
387
+ $<BUILD_INTERFACE:restraint>
388
+ $<BUILD_INTERFACE:selection>
389
+ $<BUILD_INTERFACE:simd>
390
+ $<BUILD_INTERFACE:statistics>
391
+ $<BUILD_INTERFACE:swap>
392
+ $<BUILD_INTERFACE:tables>
393
+ $<BUILD_INTERFACE:taskassignment>
394
+ $<BUILD_INTERFACE:timing>
395
+ $<BUILD_INTERFACE:tools>
396
+ $<BUILD_INTERFACE:topology>
397
+ $<BUILD_INTERFACE:trajectory>
398
+ $<BUILD_INTERFACE:trajectoryanalysis>
399
+ $<BUILD_INTERFACE:utility>
400
+ )
401
+ if (GMX_OPENMP)
402
+ target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
403
+ endif()
404
+ set_target_properties(libgromacs PROPERTIES
405
+ OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
406
+ SOVERSION ${LIBRARY_SOVERSION_MAJOR}
407
+ VERSION ${LIBRARY_VERSION}
408
+ )
409
+
410
+ gmx_manage_lmfit()
411
+ target_link_libraries(libgromacs PRIVATE lmfit)
412
+ target_link_libraries(libgromacs PRIVATE muparser::muparser)
413
+
414
+ # Make sure we fix "everything" found by compilers that support that
415
+ gmx_warn_on_everything(libgromacs)
416
+ if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
417
+ target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
418
+ #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
419
+ #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
420
+ /wd6001 #unitialized memory
421
+ /wd6011 #derefencing NULL
422
+ /wd6053 #prior call not zero-terminate
423
+ /wd6054 #might not be zero-terminated
424
+ /wd6385 #reading invalid data
425
+ /wd6386 #buffer overrun
426
+ /wd6387 #could be '0'
427
+ /wd28199 #uninitialized memory
428
+ # For compile time constant (e.g. templates) the following warnings have flase postives
429
+ /wd6239 #(<non-zero> && <expr>)
430
+ /wd6240 #(<expr> && <non-zero>)
431
+ /wd6294 #Ill-defined for-loop
432
+ /wd6326 #comparison of constant with other constant
433
+ /wd28020 #expression involving paramter is not true
434
+ # Misc
435
+ /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
436
+ /wd6993 #OpenMP ignored
437
+ #TODO
438
+ /wd6031 #return value ignored (important - mostly warnigns about sscanf)
439
+ /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
440
+ /wd6246 #hides declaration
441
+ >
442
+ )
443
+ endif()
444
+
445
+ if (GMX_CLANG_TIDY)
446
+ set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
447
+ "${CLANG_TIDY_EXE};-warnings-as-errors=*")
448
+ endif()
449
+
450
+ # TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
451
+ if (BUILD_SHARED_LIBS)
452
+ install(TARGETS libgromacs
453
+ EXPORT libgromacs
454
+ LIBRARY
455
+ DESTINATION ${CMAKE_INSTALL_LIBDIR}
456
+ COMPONENT libraries
457
+ RUNTIME
458
+ DESTINATION ${CMAKE_INSTALL_BINDIR}
459
+ COMPONENT libraries
460
+ ARCHIVE
461
+ DESTINATION ${CMAKE_INSTALL_LIBDIR}
462
+ COMPONENT libraries
463
+ INCLUDES DESTINATION include)
464
+ target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
465
+ # legacy headers use c++17 features, so consumer codes need to use that standard, too
466
+ if(GMX_INSTALL_LEGACY_API)
467
+ target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
468
+ endif()
469
+ # only install pkg-config and cmake target files when library is installed
470
+ include(InstallLibInfo.cmake)
471
+ endif()
472
+ add_library(Gromacs::libgromacs ALIAS libgromacs)
473
+
474
+
475
+ # Technically, the user could want to do this for an OpenCL build
476
+ # using the CUDA runtime, but currently there's no reason to want to
477
+ # do that.
478
+ if (INSTALL_CUDART_LIB) #can be set manual by user
479
+ if (GMX_GPU_CUDA)
480
+ foreach(CUDA_LIB ${CUDA_LIBRARIES})
481
+ string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
482
+ if(IS_CUDART) #libcuda should not be installed
483
+ #install also name-links (linker uses those)
484
+ file(GLOB CUDA_LIBS ${CUDA_LIB}*)
485
+ install(FILES ${CUDA_LIBS} DESTINATION
486
+ ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
487
+ endif()
488
+ endforeach()
489
+ else()
490
+ message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
491
+ endif()
492
+ endif()
493
+
494
+ if(GMX_GPU_OPENCL)
495
+ # Install the utility headers
496
+ file(GLOB OPENCL_INSTALLED_FILES
497
+ gpu_utils/vectype_ops.clh
498
+ gpu_utils/device_utils.clh
499
+ )
500
+ install(FILES ${OPENCL_INSTALLED_FILES}
501
+ DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
502
+ COMPONENT libraries)
503
+ file(GLOB OPENCL_INSTALLED_FILES
504
+ pbcutil/ishift.h
505
+ )
506
+ install(FILES ${OPENCL_INSTALLED_FILES}
507
+ DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
508
+ COMPONENT libraries)
509
+
510
+ # Install the NBNXM source and headers
511
+ file(GLOB OPENCL_INSTALLED_FILES
512
+ nbnxm/constants.h
513
+ )
514
+ install(FILES ${OPENCL_INSTALLED_FILES}
515
+ DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
516
+ COMPONENT libraries)
517
+ file(GLOB OPENCL_INSTALLED_FILES
518
+ nbnxm/opencl/nbnxm_ocl_kernels.cl
519
+ nbnxm/opencl/nbnxm_ocl_kernel.clh
520
+ nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
521
+ nbnxm/opencl/nbnxm_ocl_kernels.clh
522
+ nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
523
+ nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
524
+ nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
525
+ nbnxm/opencl/nbnxm_ocl_consts.h
526
+ )
527
+ install(FILES ${OPENCL_INSTALLED_FILES}
528
+ DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
529
+ COMPONENT libraries)
530
+
531
+ # Install the PME source and headers
532
+ file(GLOB OPENCL_INSTALLED_FILES
533
+ ewald/pme_spread.clh
534
+ ewald/pme_solve.clh
535
+ ewald/pme_gather.clh
536
+ ewald/pme_gpu_calculate_splines.clh
537
+ ewald/pme_program.cl
538
+ ewald/pme_gpu_types.h
539
+ )
540
+ install(FILES ${OPENCL_INSTALLED_FILES}
541
+ DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald
542
+ COMPONENT libraries)
543
+ endif()
544
+
545
+ include(GenerateExportHeader)
546
+ generate_export_header(libgromacs EXPORT_FILE_NAME "${CMAKE_BINARY_DIR}/api/legacy/include/gromacs/libgromacs_export.h")