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
  295. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/md.cpp +2348 -0
  296. plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/md.cpp.preplumed +2091 -0
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@@ -0,0 +1,422 @@
1
+ !
2
+ ! Copyright (C) 2001-2011 Quantum ESPRESSO group
3
+ ! This file is distributed under the terms of the
4
+ ! GNU General Public License. See the file `License'
5
+ ! in the root directory of the present distribution,
6
+ ! or http://www.gnu.org/copyleft/gpl.txt .
7
+ !
8
+ !----------------------------------------------------------------------------
9
+ ! TB
10
+ ! included gate related forces
11
+ !----------------------------------------------------------------------------
12
+ !
13
+ !----------------------------------------------------------------------------
14
+ SUBROUTINE forces()
15
+ !----------------------------------------------------------------------------
16
+ !
17
+ ! ... This routine is a driver routine which computes the forces
18
+ ! ... acting on the atoms. The complete expression of the forces
19
+ ! ... contains four parts which are computed by different routines:
20
+ !
21
+ ! ... a) force_lc, local contribution to the forces
22
+ ! ... b) force_cc, contribution due to NLCC
23
+ ! ... c) force_ew, contribution due to the electrostatic ewald term
24
+ ! ... d) force_us, contribution due to the non-local potential
25
+ ! ... e) force_corr, correction term for incomplete self-consistency
26
+ ! ... f) force_hub, contribution due to the Hubbard term
27
+ ! ... g) force_london, semi-empirical correction for dispersion forces
28
+ ! ... h) force_d3, Grimme-D3 (DFT-D3) correction to dispersion forces
29
+ !
30
+ !
31
+ USE kinds, ONLY : DP
32
+ USE io_global, ONLY : stdout
33
+ USE cell_base, ONLY : at, bg, alat, omega
34
+ USE ions_base, ONLY : nat, ntyp => nsp, ityp, tau, zv, amass, extfor, atm
35
+ USE fft_base, ONLY : dfftp
36
+ USE gvect, ONLY : ngm, gstart, ngl, nl, igtongl, g, gg, gcutm
37
+ USE lsda_mod, ONLY : nspin
38
+ USE symme, ONLY : symvector
39
+ USE vlocal, ONLY : strf, vloc
40
+ USE force_mod, ONLY : force, lforce, sumfor
41
+ USE scf, ONLY : rho
42
+ USE ions_base, ONLY : if_pos
43
+ USE ldaU, ONLY : lda_plus_u, U_projection
44
+ USE extfield, ONLY : tefield, forcefield, gate, forcegate, relaxz
45
+ USE control_flags, ONLY : gamma_only, remove_rigid_rot, textfor, &
46
+ iverbosity, llondon, ldftd3, lxdm, ts_vdw
47
+ USE plugin_flags
48
+ USE bp, ONLY : lelfield, gdir, l3dstring, efield_cart, &
49
+ efield_cry,efield
50
+ USE uspp, ONLY : okvan
51
+ USE martyna_tuckerman, ONLY: do_comp_mt, wg_corr_force
52
+ USE london_module, ONLY : force_london
53
+ USE dftd3_api, ONLY : get_atomic_number, dftd3_calc
54
+ USE dftd3_qe, ONLY: dftd3_pbc_gdisp, dftd3
55
+
56
+ USE xdm_module, ONLY : force_xdm
57
+ USE tsvdw_module, ONLY : FtsvdW
58
+ USE esm, ONLY : do_comp_esm, esm_bc, esm_force_ew
59
+ USE qmmm, ONLY : qmmm_mode
60
+ !
61
+ IMPLICIT NONE
62
+ !
63
+ REAL(DP), ALLOCATABLE :: forcenl(:,:), &
64
+ forcelc(:,:), &
65
+ forcecc(:,:), &
66
+ forceion(:,:), &
67
+ force_disp(:,:),&
68
+ force_d3(:,:),&
69
+ force_disp_xdm(:,:),&
70
+ force_mt(:,:), &
71
+ forcescc(:,:), &
72
+ forces_bp_efield(:,:), &
73
+ forceh(:,:)
74
+ ! nonlocal, local, core-correction, ewald, scf correction terms, and hubbard
75
+ !
76
+ ! aux is used to store a possible additional density
77
+ ! now defined in real space
78
+ !
79
+ COMPLEX(DP), ALLOCATABLE :: auxg(:), auxr(:)
80
+ !
81
+ REAL(DP) :: sumscf, sum_mm
82
+ REAL(DP), PARAMETER :: eps = 1.e-12_dp
83
+ INTEGER :: ipol, na
84
+ ! counter on polarization
85
+ ! counter on atoms
86
+ !
87
+ REAL(DP) :: latvecs(3,3)
88
+ INTEGER :: atnum(1:nat)
89
+ REAL(DP) :: stress_dftd3(3,3)
90
+ !
91
+ !
92
+ CALL start_clock( 'forces' )
93
+ !
94
+ ALLOCATE( forcenl( 3, nat ), forcelc( 3, nat ), forcecc( 3, nat ), &
95
+ forceh( 3, nat ), forceion( 3, nat ), forcescc( 3, nat ) )
96
+ !
97
+ forcescc(:,:) = 0.D0
98
+ forceh(:,:) = 0.D0
99
+ force (:,:) = 0.D0
100
+ !
101
+ ! ... The nonlocal contribution is computed here
102
+ !
103
+ CALL force_us( forcenl )
104
+ !
105
+ ! ... The local contribution
106
+ !
107
+ CALL force_lc( nat, tau, ityp, alat, omega, ngm, ngl, igtongl, &
108
+ g, rho%of_r, nl, nspin, gstart, gamma_only, vloc, &
109
+ forcelc )
110
+ !
111
+ ! ... The NLCC contribution
112
+ !
113
+ CALL force_cc( forcecc )
114
+ !
115
+ ! ... The Hubbard contribution
116
+ ! (included by force_us if using beta as local projectors)
117
+ !
118
+ IF ( lda_plus_u .AND. U_projection.NE.'pseudo' ) CALL force_hub( forceh )
119
+ !
120
+ ! ... The ionic contribution is computed here
121
+ !
122
+ IF( do_comp_esm ) THEN
123
+ CALL esm_force_ew( forceion )
124
+ ELSE
125
+ CALL force_ew( alat, nat, ntyp, ityp, zv, at, bg, tau, omega, g, &
126
+ gg, ngm, gstart, gamma_only, gcutm, strf, forceion )
127
+ END IF
128
+ !
129
+ ! ... the semi-empirical dispersion correction
130
+ !
131
+ IF ( llondon ) THEN
132
+ !
133
+ ALLOCATE ( force_disp ( 3 , nat ) )
134
+ force_disp ( : , : ) = 0.0_DP
135
+ force_disp = force_london( alat , nat , ityp , at , bg , tau )
136
+ !
137
+ END IF
138
+ !
139
+ ! ... The Grimme-D3 dispersion correction
140
+ !
141
+ IF ( ldftd3 ) THEN
142
+ !
143
+ ALLOCATE ( force_d3 (3, nat))
144
+ force_d3 ( : , : ) = 0.0_DP
145
+ latvecs(:,:) = at(:,:)*alat
146
+ tau(:,:)=tau(:,:)*alat
147
+ atnum(:) = get_atomic_number(atm(ityp(:)))
148
+ call dftd3_pbc_gdisp(dftd3, tau, atnum, latvecs, &
149
+ force_d3, stress_dftd3)
150
+ force_d3 = -2.d0*force_d3
151
+ tau(:,:)=tau(:,:)/alat
152
+ END IF
153
+ !
154
+ !
155
+ IF (lxdm) THEN
156
+ ALLOCATE (force_disp_xdm(3,nat))
157
+ force_disp_xdm = 0._dp
158
+ force_disp_xdm = force_xdm(nat)
159
+ end if
160
+
161
+ !
162
+ ! ... The SCF contribution
163
+ !
164
+ CALL force_corr( forcescc )
165
+ !
166
+ IF (do_comp_mt) THEN
167
+ !
168
+ ALLOCATE ( force_mt ( 3 , nat ) )
169
+ CALL wg_corr_force( .true.,omega, nat, ntyp, ityp, ngm, g, tau, zv, strf, &
170
+ nspin, rho%of_g, force_mt )
171
+ END IF
172
+ !
173
+ ! ... call void routine for user define/ plugin patches on internal forces
174
+ !
175
+ call plugin_int_forces()
176
+ !
177
+ ! Berry's phase electric field terms
178
+ !
179
+ if(lelfield) then
180
+ ALLOCATE ( forces_bp_efield (3,nat) )
181
+ forces_bp_efield(:,:)=0.d0
182
+ if(.not.l3dstring) then
183
+ if(okvan) call forces_us_efield(forces_bp_efield,gdir,efield)
184
+ call forces_ion_efield(forces_bp_efield,gdir,efield)
185
+ else
186
+ if(okvan)then
187
+ do ipol=1,3
188
+ call forces_us_efield(forces_bp_efield,ipol,efield_cry(ipol))
189
+ enddo
190
+ endif
191
+ do ipol=1,3
192
+ call forces_ion_efield(forces_bp_efield,ipol,efield_cart(ipol))
193
+ enddo
194
+ endif
195
+ endif
196
+ !
197
+ ! ... here we sum all the contributions and compute the total force acting
198
+ ! ... on the crystal
199
+ !
200
+ DO ipol = 1, 3
201
+ !
202
+ sumfor = 0.D0
203
+ !
204
+ DO na = 1, nat
205
+ !
206
+ force(ipol,na) = force(ipol,na) + &
207
+ forcenl(ipol,na) + &
208
+ forceion(ipol,na) + &
209
+ forcelc(ipol,na) + &
210
+ forcecc(ipol,na) + &
211
+ forceh(ipol,na) + &
212
+ forcescc(ipol,na)
213
+ !
214
+ IF ( llondon ) force(ipol,na) = force(ipol,na) + force_disp(ipol,na)
215
+ IF ( ldftd3 ) force(ipol,na) = force(ipol,na) + force_d3(ipol,na)
216
+ IF ( lxdm ) force(ipol,na) = force(ipol,na) + force_disp_xdm(ipol,na)
217
+ ! factor 2 converts from Ha to Ry a.u.
218
+ IF ( ts_vdw ) force(ipol,na) = force(ipol,na) + 2.0_dp*FtsvdW(ipol,na)
219
+ IF ( tefield ) force(ipol,na) = force(ipol,na) + forcefield(ipol,na)
220
+ IF ( gate ) force(ipol,na) = force(ipol,na) + forcegate(ipol,na) ! TB
221
+ IF (lelfield) force(ipol,na) = force(ipol,na) + forces_bp_efield(ipol,na)
222
+ IF (do_comp_mt)force(ipol,na) = force(ipol,na) + force_mt(ipol,na)
223
+
224
+ sumfor = sumfor + force(ipol,na)
225
+ !
226
+ END DO
227
+ !
228
+ !TB
229
+ IF ((gate.and.relaxz).AND.(ipol==3)) WRITE( stdout, '("Total force in z direction = 0 disabled")')
230
+ !
231
+ IF ( (do_comp_esm .and. ( esm_bc .ne. 'pbc' )).or.(gate.and.relaxz) ) THEN
232
+ !
233
+ ! ... impose total force along xy = 0
234
+ !
235
+ DO na = 1, nat
236
+ IF ( ipol .ne. 3) force(ipol,na) = force(ipol,na) &
237
+ - sumfor / DBLE ( nat )
238
+ END DO
239
+ !
240
+ ELSE IF ( qmmm_mode < 0 ) THEN
241
+ !
242
+ ! ... impose total force = 0 except in a QM-MM calculation
243
+ !
244
+ DO na = 1, nat
245
+ force(ipol,na) = force(ipol,na) - sumfor / DBLE( nat )
246
+ END DO
247
+ !
248
+ ENDIF
249
+ !
250
+ END DO
251
+ !
252
+ ! ... resymmetrize (should not be needed, but ...)
253
+ !
254
+ CALL symvector ( nat, force )
255
+ !
256
+ IF ( remove_rigid_rot ) &
257
+ CALL remove_tot_torque( nat, tau, amass(ityp(:)), force )
258
+ !
259
+ IF( textfor ) force(:,:) = force(:,:) + extfor(:,:)
260
+ !
261
+ ! ... call void routine for user define/ plugin patches on external forces
262
+ !
263
+ ! plugin should be called after stress has been computed
264
+ ! look in run_pwscf.f90
265
+ !CALL plugin_ext_forces()
266
+ !
267
+ ! ... write on output the forces
268
+ !
269
+ WRITE( stdout, '(/,5x,"Forces acting on atoms (cartesian axes, Ry/au):", / )')
270
+ DO na = 1, nat
271
+ WRITE( stdout, 9035) na, ityp(na), force(:,na)
272
+ END DO
273
+ !
274
+ ! ... forces on fixed coordinates are set to zero ( C.S. 15/10/2003 )
275
+ !
276
+ force(:,:) = force(:,:) * DBLE( if_pos )
277
+ forcescc(:,:) = forcescc(:,:) * DBLE( if_pos )
278
+ !
279
+ IF ( iverbosity > 0 ) THEN
280
+ IF ( do_comp_mt ) THEN
281
+ WRITE( stdout, '(5x,"The Martyna-Tuckerman correction term to forces")')
282
+ DO na = 1, nat
283
+ WRITE( stdout, 9035) na, ityp(na), ( force_mt(ipol,na), ipol = 1, 3 )
284
+ END DO
285
+ END IF
286
+ !
287
+ WRITE( stdout, '(5x,"The non-local contrib. to forces")')
288
+ DO na = 1, nat
289
+ WRITE( stdout, 9035) na, ityp(na), ( forcenl(ipol,na), ipol = 1, 3 )
290
+ END DO
291
+ WRITE( stdout, '(5x,"The ionic contribution to forces")')
292
+ DO na = 1, nat
293
+ WRITE( stdout, 9035) na, ityp(na), ( forceion(ipol,na), ipol = 1, 3 )
294
+ END DO
295
+ WRITE( stdout, '(5x,"The local contribution to forces")')
296
+ DO na = 1, nat
297
+ WRITE( stdout, 9035) na, ityp(na), ( forcelc(ipol,na), ipol = 1, 3 )
298
+ END DO
299
+ WRITE( stdout, '(5x,"The core correction contribution to forces")')
300
+ DO na = 1, nat
301
+ WRITE( stdout, 9035) na, ityp(na), ( forcecc(ipol,na), ipol = 1, 3 )
302
+ END DO
303
+ WRITE( stdout, '(5x,"The Hubbard contrib. to forces")')
304
+ DO na = 1, nat
305
+ WRITE( stdout, 9035) na, ityp(na), ( forceh(ipol,na), ipol = 1, 3 )
306
+ END DO
307
+ WRITE( stdout, '(5x,"The SCF correction term to forces")')
308
+ DO na = 1, nat
309
+ WRITE( stdout, 9035) na, ityp(na), ( forcescc(ipol,na), ipol = 1, 3 )
310
+ END DO
311
+ !
312
+ IF ( llondon) THEN
313
+ WRITE( stdout, '(/,5x,"Dispersion contribution to forces:")')
314
+ DO na = 1, nat
315
+ WRITE( stdout, 9035) na, ityp(na), (force_disp(ipol,na), ipol = 1, 3)
316
+ END DO
317
+ END IF
318
+ !
319
+ IF ( ldftd3 ) THEN
320
+ WRITE( stdout, '(/,5x,"DFT-D3 dispersion contribution to forces:")')
321
+ DO na = 1, nat
322
+ WRITE( stdout, 9035) na, ityp(na), (force_d3(ipol,na), ipol = 1, 3)
323
+ END DO
324
+ END IF
325
+ !
326
+ IF (lxdm) THEN
327
+ WRITE( stdout, '(/,5x,"XDM contribution to forces:")')
328
+ DO na = 1, nat
329
+ WRITE( stdout, 9035) na, ityp(na), (force_disp_xdm(ipol,na), ipol = 1, 3)
330
+ END DO
331
+ END IF
332
+ !
333
+ IF ( ts_vdw) THEN
334
+ WRITE( stdout, '(/,5x,"TS-VDW contribution to forces:")')
335
+ DO na = 1, nat
336
+ WRITE( stdout, 9035) na, ityp(na), (2.0d0*FtsvdW(ipol,na), ipol=1,3)
337
+ END DO
338
+ END IF
339
+ !
340
+ ! TB gate forces
341
+ IF ( gate ) THEN
342
+ WRITE( stdout, '(/,5x,"Gate contribution to forces:")')
343
+ DO na = 1, nat
344
+ WRITE( stdout, 9035) na, ityp(na), (forcegate(ipol,na), ipol = 1, 3)
345
+ END DO
346
+ END IF
347
+ !
348
+ END IF
349
+ !
350
+ sumfor = 0.D0
351
+ sumscf = 0.D0
352
+ !
353
+ DO na = 1, nat
354
+ !
355
+ sumfor = sumfor + force(1,na)**2 + force(2,na)**2 + force(3,na)**2
356
+ sumscf = sumscf + forcescc(1,na)**2 + forcescc(2,na)**2+ forcescc(3,na)**2
357
+ !
358
+ END DO
359
+ !
360
+ sumfor = SQRT( sumfor )
361
+ sumscf = SQRT( sumscf )
362
+ !
363
+ WRITE( stdout, '(/5x,"Total force = ",F12.6,5X, &
364
+ & "Total SCF correction = ",F12.6)') sumfor, sumscf
365
+ !
366
+ IF ( llondon .AND. iverbosity > 0 ) THEN
367
+ !
368
+ sum_mm = 0.D0
369
+ DO na = 1, nat
370
+ sum_mm = sum_mm + &
371
+ force_disp(1,na)**2 + force_disp(2,na)**2 + force_disp(3,na)**2
372
+ END DO
373
+ sum_mm = SQRT( sum_mm )
374
+ WRITE ( stdout, '(/,5x, "Total Dispersion Force = ",F12.6)') sum_mm
375
+ !
376
+ END IF
377
+ !
378
+ IF ( ldftd3 .AND. iverbosity > 0 ) THEN
379
+ !
380
+ sum_mm = 0.D0
381
+ DO na = 1, nat
382
+ sum_mm = sum_mm + &
383
+ force_d3(1,na)**2 + force_d3(2,na)**2 + force_d3(3,na)**2
384
+ END DO
385
+ sum_mm = SQRT( sum_mm )
386
+ WRITE ( stdout, '(/,5x, "DFT-D3 dispersion Force = ",F12.6)') sum_mm
387
+ !
388
+ END IF
389
+ !
390
+ IF ( lxdm .AND. iverbosity > 0 ) THEN
391
+ !
392
+ sum_mm = 0.D0
393
+ DO na = 1, nat
394
+ sum_mm = sum_mm + &
395
+ force_disp_xdm(1,na)**2 + force_disp_xdm(2,na)**2 + force_disp_xdm(3,na)**2
396
+ END DO
397
+ sum_mm = SQRT( sum_mm )
398
+ WRITE ( stdout, '(/,5x, "Total XDM Force = ",F12.6)') sum_mm
399
+ !
400
+ END IF
401
+ !
402
+ DEALLOCATE( forcenl, forcelc, forcecc, forceh, forceion, forcescc )
403
+ IF ( llondon ) DEALLOCATE ( force_disp )
404
+ IF ( ldftd3 ) DEALLOCATE ( force_d3 )
405
+ IF ( lxdm ) DEALLOCATE( force_disp_xdm )
406
+ IF ( lelfield ) DEALLOCATE ( forces_bp_efield )
407
+ !
408
+ lforce = .TRUE.
409
+ !
410
+ CALL stop_clock( 'forces' )
411
+ !
412
+ IF ( ( sumfor < 10.D0*sumscf ) .AND. ( sumfor > nat*eps ) ) &
413
+ WRITE( stdout,'(5x,"SCF correction compared to forces is large: ", &
414
+ & "reduce conv_thr to get better values")')
415
+ !
416
+ IF(ALLOCATED(force_mt)) DEALLOCATE( force_mt )
417
+
418
+ RETURN
419
+ !
420
+ 9035 FORMAT(5X,'atom ',I4,' type ',I2,' force = ',3F14.8)
421
+ !
422
+ END SUBROUTINE forces