umappp 0.1.2

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Files changed (395) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE.txt +25 -0
  3. data/README.md +110 -0
  4. data/ext/umappp/extconf.rb +25 -0
  5. data/ext/umappp/numo.hpp +867 -0
  6. data/ext/umappp/umappp.cpp +225 -0
  7. data/lib/umappp/version.rb +5 -0
  8. data/lib/umappp.rb +41 -0
  9. data/vendor/Eigen/Cholesky +45 -0
  10. data/vendor/Eigen/CholmodSupport +48 -0
  11. data/vendor/Eigen/Core +384 -0
  12. data/vendor/Eigen/Dense +7 -0
  13. data/vendor/Eigen/Eigen +2 -0
  14. data/vendor/Eigen/Eigenvalues +60 -0
  15. data/vendor/Eigen/Geometry +59 -0
  16. data/vendor/Eigen/Householder +29 -0
  17. data/vendor/Eigen/IterativeLinearSolvers +48 -0
  18. data/vendor/Eigen/Jacobi +32 -0
  19. data/vendor/Eigen/KLUSupport +41 -0
  20. data/vendor/Eigen/LU +47 -0
  21. data/vendor/Eigen/MetisSupport +35 -0
  22. data/vendor/Eigen/OrderingMethods +70 -0
  23. data/vendor/Eigen/PaStiXSupport +49 -0
  24. data/vendor/Eigen/PardisoSupport +35 -0
  25. data/vendor/Eigen/QR +50 -0
  26. data/vendor/Eigen/QtAlignedMalloc +39 -0
  27. data/vendor/Eigen/SPQRSupport +34 -0
  28. data/vendor/Eigen/SVD +50 -0
  29. data/vendor/Eigen/Sparse +34 -0
  30. data/vendor/Eigen/SparseCholesky +37 -0
  31. data/vendor/Eigen/SparseCore +69 -0
  32. data/vendor/Eigen/SparseLU +50 -0
  33. data/vendor/Eigen/SparseQR +36 -0
  34. data/vendor/Eigen/StdDeque +27 -0
  35. data/vendor/Eigen/StdList +26 -0
  36. data/vendor/Eigen/StdVector +27 -0
  37. data/vendor/Eigen/SuperLUSupport +64 -0
  38. data/vendor/Eigen/UmfPackSupport +40 -0
  39. data/vendor/Eigen/src/Cholesky/LDLT.h +688 -0
  40. data/vendor/Eigen/src/Cholesky/LLT.h +558 -0
  41. data/vendor/Eigen/src/Cholesky/LLT_LAPACKE.h +99 -0
  42. data/vendor/Eigen/src/CholmodSupport/CholmodSupport.h +682 -0
  43. data/vendor/Eigen/src/Core/ArithmeticSequence.h +413 -0
  44. data/vendor/Eigen/src/Core/Array.h +417 -0
  45. data/vendor/Eigen/src/Core/ArrayBase.h +226 -0
  46. data/vendor/Eigen/src/Core/ArrayWrapper.h +209 -0
  47. data/vendor/Eigen/src/Core/Assign.h +90 -0
  48. data/vendor/Eigen/src/Core/AssignEvaluator.h +1010 -0
  49. data/vendor/Eigen/src/Core/Assign_MKL.h +178 -0
  50. data/vendor/Eigen/src/Core/BandMatrix.h +353 -0
  51. data/vendor/Eigen/src/Core/Block.h +448 -0
  52. data/vendor/Eigen/src/Core/BooleanRedux.h +162 -0
  53. data/vendor/Eigen/src/Core/CommaInitializer.h +164 -0
  54. data/vendor/Eigen/src/Core/ConditionEstimator.h +175 -0
  55. data/vendor/Eigen/src/Core/CoreEvaluators.h +1741 -0
  56. data/vendor/Eigen/src/Core/CoreIterators.h +132 -0
  57. data/vendor/Eigen/src/Core/CwiseBinaryOp.h +183 -0
  58. data/vendor/Eigen/src/Core/CwiseNullaryOp.h +1001 -0
  59. data/vendor/Eigen/src/Core/CwiseTernaryOp.h +197 -0
  60. data/vendor/Eigen/src/Core/CwiseUnaryOp.h +103 -0
  61. data/vendor/Eigen/src/Core/CwiseUnaryView.h +132 -0
  62. data/vendor/Eigen/src/Core/DenseBase.h +701 -0
  63. data/vendor/Eigen/src/Core/DenseCoeffsBase.h +685 -0
  64. data/vendor/Eigen/src/Core/DenseStorage.h +652 -0
  65. data/vendor/Eigen/src/Core/Diagonal.h +258 -0
  66. data/vendor/Eigen/src/Core/DiagonalMatrix.h +391 -0
  67. data/vendor/Eigen/src/Core/DiagonalProduct.h +28 -0
  68. data/vendor/Eigen/src/Core/Dot.h +318 -0
  69. data/vendor/Eigen/src/Core/EigenBase.h +160 -0
  70. data/vendor/Eigen/src/Core/ForceAlignedAccess.h +150 -0
  71. data/vendor/Eigen/src/Core/Fuzzy.h +155 -0
  72. data/vendor/Eigen/src/Core/GeneralProduct.h +465 -0
  73. data/vendor/Eigen/src/Core/GenericPacketMath.h +1040 -0
  74. data/vendor/Eigen/src/Core/GlobalFunctions.h +194 -0
  75. data/vendor/Eigen/src/Core/IO.h +258 -0
  76. data/vendor/Eigen/src/Core/IndexedView.h +237 -0
  77. data/vendor/Eigen/src/Core/Inverse.h +117 -0
  78. data/vendor/Eigen/src/Core/Map.h +171 -0
  79. data/vendor/Eigen/src/Core/MapBase.h +310 -0
  80. data/vendor/Eigen/src/Core/MathFunctions.h +2057 -0
  81. data/vendor/Eigen/src/Core/MathFunctionsImpl.h +200 -0
  82. data/vendor/Eigen/src/Core/Matrix.h +565 -0
  83. data/vendor/Eigen/src/Core/MatrixBase.h +547 -0
  84. data/vendor/Eigen/src/Core/NestByValue.h +85 -0
  85. data/vendor/Eigen/src/Core/NoAlias.h +109 -0
  86. data/vendor/Eigen/src/Core/NumTraits.h +335 -0
  87. data/vendor/Eigen/src/Core/PartialReduxEvaluator.h +232 -0
  88. data/vendor/Eigen/src/Core/PermutationMatrix.h +605 -0
  89. data/vendor/Eigen/src/Core/PlainObjectBase.h +1128 -0
  90. data/vendor/Eigen/src/Core/Product.h +191 -0
  91. data/vendor/Eigen/src/Core/ProductEvaluators.h +1179 -0
  92. data/vendor/Eigen/src/Core/Random.h +218 -0
  93. data/vendor/Eigen/src/Core/Redux.h +515 -0
  94. data/vendor/Eigen/src/Core/Ref.h +381 -0
  95. data/vendor/Eigen/src/Core/Replicate.h +142 -0
  96. data/vendor/Eigen/src/Core/Reshaped.h +454 -0
  97. data/vendor/Eigen/src/Core/ReturnByValue.h +119 -0
  98. data/vendor/Eigen/src/Core/Reverse.h +217 -0
  99. data/vendor/Eigen/src/Core/Select.h +164 -0
  100. data/vendor/Eigen/src/Core/SelfAdjointView.h +365 -0
  101. data/vendor/Eigen/src/Core/SelfCwiseBinaryOp.h +47 -0
  102. data/vendor/Eigen/src/Core/Solve.h +188 -0
  103. data/vendor/Eigen/src/Core/SolveTriangular.h +235 -0
  104. data/vendor/Eigen/src/Core/SolverBase.h +168 -0
  105. data/vendor/Eigen/src/Core/StableNorm.h +251 -0
  106. data/vendor/Eigen/src/Core/StlIterators.h +463 -0
  107. data/vendor/Eigen/src/Core/Stride.h +116 -0
  108. data/vendor/Eigen/src/Core/Swap.h +68 -0
  109. data/vendor/Eigen/src/Core/Transpose.h +464 -0
  110. data/vendor/Eigen/src/Core/Transpositions.h +386 -0
  111. data/vendor/Eigen/src/Core/TriangularMatrix.h +1001 -0
  112. data/vendor/Eigen/src/Core/VectorBlock.h +96 -0
  113. data/vendor/Eigen/src/Core/VectorwiseOp.h +784 -0
  114. data/vendor/Eigen/src/Core/Visitor.h +381 -0
  115. data/vendor/Eigen/src/Core/arch/AVX/Complex.h +372 -0
  116. data/vendor/Eigen/src/Core/arch/AVX/MathFunctions.h +228 -0
  117. data/vendor/Eigen/src/Core/arch/AVX/PacketMath.h +1574 -0
  118. data/vendor/Eigen/src/Core/arch/AVX/TypeCasting.h +115 -0
  119. data/vendor/Eigen/src/Core/arch/AVX512/Complex.h +422 -0
  120. data/vendor/Eigen/src/Core/arch/AVX512/MathFunctions.h +362 -0
  121. data/vendor/Eigen/src/Core/arch/AVX512/PacketMath.h +2303 -0
  122. data/vendor/Eigen/src/Core/arch/AVX512/TypeCasting.h +89 -0
  123. data/vendor/Eigen/src/Core/arch/AltiVec/Complex.h +417 -0
  124. data/vendor/Eigen/src/Core/arch/AltiVec/MathFunctions.h +90 -0
  125. data/vendor/Eigen/src/Core/arch/AltiVec/MatrixProduct.h +2937 -0
  126. data/vendor/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h +221 -0
  127. data/vendor/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h +629 -0
  128. data/vendor/Eigen/src/Core/arch/AltiVec/PacketMath.h +2711 -0
  129. data/vendor/Eigen/src/Core/arch/CUDA/Complex.h +258 -0
  130. data/vendor/Eigen/src/Core/arch/Default/BFloat16.h +700 -0
  131. data/vendor/Eigen/src/Core/arch/Default/ConjHelper.h +117 -0
  132. data/vendor/Eigen/src/Core/arch/Default/GenericPacketMathFunctions.h +1649 -0
  133. data/vendor/Eigen/src/Core/arch/Default/GenericPacketMathFunctionsFwd.h +110 -0
  134. data/vendor/Eigen/src/Core/arch/Default/Half.h +942 -0
  135. data/vendor/Eigen/src/Core/arch/Default/Settings.h +49 -0
  136. data/vendor/Eigen/src/Core/arch/Default/TypeCasting.h +120 -0
  137. data/vendor/Eigen/src/Core/arch/GPU/MathFunctions.h +103 -0
  138. data/vendor/Eigen/src/Core/arch/GPU/PacketMath.h +1685 -0
  139. data/vendor/Eigen/src/Core/arch/GPU/TypeCasting.h +80 -0
  140. data/vendor/Eigen/src/Core/arch/HIP/hcc/math_constants.h +23 -0
  141. data/vendor/Eigen/src/Core/arch/MSA/Complex.h +648 -0
  142. data/vendor/Eigen/src/Core/arch/MSA/MathFunctions.h +387 -0
  143. data/vendor/Eigen/src/Core/arch/MSA/PacketMath.h +1233 -0
  144. data/vendor/Eigen/src/Core/arch/NEON/Complex.h +584 -0
  145. data/vendor/Eigen/src/Core/arch/NEON/GeneralBlockPanelKernel.h +183 -0
  146. data/vendor/Eigen/src/Core/arch/NEON/MathFunctions.h +75 -0
  147. data/vendor/Eigen/src/Core/arch/NEON/PacketMath.h +4587 -0
  148. data/vendor/Eigen/src/Core/arch/NEON/TypeCasting.h +1419 -0
  149. data/vendor/Eigen/src/Core/arch/SSE/Complex.h +351 -0
  150. data/vendor/Eigen/src/Core/arch/SSE/MathFunctions.h +199 -0
  151. data/vendor/Eigen/src/Core/arch/SSE/PacketMath.h +1505 -0
  152. data/vendor/Eigen/src/Core/arch/SSE/TypeCasting.h +142 -0
  153. data/vendor/Eigen/src/Core/arch/SVE/MathFunctions.h +44 -0
  154. data/vendor/Eigen/src/Core/arch/SVE/PacketMath.h +752 -0
  155. data/vendor/Eigen/src/Core/arch/SVE/TypeCasting.h +49 -0
  156. data/vendor/Eigen/src/Core/arch/SYCL/InteropHeaders.h +232 -0
  157. data/vendor/Eigen/src/Core/arch/SYCL/MathFunctions.h +301 -0
  158. data/vendor/Eigen/src/Core/arch/SYCL/PacketMath.h +670 -0
  159. data/vendor/Eigen/src/Core/arch/SYCL/SyclMemoryModel.h +694 -0
  160. data/vendor/Eigen/src/Core/arch/SYCL/TypeCasting.h +85 -0
  161. data/vendor/Eigen/src/Core/arch/ZVector/Complex.h +426 -0
  162. data/vendor/Eigen/src/Core/arch/ZVector/MathFunctions.h +233 -0
  163. data/vendor/Eigen/src/Core/arch/ZVector/PacketMath.h +1060 -0
  164. data/vendor/Eigen/src/Core/functors/AssignmentFunctors.h +177 -0
  165. data/vendor/Eigen/src/Core/functors/BinaryFunctors.h +541 -0
  166. data/vendor/Eigen/src/Core/functors/NullaryFunctors.h +189 -0
  167. data/vendor/Eigen/src/Core/functors/StlFunctors.h +166 -0
  168. data/vendor/Eigen/src/Core/functors/TernaryFunctors.h +25 -0
  169. data/vendor/Eigen/src/Core/functors/UnaryFunctors.h +1131 -0
  170. data/vendor/Eigen/src/Core/products/GeneralBlockPanelKernel.h +2645 -0
  171. data/vendor/Eigen/src/Core/products/GeneralMatrixMatrix.h +517 -0
  172. data/vendor/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h +317 -0
  173. data/vendor/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h +145 -0
  174. data/vendor/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h +124 -0
  175. data/vendor/Eigen/src/Core/products/GeneralMatrixVector.h +518 -0
  176. data/vendor/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h +136 -0
  177. data/vendor/Eigen/src/Core/products/Parallelizer.h +180 -0
  178. data/vendor/Eigen/src/Core/products/SelfadjointMatrixMatrix.h +544 -0
  179. data/vendor/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h +295 -0
  180. data/vendor/Eigen/src/Core/products/SelfadjointMatrixVector.h +262 -0
  181. data/vendor/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h +118 -0
  182. data/vendor/Eigen/src/Core/products/SelfadjointProduct.h +133 -0
  183. data/vendor/Eigen/src/Core/products/SelfadjointRank2Update.h +94 -0
  184. data/vendor/Eigen/src/Core/products/TriangularMatrixMatrix.h +472 -0
  185. data/vendor/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h +317 -0
  186. data/vendor/Eigen/src/Core/products/TriangularMatrixVector.h +350 -0
  187. data/vendor/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h +255 -0
  188. data/vendor/Eigen/src/Core/products/TriangularSolverMatrix.h +337 -0
  189. data/vendor/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h +167 -0
  190. data/vendor/Eigen/src/Core/products/TriangularSolverVector.h +148 -0
  191. data/vendor/Eigen/src/Core/util/BlasUtil.h +583 -0
  192. data/vendor/Eigen/src/Core/util/ConfigureVectorization.h +512 -0
  193. data/vendor/Eigen/src/Core/util/Constants.h +563 -0
  194. data/vendor/Eigen/src/Core/util/DisableStupidWarnings.h +106 -0
  195. data/vendor/Eigen/src/Core/util/ForwardDeclarations.h +322 -0
  196. data/vendor/Eigen/src/Core/util/IndexedViewHelper.h +186 -0
  197. data/vendor/Eigen/src/Core/util/IntegralConstant.h +272 -0
  198. data/vendor/Eigen/src/Core/util/MKL_support.h +137 -0
  199. data/vendor/Eigen/src/Core/util/Macros.h +1464 -0
  200. data/vendor/Eigen/src/Core/util/Memory.h +1163 -0
  201. data/vendor/Eigen/src/Core/util/Meta.h +812 -0
  202. data/vendor/Eigen/src/Core/util/NonMPL2.h +3 -0
  203. data/vendor/Eigen/src/Core/util/ReenableStupidWarnings.h +31 -0
  204. data/vendor/Eigen/src/Core/util/ReshapedHelper.h +51 -0
  205. data/vendor/Eigen/src/Core/util/StaticAssert.h +221 -0
  206. data/vendor/Eigen/src/Core/util/SymbolicIndex.h +293 -0
  207. data/vendor/Eigen/src/Core/util/XprHelper.h +856 -0
  208. data/vendor/Eigen/src/Eigenvalues/ComplexEigenSolver.h +346 -0
  209. data/vendor/Eigen/src/Eigenvalues/ComplexSchur.h +462 -0
  210. data/vendor/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +91 -0
  211. data/vendor/Eigen/src/Eigenvalues/EigenSolver.h +622 -0
  212. data/vendor/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +418 -0
  213. data/vendor/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +226 -0
  214. data/vendor/Eigen/src/Eigenvalues/HessenbergDecomposition.h +374 -0
  215. data/vendor/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +158 -0
  216. data/vendor/Eigen/src/Eigenvalues/RealQZ.h +657 -0
  217. data/vendor/Eigen/src/Eigenvalues/RealSchur.h +558 -0
  218. data/vendor/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +77 -0
  219. data/vendor/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +904 -0
  220. data/vendor/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +87 -0
  221. data/vendor/Eigen/src/Eigenvalues/Tridiagonalization.h +561 -0
  222. data/vendor/Eigen/src/Geometry/AlignedBox.h +486 -0
  223. data/vendor/Eigen/src/Geometry/AngleAxis.h +247 -0
  224. data/vendor/Eigen/src/Geometry/EulerAngles.h +114 -0
  225. data/vendor/Eigen/src/Geometry/Homogeneous.h +501 -0
  226. data/vendor/Eigen/src/Geometry/Hyperplane.h +282 -0
  227. data/vendor/Eigen/src/Geometry/OrthoMethods.h +235 -0
  228. data/vendor/Eigen/src/Geometry/ParametrizedLine.h +232 -0
  229. data/vendor/Eigen/src/Geometry/Quaternion.h +870 -0
  230. data/vendor/Eigen/src/Geometry/Rotation2D.h +199 -0
  231. data/vendor/Eigen/src/Geometry/RotationBase.h +206 -0
  232. data/vendor/Eigen/src/Geometry/Scaling.h +188 -0
  233. data/vendor/Eigen/src/Geometry/Transform.h +1563 -0
  234. data/vendor/Eigen/src/Geometry/Translation.h +202 -0
  235. data/vendor/Eigen/src/Geometry/Umeyama.h +166 -0
  236. data/vendor/Eigen/src/Geometry/arch/Geometry_SIMD.h +168 -0
  237. data/vendor/Eigen/src/Householder/BlockHouseholder.h +110 -0
  238. data/vendor/Eigen/src/Householder/Householder.h +176 -0
  239. data/vendor/Eigen/src/Householder/HouseholderSequence.h +545 -0
  240. data/vendor/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +226 -0
  241. data/vendor/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +212 -0
  242. data/vendor/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +229 -0
  243. data/vendor/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +394 -0
  244. data/vendor/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +453 -0
  245. data/vendor/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +444 -0
  246. data/vendor/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +198 -0
  247. data/vendor/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +117 -0
  248. data/vendor/Eigen/src/Jacobi/Jacobi.h +483 -0
  249. data/vendor/Eigen/src/KLUSupport/KLUSupport.h +358 -0
  250. data/vendor/Eigen/src/LU/Determinant.h +117 -0
  251. data/vendor/Eigen/src/LU/FullPivLU.h +877 -0
  252. data/vendor/Eigen/src/LU/InverseImpl.h +432 -0
  253. data/vendor/Eigen/src/LU/PartialPivLU.h +624 -0
  254. data/vendor/Eigen/src/LU/PartialPivLU_LAPACKE.h +83 -0
  255. data/vendor/Eigen/src/LU/arch/InverseSize4.h +351 -0
  256. data/vendor/Eigen/src/MetisSupport/MetisSupport.h +137 -0
  257. data/vendor/Eigen/src/OrderingMethods/Amd.h +435 -0
  258. data/vendor/Eigen/src/OrderingMethods/Eigen_Colamd.h +1863 -0
  259. data/vendor/Eigen/src/OrderingMethods/Ordering.h +153 -0
  260. data/vendor/Eigen/src/PaStiXSupport/PaStiXSupport.h +678 -0
  261. data/vendor/Eigen/src/PardisoSupport/PardisoSupport.h +545 -0
  262. data/vendor/Eigen/src/QR/ColPivHouseholderQR.h +674 -0
  263. data/vendor/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +97 -0
  264. data/vendor/Eigen/src/QR/CompleteOrthogonalDecomposition.h +635 -0
  265. data/vendor/Eigen/src/QR/FullPivHouseholderQR.h +713 -0
  266. data/vendor/Eigen/src/QR/HouseholderQR.h +434 -0
  267. data/vendor/Eigen/src/QR/HouseholderQR_LAPACKE.h +68 -0
  268. data/vendor/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +335 -0
  269. data/vendor/Eigen/src/SVD/BDCSVD.h +1366 -0
  270. data/vendor/Eigen/src/SVD/JacobiSVD.h +812 -0
  271. data/vendor/Eigen/src/SVD/JacobiSVD_LAPACKE.h +91 -0
  272. data/vendor/Eigen/src/SVD/SVDBase.h +376 -0
  273. data/vendor/Eigen/src/SVD/UpperBidiagonalization.h +414 -0
  274. data/vendor/Eigen/src/SparseCholesky/SimplicialCholesky.h +697 -0
  275. data/vendor/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +174 -0
  276. data/vendor/Eigen/src/SparseCore/AmbiVector.h +378 -0
  277. data/vendor/Eigen/src/SparseCore/CompressedStorage.h +274 -0
  278. data/vendor/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +352 -0
  279. data/vendor/Eigen/src/SparseCore/MappedSparseMatrix.h +67 -0
  280. data/vendor/Eigen/src/SparseCore/SparseAssign.h +270 -0
  281. data/vendor/Eigen/src/SparseCore/SparseBlock.h +571 -0
  282. data/vendor/Eigen/src/SparseCore/SparseColEtree.h +206 -0
  283. data/vendor/Eigen/src/SparseCore/SparseCompressedBase.h +370 -0
  284. data/vendor/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +722 -0
  285. data/vendor/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +150 -0
  286. data/vendor/Eigen/src/SparseCore/SparseDenseProduct.h +342 -0
  287. data/vendor/Eigen/src/SparseCore/SparseDiagonalProduct.h +138 -0
  288. data/vendor/Eigen/src/SparseCore/SparseDot.h +98 -0
  289. data/vendor/Eigen/src/SparseCore/SparseFuzzy.h +29 -0
  290. data/vendor/Eigen/src/SparseCore/SparseMap.h +305 -0
  291. data/vendor/Eigen/src/SparseCore/SparseMatrix.h +1518 -0
  292. data/vendor/Eigen/src/SparseCore/SparseMatrixBase.h +398 -0
  293. data/vendor/Eigen/src/SparseCore/SparsePermutation.h +178 -0
  294. data/vendor/Eigen/src/SparseCore/SparseProduct.h +181 -0
  295. data/vendor/Eigen/src/SparseCore/SparseRedux.h +49 -0
  296. data/vendor/Eigen/src/SparseCore/SparseRef.h +397 -0
  297. data/vendor/Eigen/src/SparseCore/SparseSelfAdjointView.h +659 -0
  298. data/vendor/Eigen/src/SparseCore/SparseSolverBase.h +124 -0
  299. data/vendor/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +198 -0
  300. data/vendor/Eigen/src/SparseCore/SparseTranspose.h +92 -0
  301. data/vendor/Eigen/src/SparseCore/SparseTriangularView.h +189 -0
  302. data/vendor/Eigen/src/SparseCore/SparseUtil.h +186 -0
  303. data/vendor/Eigen/src/SparseCore/SparseVector.h +478 -0
  304. data/vendor/Eigen/src/SparseCore/SparseView.h +254 -0
  305. data/vendor/Eigen/src/SparseCore/TriangularSolver.h +315 -0
  306. data/vendor/Eigen/src/SparseLU/SparseLU.h +923 -0
  307. data/vendor/Eigen/src/SparseLU/SparseLUImpl.h +66 -0
  308. data/vendor/Eigen/src/SparseLU/SparseLU_Memory.h +226 -0
  309. data/vendor/Eigen/src/SparseLU/SparseLU_Structs.h +110 -0
  310. data/vendor/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +375 -0
  311. data/vendor/Eigen/src/SparseLU/SparseLU_Utils.h +80 -0
  312. data/vendor/Eigen/src/SparseLU/SparseLU_column_bmod.h +181 -0
  313. data/vendor/Eigen/src/SparseLU/SparseLU_column_dfs.h +179 -0
  314. data/vendor/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +107 -0
  315. data/vendor/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +280 -0
  316. data/vendor/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +126 -0
  317. data/vendor/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +130 -0
  318. data/vendor/Eigen/src/SparseLU/SparseLU_panel_bmod.h +223 -0
  319. data/vendor/Eigen/src/SparseLU/SparseLU_panel_dfs.h +258 -0
  320. data/vendor/Eigen/src/SparseLU/SparseLU_pivotL.h +137 -0
  321. data/vendor/Eigen/src/SparseLU/SparseLU_pruneL.h +136 -0
  322. data/vendor/Eigen/src/SparseLU/SparseLU_relax_snode.h +83 -0
  323. data/vendor/Eigen/src/SparseQR/SparseQR.h +758 -0
  324. data/vendor/Eigen/src/StlSupport/StdDeque.h +116 -0
  325. data/vendor/Eigen/src/StlSupport/StdList.h +106 -0
  326. data/vendor/Eigen/src/StlSupport/StdVector.h +131 -0
  327. data/vendor/Eigen/src/StlSupport/details.h +84 -0
  328. data/vendor/Eigen/src/SuperLUSupport/SuperLUSupport.h +1025 -0
  329. data/vendor/Eigen/src/UmfPackSupport/UmfPackSupport.h +642 -0
  330. data/vendor/Eigen/src/misc/Image.h +82 -0
  331. data/vendor/Eigen/src/misc/Kernel.h +79 -0
  332. data/vendor/Eigen/src/misc/RealSvd2x2.h +55 -0
  333. data/vendor/Eigen/src/misc/blas.h +440 -0
  334. data/vendor/Eigen/src/misc/lapack.h +152 -0
  335. data/vendor/Eigen/src/misc/lapacke.h +16292 -0
  336. data/vendor/Eigen/src/misc/lapacke_mangling.h +17 -0
  337. data/vendor/Eigen/src/plugins/ArrayCwiseBinaryOps.h +358 -0
  338. data/vendor/Eigen/src/plugins/ArrayCwiseUnaryOps.h +696 -0
  339. data/vendor/Eigen/src/plugins/BlockMethods.h +1442 -0
  340. data/vendor/Eigen/src/plugins/CommonCwiseBinaryOps.h +115 -0
  341. data/vendor/Eigen/src/plugins/CommonCwiseUnaryOps.h +177 -0
  342. data/vendor/Eigen/src/plugins/IndexedViewMethods.h +262 -0
  343. data/vendor/Eigen/src/plugins/MatrixCwiseBinaryOps.h +152 -0
  344. data/vendor/Eigen/src/plugins/MatrixCwiseUnaryOps.h +95 -0
  345. data/vendor/Eigen/src/plugins/ReshapedMethods.h +149 -0
  346. data/vendor/aarand/aarand.hpp +114 -0
  347. data/vendor/annoy/annoylib.h +1495 -0
  348. data/vendor/annoy/kissrandom.h +120 -0
  349. data/vendor/annoy/mman.h +242 -0
  350. data/vendor/hnswlib/bruteforce.h +152 -0
  351. data/vendor/hnswlib/hnswalg.h +1192 -0
  352. data/vendor/hnswlib/hnswlib.h +108 -0
  353. data/vendor/hnswlib/space_ip.h +282 -0
  354. data/vendor/hnswlib/space_l2.h +281 -0
  355. data/vendor/hnswlib/visited_list_pool.h +79 -0
  356. data/vendor/irlba/irlba.hpp +575 -0
  357. data/vendor/irlba/lanczos.hpp +212 -0
  358. data/vendor/irlba/parallel.hpp +474 -0
  359. data/vendor/irlba/utils.hpp +224 -0
  360. data/vendor/irlba/wrappers.hpp +228 -0
  361. data/vendor/kmeans/Base.hpp +75 -0
  362. data/vendor/kmeans/Details.hpp +79 -0
  363. data/vendor/kmeans/HartiganWong.hpp +492 -0
  364. data/vendor/kmeans/InitializeKmeansPP.hpp +144 -0
  365. data/vendor/kmeans/InitializeNone.hpp +44 -0
  366. data/vendor/kmeans/InitializePCAPartition.hpp +309 -0
  367. data/vendor/kmeans/InitializeRandom.hpp +91 -0
  368. data/vendor/kmeans/Kmeans.hpp +161 -0
  369. data/vendor/kmeans/Lloyd.hpp +134 -0
  370. data/vendor/kmeans/MiniBatch.hpp +269 -0
  371. data/vendor/kmeans/QuickSearch.hpp +179 -0
  372. data/vendor/kmeans/compute_centroids.hpp +32 -0
  373. data/vendor/kmeans/compute_wcss.hpp +27 -0
  374. data/vendor/kmeans/is_edge_case.hpp +42 -0
  375. data/vendor/kmeans/random.hpp +55 -0
  376. data/vendor/knncolle/Annoy/Annoy.hpp +193 -0
  377. data/vendor/knncolle/BruteForce/BruteForce.hpp +120 -0
  378. data/vendor/knncolle/Hnsw/Hnsw.hpp +225 -0
  379. data/vendor/knncolle/Kmknn/Kmknn.hpp +286 -0
  380. data/vendor/knncolle/VpTree/VpTree.hpp +256 -0
  381. data/vendor/knncolle/knncolle.hpp +34 -0
  382. data/vendor/knncolle/utils/Base.hpp +100 -0
  383. data/vendor/knncolle/utils/NeighborQueue.hpp +94 -0
  384. data/vendor/knncolle/utils/distances.hpp +98 -0
  385. data/vendor/knncolle/utils/find_nearest_neighbors.hpp +112 -0
  386. data/vendor/powerit/PowerIterations.hpp +157 -0
  387. data/vendor/umappp/NeighborList.hpp +37 -0
  388. data/vendor/umappp/Umap.hpp +662 -0
  389. data/vendor/umappp/combine_neighbor_sets.hpp +95 -0
  390. data/vendor/umappp/find_ab.hpp +157 -0
  391. data/vendor/umappp/neighbor_similarities.hpp +136 -0
  392. data/vendor/umappp/optimize_layout.hpp +285 -0
  393. data/vendor/umappp/spectral_init.hpp +181 -0
  394. data/vendor/umappp/umappp.hpp +13 -0
  395. metadata +465 -0
@@ -0,0 +1,226 @@
1
+ // This file is part of Eigen, a lightweight C++ template library
2
+ // for linear algebra.
3
+ //
4
+ // Copyright (C) 2011-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
5
+ //
6
+ // This Source Code Form is subject to the terms of the Mozilla
7
+ // Public License v. 2.0. If a copy of the MPL was not distributed
8
+ // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
+
10
+ #ifndef EIGEN_BASIC_PRECONDITIONERS_H
11
+ #define EIGEN_BASIC_PRECONDITIONERS_H
12
+
13
+ namespace Eigen {
14
+
15
+ /** \ingroup IterativeLinearSolvers_Module
16
+ * \brief A preconditioner based on the digonal entries
17
+ *
18
+ * This class allows to approximately solve for A.x = b problems assuming A is a diagonal matrix.
19
+ * In other words, this preconditioner neglects all off diagonal entries and, in Eigen's language, solves for:
20
+ \code
21
+ A.diagonal().asDiagonal() . x = b
22
+ \endcode
23
+ *
24
+ * \tparam _Scalar the type of the scalar.
25
+ *
26
+ * \implsparsesolverconcept
27
+ *
28
+ * This preconditioner is suitable for both selfadjoint and general problems.
29
+ * The diagonal entries are pre-inverted and stored into a dense vector.
30
+ *
31
+ * \note A variant that has yet to be implemented would attempt to preserve the norm of each column.
32
+ *
33
+ * \sa class LeastSquareDiagonalPreconditioner, class ConjugateGradient
34
+ */
35
+ template <typename _Scalar>
36
+ class DiagonalPreconditioner
37
+ {
38
+ typedef _Scalar Scalar;
39
+ typedef Matrix<Scalar,Dynamic,1> Vector;
40
+ public:
41
+ typedef typename Vector::StorageIndex StorageIndex;
42
+ enum {
43
+ ColsAtCompileTime = Dynamic,
44
+ MaxColsAtCompileTime = Dynamic
45
+ };
46
+
47
+ DiagonalPreconditioner() : m_isInitialized(false) {}
48
+
49
+ template<typename MatType>
50
+ explicit DiagonalPreconditioner(const MatType& mat) : m_invdiag(mat.cols())
51
+ {
52
+ compute(mat);
53
+ }
54
+
55
+ EIGEN_CONSTEXPR Index rows() const EIGEN_NOEXCEPT { return m_invdiag.size(); }
56
+ EIGEN_CONSTEXPR Index cols() const EIGEN_NOEXCEPT { return m_invdiag.size(); }
57
+
58
+ template<typename MatType>
59
+ DiagonalPreconditioner& analyzePattern(const MatType& )
60
+ {
61
+ return *this;
62
+ }
63
+
64
+ template<typename MatType>
65
+ DiagonalPreconditioner& factorize(const MatType& mat)
66
+ {
67
+ m_invdiag.resize(mat.cols());
68
+ for(int j=0; j<mat.outerSize(); ++j)
69
+ {
70
+ typename MatType::InnerIterator it(mat,j);
71
+ while(it && it.index()!=j) ++it;
72
+ if(it && it.index()==j && it.value()!=Scalar(0))
73
+ m_invdiag(j) = Scalar(1)/it.value();
74
+ else
75
+ m_invdiag(j) = Scalar(1);
76
+ }
77
+ m_isInitialized = true;
78
+ return *this;
79
+ }
80
+
81
+ template<typename MatType>
82
+ DiagonalPreconditioner& compute(const MatType& mat)
83
+ {
84
+ return factorize(mat);
85
+ }
86
+
87
+ /** \internal */
88
+ template<typename Rhs, typename Dest>
89
+ void _solve_impl(const Rhs& b, Dest& x) const
90
+ {
91
+ x = m_invdiag.array() * b.array() ;
92
+ }
93
+
94
+ template<typename Rhs> inline const Solve<DiagonalPreconditioner, Rhs>
95
+ solve(const MatrixBase<Rhs>& b) const
96
+ {
97
+ eigen_assert(m_isInitialized && "DiagonalPreconditioner is not initialized.");
98
+ eigen_assert(m_invdiag.size()==b.rows()
99
+ && "DiagonalPreconditioner::solve(): invalid number of rows of the right hand side matrix b");
100
+ return Solve<DiagonalPreconditioner, Rhs>(*this, b.derived());
101
+ }
102
+
103
+ ComputationInfo info() { return Success; }
104
+
105
+ protected:
106
+ Vector m_invdiag;
107
+ bool m_isInitialized;
108
+ };
109
+
110
+ /** \ingroup IterativeLinearSolvers_Module
111
+ * \brief Jacobi preconditioner for LeastSquaresConjugateGradient
112
+ *
113
+ * This class allows to approximately solve for A' A x = A' b problems assuming A' A is a diagonal matrix.
114
+ * In other words, this preconditioner neglects all off diagonal entries and, in Eigen's language, solves for:
115
+ \code
116
+ (A.adjoint() * A).diagonal().asDiagonal() * x = b
117
+ \endcode
118
+ *
119
+ * \tparam _Scalar the type of the scalar.
120
+ *
121
+ * \implsparsesolverconcept
122
+ *
123
+ * The diagonal entries are pre-inverted and stored into a dense vector.
124
+ *
125
+ * \sa class LeastSquaresConjugateGradient, class DiagonalPreconditioner
126
+ */
127
+ template <typename _Scalar>
128
+ class LeastSquareDiagonalPreconditioner : public DiagonalPreconditioner<_Scalar>
129
+ {
130
+ typedef _Scalar Scalar;
131
+ typedef typename NumTraits<Scalar>::Real RealScalar;
132
+ typedef DiagonalPreconditioner<_Scalar> Base;
133
+ using Base::m_invdiag;
134
+ public:
135
+
136
+ LeastSquareDiagonalPreconditioner() : Base() {}
137
+
138
+ template<typename MatType>
139
+ explicit LeastSquareDiagonalPreconditioner(const MatType& mat) : Base()
140
+ {
141
+ compute(mat);
142
+ }
143
+
144
+ template<typename MatType>
145
+ LeastSquareDiagonalPreconditioner& analyzePattern(const MatType& )
146
+ {
147
+ return *this;
148
+ }
149
+
150
+ template<typename MatType>
151
+ LeastSquareDiagonalPreconditioner& factorize(const MatType& mat)
152
+ {
153
+ // Compute the inverse squared-norm of each column of mat
154
+ m_invdiag.resize(mat.cols());
155
+ if(MatType::IsRowMajor)
156
+ {
157
+ m_invdiag.setZero();
158
+ for(Index j=0; j<mat.outerSize(); ++j)
159
+ {
160
+ for(typename MatType::InnerIterator it(mat,j); it; ++it)
161
+ m_invdiag(it.index()) += numext::abs2(it.value());
162
+ }
163
+ for(Index j=0; j<mat.cols(); ++j)
164
+ if(numext::real(m_invdiag(j))>RealScalar(0))
165
+ m_invdiag(j) = RealScalar(1)/numext::real(m_invdiag(j));
166
+ }
167
+ else
168
+ {
169
+ for(Index j=0; j<mat.outerSize(); ++j)
170
+ {
171
+ RealScalar sum = mat.col(j).squaredNorm();
172
+ if(sum>RealScalar(0))
173
+ m_invdiag(j) = RealScalar(1)/sum;
174
+ else
175
+ m_invdiag(j) = RealScalar(1);
176
+ }
177
+ }
178
+ Base::m_isInitialized = true;
179
+ return *this;
180
+ }
181
+
182
+ template<typename MatType>
183
+ LeastSquareDiagonalPreconditioner& compute(const MatType& mat)
184
+ {
185
+ return factorize(mat);
186
+ }
187
+
188
+ ComputationInfo info() { return Success; }
189
+
190
+ protected:
191
+ };
192
+
193
+ /** \ingroup IterativeLinearSolvers_Module
194
+ * \brief A naive preconditioner which approximates any matrix as the identity matrix
195
+ *
196
+ * \implsparsesolverconcept
197
+ *
198
+ * \sa class DiagonalPreconditioner
199
+ */
200
+ class IdentityPreconditioner
201
+ {
202
+ public:
203
+
204
+ IdentityPreconditioner() {}
205
+
206
+ template<typename MatrixType>
207
+ explicit IdentityPreconditioner(const MatrixType& ) {}
208
+
209
+ template<typename MatrixType>
210
+ IdentityPreconditioner& analyzePattern(const MatrixType& ) { return *this; }
211
+
212
+ template<typename MatrixType>
213
+ IdentityPreconditioner& factorize(const MatrixType& ) { return *this; }
214
+
215
+ template<typename MatrixType>
216
+ IdentityPreconditioner& compute(const MatrixType& ) { return *this; }
217
+
218
+ template<typename Rhs>
219
+ inline const Rhs& solve(const Rhs& b) const { return b; }
220
+
221
+ ComputationInfo info() { return Success; }
222
+ };
223
+
224
+ } // end namespace Eigen
225
+
226
+ #endif // EIGEN_BASIC_PRECONDITIONERS_H
@@ -0,0 +1,212 @@
1
+ // This file is part of Eigen, a lightweight C++ template library
2
+ // for linear algebra.
3
+ //
4
+ // Copyright (C) 2011-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
5
+ // Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
6
+ //
7
+ // This Source Code Form is subject to the terms of the Mozilla
8
+ // Public License v. 2.0. If a copy of the MPL was not distributed
9
+ // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10
+
11
+ #ifndef EIGEN_BICGSTAB_H
12
+ #define EIGEN_BICGSTAB_H
13
+
14
+ namespace Eigen {
15
+
16
+ namespace internal {
17
+
18
+ /** \internal Low-level bi conjugate gradient stabilized algorithm
19
+ * \param mat The matrix A
20
+ * \param rhs The right hand side vector b
21
+ * \param x On input and initial solution, on output the computed solution.
22
+ * \param precond A preconditioner being able to efficiently solve for an
23
+ * approximation of Ax=b (regardless of b)
24
+ * \param iters On input the max number of iteration, on output the number of performed iterations.
25
+ * \param tol_error On input the tolerance error, on output an estimation of the relative error.
26
+ * \return false in the case of numerical issue, for example a break down of BiCGSTAB.
27
+ */
28
+ template<typename MatrixType, typename Rhs, typename Dest, typename Preconditioner>
29
+ bool bicgstab(const MatrixType& mat, const Rhs& rhs, Dest& x,
30
+ const Preconditioner& precond, Index& iters,
31
+ typename Dest::RealScalar& tol_error)
32
+ {
33
+ using std::sqrt;
34
+ using std::abs;
35
+ typedef typename Dest::RealScalar RealScalar;
36
+ typedef typename Dest::Scalar Scalar;
37
+ typedef Matrix<Scalar,Dynamic,1> VectorType;
38
+ RealScalar tol = tol_error;
39
+ Index maxIters = iters;
40
+
41
+ Index n = mat.cols();
42
+ VectorType r = rhs - mat * x;
43
+ VectorType r0 = r;
44
+
45
+ RealScalar r0_sqnorm = r0.squaredNorm();
46
+ RealScalar rhs_sqnorm = rhs.squaredNorm();
47
+ if(rhs_sqnorm == 0)
48
+ {
49
+ x.setZero();
50
+ return true;
51
+ }
52
+ Scalar rho = 1;
53
+ Scalar alpha = 1;
54
+ Scalar w = 1;
55
+
56
+ VectorType v = VectorType::Zero(n), p = VectorType::Zero(n);
57
+ VectorType y(n), z(n);
58
+ VectorType kt(n), ks(n);
59
+
60
+ VectorType s(n), t(n);
61
+
62
+ RealScalar tol2 = tol*tol*rhs_sqnorm;
63
+ RealScalar eps2 = NumTraits<Scalar>::epsilon()*NumTraits<Scalar>::epsilon();
64
+ Index i = 0;
65
+ Index restarts = 0;
66
+
67
+ while ( r.squaredNorm() > tol2 && i<maxIters )
68
+ {
69
+ Scalar rho_old = rho;
70
+
71
+ rho = r0.dot(r);
72
+ if (abs(rho) < eps2*r0_sqnorm)
73
+ {
74
+ // The new residual vector became too orthogonal to the arbitrarily chosen direction r0
75
+ // Let's restart with a new r0:
76
+ r = rhs - mat * x;
77
+ r0 = r;
78
+ rho = r0_sqnorm = r.squaredNorm();
79
+ if(restarts++ == 0)
80
+ i = 0;
81
+ }
82
+ Scalar beta = (rho/rho_old) * (alpha / w);
83
+ p = r + beta * (p - w * v);
84
+
85
+ y = precond.solve(p);
86
+
87
+ v.noalias() = mat * y;
88
+
89
+ alpha = rho / r0.dot(v);
90
+ s = r - alpha * v;
91
+
92
+ z = precond.solve(s);
93
+ t.noalias() = mat * z;
94
+
95
+ RealScalar tmp = t.squaredNorm();
96
+ if(tmp>RealScalar(0))
97
+ w = t.dot(s) / tmp;
98
+ else
99
+ w = Scalar(0);
100
+ x += alpha * y + w * z;
101
+ r = s - w * t;
102
+ ++i;
103
+ }
104
+ tol_error = sqrt(r.squaredNorm()/rhs_sqnorm);
105
+ iters = i;
106
+ return true;
107
+ }
108
+
109
+ }
110
+
111
+ template< typename _MatrixType,
112
+ typename _Preconditioner = DiagonalPreconditioner<typename _MatrixType::Scalar> >
113
+ class BiCGSTAB;
114
+
115
+ namespace internal {
116
+
117
+ template< typename _MatrixType, typename _Preconditioner>
118
+ struct traits<BiCGSTAB<_MatrixType,_Preconditioner> >
119
+ {
120
+ typedef _MatrixType MatrixType;
121
+ typedef _Preconditioner Preconditioner;
122
+ };
123
+
124
+ }
125
+
126
+ /** \ingroup IterativeLinearSolvers_Module
127
+ * \brief A bi conjugate gradient stabilized solver for sparse square problems
128
+ *
129
+ * This class allows to solve for A.x = b sparse linear problems using a bi conjugate gradient
130
+ * stabilized algorithm. The vectors x and b can be either dense or sparse.
131
+ *
132
+ * \tparam _MatrixType the type of the sparse matrix A, can be a dense or a sparse matrix.
133
+ * \tparam _Preconditioner the type of the preconditioner. Default is DiagonalPreconditioner
134
+ *
135
+ * \implsparsesolverconcept
136
+ *
137
+ * The maximal number of iterations and tolerance value can be controlled via the setMaxIterations()
138
+ * and setTolerance() methods. The defaults are the size of the problem for the maximal number of iterations
139
+ * and NumTraits<Scalar>::epsilon() for the tolerance.
140
+ *
141
+ * The tolerance corresponds to the relative residual error: |Ax-b|/|b|
142
+ *
143
+ * \b Performance: when using sparse matrices, best performance is achied for a row-major sparse matrix format.
144
+ * Moreover, in this case multi-threading can be exploited if the user code is compiled with OpenMP enabled.
145
+ * See \ref TopicMultiThreading for details.
146
+ *
147
+ * This class can be used as the direct solver classes. Here is a typical usage example:
148
+ * \include BiCGSTAB_simple.cpp
149
+ *
150
+ * By default the iterations start with x=0 as an initial guess of the solution.
151
+ * One can control the start using the solveWithGuess() method.
152
+ *
153
+ * BiCGSTAB can also be used in a matrix-free context, see the following \link MatrixfreeSolverExample example \endlink.
154
+ *
155
+ * \sa class SimplicialCholesky, DiagonalPreconditioner, IdentityPreconditioner
156
+ */
157
+ template< typename _MatrixType, typename _Preconditioner>
158
+ class BiCGSTAB : public IterativeSolverBase<BiCGSTAB<_MatrixType,_Preconditioner> >
159
+ {
160
+ typedef IterativeSolverBase<BiCGSTAB> Base;
161
+ using Base::matrix;
162
+ using Base::m_error;
163
+ using Base::m_iterations;
164
+ using Base::m_info;
165
+ using Base::m_isInitialized;
166
+ public:
167
+ typedef _MatrixType MatrixType;
168
+ typedef typename MatrixType::Scalar Scalar;
169
+ typedef typename MatrixType::RealScalar RealScalar;
170
+ typedef _Preconditioner Preconditioner;
171
+
172
+ public:
173
+
174
+ /** Default constructor. */
175
+ BiCGSTAB() : Base() {}
176
+
177
+ /** Initialize the solver with matrix \a A for further \c Ax=b solving.
178
+ *
179
+ * This constructor is a shortcut for the default constructor followed
180
+ * by a call to compute().
181
+ *
182
+ * \warning this class stores a reference to the matrix A as well as some
183
+ * precomputed values that depend on it. Therefore, if \a A is changed
184
+ * this class becomes invalid. Call compute() to update it with the new
185
+ * matrix A, or modify a copy of A.
186
+ */
187
+ template<typename MatrixDerived>
188
+ explicit BiCGSTAB(const EigenBase<MatrixDerived>& A) : Base(A.derived()) {}
189
+
190
+ ~BiCGSTAB() {}
191
+
192
+ /** \internal */
193
+ template<typename Rhs,typename Dest>
194
+ void _solve_vector_with_guess_impl(const Rhs& b, Dest& x) const
195
+ {
196
+ m_iterations = Base::maxIterations();
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+ m_error = Base::m_tolerance;
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+
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+ bool ret = internal::bicgstab(matrix(), b, x, Base::m_preconditioner, m_iterations, m_error);
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+
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+ m_info = (!ret) ? NumericalIssue
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+ : m_error <= Base::m_tolerance ? Success
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+ : NoConvergence;
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+ }
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+
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+ protected:
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+
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+ };
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+
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+ } // end namespace Eigen
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+
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+ #endif // EIGEN_BICGSTAB_H
@@ -0,0 +1,229 @@
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+ // This file is part of Eigen, a lightweight C++ template library
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+ // for linear algebra.
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+ //
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+ // Copyright (C) 2011-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
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+ //
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+ // This Source Code Form is subject to the terms of the Mozilla
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+ // Public License v. 2.0. If a copy of the MPL was not distributed
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+ // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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+
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+ #ifndef EIGEN_CONJUGATE_GRADIENT_H
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+ #define EIGEN_CONJUGATE_GRADIENT_H
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+
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+ namespace Eigen {
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+
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+ namespace internal {
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+
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+ /** \internal Low-level conjugate gradient algorithm
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+ * \param mat The matrix A
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+ * \param rhs The right hand side vector b
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+ * \param x On input and initial solution, on output the computed solution.
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+ * \param precond A preconditioner being able to efficiently solve for an
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+ * approximation of Ax=b (regardless of b)
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+ * \param iters On input the max number of iteration, on output the number of performed iterations.
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+ * \param tol_error On input the tolerance error, on output an estimation of the relative error.
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+ */
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+ template<typename MatrixType, typename Rhs, typename Dest, typename Preconditioner>
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+ EIGEN_DONT_INLINE
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+ void conjugate_gradient(const MatrixType& mat, const Rhs& rhs, Dest& x,
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+ const Preconditioner& precond, Index& iters,
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+ typename Dest::RealScalar& tol_error)
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+ {
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+ using std::sqrt;
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+ using std::abs;
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+ typedef typename Dest::RealScalar RealScalar;
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+ typedef typename Dest::Scalar Scalar;
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+ typedef Matrix<Scalar,Dynamic,1> VectorType;
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+
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+ RealScalar tol = tol_error;
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+ Index maxIters = iters;
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+
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+ Index n = mat.cols();
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+
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+ VectorType residual = rhs - mat * x; //initial residual
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+
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+ RealScalar rhsNorm2 = rhs.squaredNorm();
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+ if(rhsNorm2 == 0)
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+ {
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+ x.setZero();
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+ iters = 0;
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+ tol_error = 0;
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+ return;
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+ }
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+ const RealScalar considerAsZero = (std::numeric_limits<RealScalar>::min)();
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+ RealScalar threshold = numext::maxi(RealScalar(tol*tol*rhsNorm2),considerAsZero);
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+ RealScalar residualNorm2 = residual.squaredNorm();
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+ if (residualNorm2 < threshold)
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+ {
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+ iters = 0;
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+ tol_error = sqrt(residualNorm2 / rhsNorm2);
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+ return;
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+ }
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+
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+ VectorType p(n);
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+ p = precond.solve(residual); // initial search direction
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+
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+ VectorType z(n), tmp(n);
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+ RealScalar absNew = numext::real(residual.dot(p)); // the square of the absolute value of r scaled by invM
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+ Index i = 0;
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+ while(i < maxIters)
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+ {
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+ tmp.noalias() = mat * p; // the bottleneck of the algorithm
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+
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+ Scalar alpha = absNew / p.dot(tmp); // the amount we travel on dir
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+ x += alpha * p; // update solution
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+ residual -= alpha * tmp; // update residual
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+
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+ residualNorm2 = residual.squaredNorm();
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+ if(residualNorm2 < threshold)
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+ break;
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+
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+ z = precond.solve(residual); // approximately solve for "A z = residual"
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+
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+ RealScalar absOld = absNew;
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+ absNew = numext::real(residual.dot(z)); // update the absolute value of r
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+ RealScalar beta = absNew / absOld; // calculate the Gram-Schmidt value used to create the new search direction
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+ p = z + beta * p; // update search direction
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+ i++;
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+ }
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+ tol_error = sqrt(residualNorm2 / rhsNorm2);
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+ iters = i;
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+ }
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+
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+ }
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+
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+ template< typename _MatrixType, int _UpLo=Lower,
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+ typename _Preconditioner = DiagonalPreconditioner<typename _MatrixType::Scalar> >
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+ class ConjugateGradient;
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+
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+ namespace internal {
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+
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+ template< typename _MatrixType, int _UpLo, typename _Preconditioner>
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+ struct traits<ConjugateGradient<_MatrixType,_UpLo,_Preconditioner> >
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+ {
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+ typedef _MatrixType MatrixType;
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+ typedef _Preconditioner Preconditioner;
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+ };
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+
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+ }
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+
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+ /** \ingroup IterativeLinearSolvers_Module
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+ * \brief A conjugate gradient solver for sparse (or dense) self-adjoint problems
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+ *
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+ * This class allows to solve for A.x = b linear problems using an iterative conjugate gradient algorithm.
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+ * The matrix A must be selfadjoint. The matrix A and the vectors x and b can be either dense or sparse.
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+ *
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+ * \tparam _MatrixType the type of the matrix A, can be a dense or a sparse matrix.
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+ * \tparam _UpLo the triangular part that will be used for the computations. It can be Lower,
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+ * \c Upper, or \c Lower|Upper in which the full matrix entries will be considered.
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+ * Default is \c Lower, best performance is \c Lower|Upper.
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+ * \tparam _Preconditioner the type of the preconditioner. Default is DiagonalPreconditioner
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+ *
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+ * \implsparsesolverconcept
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+ *
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+ * The maximal number of iterations and tolerance value can be controlled via the setMaxIterations()
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+ * and setTolerance() methods. The defaults are the size of the problem for the maximal number of iterations
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+ * and NumTraits<Scalar>::epsilon() for the tolerance.
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+ *
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+ * The tolerance corresponds to the relative residual error: |Ax-b|/|b|
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+ *
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+ * \b Performance: Even though the default value of \c _UpLo is \c Lower, significantly higher performance is
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+ * achieved when using a complete matrix and \b Lower|Upper as the \a _UpLo template parameter. Moreover, in this
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+ * case multi-threading can be exploited if the user code is compiled with OpenMP enabled.
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+ * See \ref TopicMultiThreading for details.
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+ *
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+ * This class can be used as the direct solver classes. Here is a typical usage example:
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+ \code
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+ int n = 10000;
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+ VectorXd x(n), b(n);
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+ SparseMatrix<double> A(n,n);
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+ // fill A and b
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+ ConjugateGradient<SparseMatrix<double>, Lower|Upper> cg;
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+ cg.compute(A);
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+ x = cg.solve(b);
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+ std::cout << "#iterations: " << cg.iterations() << std::endl;
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+ std::cout << "estimated error: " << cg.error() << std::endl;
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+ // update b, and solve again
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+ x = cg.solve(b);
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+ \endcode
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+ *
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+ * By default the iterations start with x=0 as an initial guess of the solution.
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+ * One can control the start using the solveWithGuess() method.
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+ *
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+ * ConjugateGradient can also be used in a matrix-free context, see the following \link MatrixfreeSolverExample example \endlink.
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+ *
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+ * \sa class LeastSquaresConjugateGradient, class SimplicialCholesky, DiagonalPreconditioner, IdentityPreconditioner
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+ */
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+ template< typename _MatrixType, int _UpLo, typename _Preconditioner>
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+ class ConjugateGradient : public IterativeSolverBase<ConjugateGradient<_MatrixType,_UpLo,_Preconditioner> >
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+ {
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+ typedef IterativeSolverBase<ConjugateGradient> Base;
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+ using Base::matrix;
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+ using Base::m_error;
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+ using Base::m_iterations;
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+ using Base::m_info;
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+ using Base::m_isInitialized;
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+ public:
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+ typedef _MatrixType MatrixType;
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+ typedef typename MatrixType::Scalar Scalar;
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+ typedef typename MatrixType::RealScalar RealScalar;
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+ typedef _Preconditioner Preconditioner;
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+
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+ enum {
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+ UpLo = _UpLo
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+ };
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+
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+ public:
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+
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+ /** Default constructor. */
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+ ConjugateGradient() : Base() {}
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+
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+ /** Initialize the solver with matrix \a A for further \c Ax=b solving.
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+ *
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+ * This constructor is a shortcut for the default constructor followed
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+ * by a call to compute().
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+ *
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+ * \warning this class stores a reference to the matrix A as well as some
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+ * precomputed values that depend on it. Therefore, if \a A is changed
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+ * this class becomes invalid. Call compute() to update it with the new
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+ * matrix A, or modify a copy of A.
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+ */
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+ template<typename MatrixDerived>
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+ explicit ConjugateGradient(const EigenBase<MatrixDerived>& A) : Base(A.derived()) {}
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+
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+ ~ConjugateGradient() {}
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+
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+ /** \internal */
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+ template<typename Rhs,typename Dest>
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+ void _solve_vector_with_guess_impl(const Rhs& b, Dest& x) const
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+ {
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+ typedef typename Base::MatrixWrapper MatrixWrapper;
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+ typedef typename Base::ActualMatrixType ActualMatrixType;
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+ enum {
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+ TransposeInput = (!MatrixWrapper::MatrixFree)
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+ && (UpLo==(Lower|Upper))
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+ && (!MatrixType::IsRowMajor)
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+ && (!NumTraits<Scalar>::IsComplex)
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+ };
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+ typedef typename internal::conditional<TransposeInput,Transpose<const ActualMatrixType>, ActualMatrixType const&>::type RowMajorWrapper;
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+ EIGEN_STATIC_ASSERT(EIGEN_IMPLIES(MatrixWrapper::MatrixFree,UpLo==(Lower|Upper)),MATRIX_FREE_CONJUGATE_GRADIENT_IS_COMPATIBLE_WITH_UPPER_UNION_LOWER_MODE_ONLY);
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+ typedef typename internal::conditional<UpLo==(Lower|Upper),
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+ RowMajorWrapper,
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+ typename MatrixWrapper::template ConstSelfAdjointViewReturnType<UpLo>::Type
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+ >::type SelfAdjointWrapper;
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+
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+ m_iterations = Base::maxIterations();
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+ m_error = Base::m_tolerance;
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+
218
+ RowMajorWrapper row_mat(matrix());
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+ internal::conjugate_gradient(SelfAdjointWrapper(row_mat), b, x, Base::m_preconditioner, m_iterations, m_error);
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+ m_info = m_error <= Base::m_tolerance ? Success : NoConvergence;
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+ }
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+
223
+ protected:
224
+
225
+ };
226
+
227
+ } // end namespace Eigen
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+
229
+ #endif // EIGEN_CONJUGATE_GRADIENT_H