sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
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  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,375 +0,0 @@
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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) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
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- // Copyright (C) 2012 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_SPARSELU_SUPERNODAL_MATRIX_H
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- #define EIGEN_SPARSELU_SUPERNODAL_MATRIX_H
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-
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- namespace Eigen {
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- namespace internal {
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-
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- /** \ingroup SparseLU_Module
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- * \brief a class to manipulate the L supernodal factor from the SparseLU factorization
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- *
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- * This class contain the data to easily store
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- * and manipulate the supernodes during the factorization and solution phase of Sparse LU.
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- * Only the lower triangular matrix has supernodes.
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- *
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- * NOTE : This class corresponds to the SCformat structure in SuperLU
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- *
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- */
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- /* TODO
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- * InnerIterator as for sparsematrix
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- * SuperInnerIterator to iterate through all supernodes
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- * Function for triangular solve
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- */
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- template <typename _Scalar, typename _StorageIndex>
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- class MappedSuperNodalMatrix
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- {
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- public:
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- typedef _Scalar Scalar;
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- typedef _StorageIndex StorageIndex;
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- typedef Matrix<StorageIndex,Dynamic,1> IndexVector;
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- typedef Matrix<Scalar,Dynamic,1> ScalarVector;
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- public:
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- MappedSuperNodalMatrix()
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- {
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-
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- }
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- MappedSuperNodalMatrix(Index m, Index n, ScalarVector& nzval, IndexVector& nzval_colptr, IndexVector& rowind,
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- IndexVector& rowind_colptr, IndexVector& col_to_sup, IndexVector& sup_to_col )
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- {
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- setInfos(m, n, nzval, nzval_colptr, rowind, rowind_colptr, col_to_sup, sup_to_col);
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- }
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-
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- ~MappedSuperNodalMatrix()
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- {
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-
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- }
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- /**
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- * Set appropriate pointers for the lower triangular supernodal matrix
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- * These infos are available at the end of the numerical factorization
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- * FIXME This class will be modified such that it can be use in the course
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- * of the factorization.
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- */
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- void setInfos(Index m, Index n, ScalarVector& nzval, IndexVector& nzval_colptr, IndexVector& rowind,
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- IndexVector& rowind_colptr, IndexVector& col_to_sup, IndexVector& sup_to_col )
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- {
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- m_row = m;
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- m_col = n;
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- m_nzval = nzval.data();
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- m_nzval_colptr = nzval_colptr.data();
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- m_rowind = rowind.data();
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- m_rowind_colptr = rowind_colptr.data();
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- m_nsuper = col_to_sup(n);
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- m_col_to_sup = col_to_sup.data();
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- m_sup_to_col = sup_to_col.data();
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- }
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-
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- /**
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- * Number of rows
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- */
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- Index rows() const { return m_row; }
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-
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- /**
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- * Number of columns
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- */
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- Index cols() const { return m_col; }
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-
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- /**
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- * Return the array of nonzero values packed by column
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- *
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- * The size is nnz
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- */
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- Scalar* valuePtr() { return m_nzval; }
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-
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- const Scalar* valuePtr() const
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- {
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- return m_nzval;
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- }
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- /**
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- * Return the pointers to the beginning of each column in \ref valuePtr()
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- */
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- StorageIndex* colIndexPtr()
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- {
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- return m_nzval_colptr;
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- }
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-
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- const StorageIndex* colIndexPtr() const
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- {
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- return m_nzval_colptr;
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- }
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-
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- /**
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- * Return the array of compressed row indices of all supernodes
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- */
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- StorageIndex* rowIndex() { return m_rowind; }
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-
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- const StorageIndex* rowIndex() const
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- {
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- return m_rowind;
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- }
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-
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- /**
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- * Return the location in \em rowvaluePtr() which starts each column
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- */
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- StorageIndex* rowIndexPtr() { return m_rowind_colptr; }
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-
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- const StorageIndex* rowIndexPtr() const
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- {
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- return m_rowind_colptr;
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- }
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-
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- /**
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- * Return the array of column-to-supernode mapping
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- */
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- StorageIndex* colToSup() { return m_col_to_sup; }
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-
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- const StorageIndex* colToSup() const
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- {
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- return m_col_to_sup;
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- }
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- /**
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- * Return the array of supernode-to-column mapping
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- */
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- StorageIndex* supToCol() { return m_sup_to_col; }
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-
143
- const StorageIndex* supToCol() const
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- {
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- return m_sup_to_col;
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- }
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-
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- /**
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- * Return the number of supernodes
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- */
151
- Index nsuper() const
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- {
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- return m_nsuper;
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- }
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-
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- class InnerIterator;
157
- template<typename Dest>
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- void solveInPlace( MatrixBase<Dest>&X) const;
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- template<bool Conjugate, typename Dest>
160
- void solveTransposedInPlace( MatrixBase<Dest>&X) const;
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-
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-
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-
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-
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-
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- protected:
167
- Index m_row; // Number of rows
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- Index m_col; // Number of columns
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- Index m_nsuper; // Number of supernodes
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- Scalar* m_nzval; //array of nonzero values packed by column
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- StorageIndex* m_nzval_colptr; //nzval_colptr[j] Stores the location in nzval[] which starts column j
172
- StorageIndex* m_rowind; // Array of compressed row indices of rectangular supernodes
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- StorageIndex* m_rowind_colptr; //rowind_colptr[j] stores the location in rowind[] which starts column j
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- StorageIndex* m_col_to_sup; // col_to_sup[j] is the supernode number to which column j belongs
175
- StorageIndex* m_sup_to_col; //sup_to_col[s] points to the starting column of the s-th supernode
176
-
177
- private :
178
- };
179
-
180
- /**
181
- * \brief InnerIterator class to iterate over nonzero values of the current column in the supernodal matrix L
182
- *
183
- */
184
- template<typename Scalar, typename StorageIndex>
185
- class MappedSuperNodalMatrix<Scalar,StorageIndex>::InnerIterator
186
- {
187
- public:
188
- InnerIterator(const MappedSuperNodalMatrix& mat, Index outer)
189
- : m_matrix(mat),
190
- m_outer(outer),
191
- m_supno(mat.colToSup()[outer]),
192
- m_idval(mat.colIndexPtr()[outer]),
193
- m_startidval(m_idval),
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- m_endidval(mat.colIndexPtr()[outer+1]),
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- m_idrow(mat.rowIndexPtr()[mat.supToCol()[mat.colToSup()[outer]]]),
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- m_endidrow(mat.rowIndexPtr()[mat.supToCol()[mat.colToSup()[outer]]+1])
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- {}
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- inline InnerIterator& operator++()
199
- {
200
- m_idval++;
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- m_idrow++;
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- return *this;
203
- }
204
- inline Scalar value() const { return m_matrix.valuePtr()[m_idval]; }
205
-
206
- inline Scalar& valueRef() { return const_cast<Scalar&>(m_matrix.valuePtr()[m_idval]); }
207
-
208
- inline Index index() const { return m_matrix.rowIndex()[m_idrow]; }
209
- inline Index row() const { return index(); }
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- inline Index col() const { return m_outer; }
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-
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- inline Index supIndex() const { return m_supno; }
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-
214
- inline operator bool() const
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- {
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- return ( (m_idval < m_endidval) && (m_idval >= m_startidval)
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- && (m_idrow < m_endidrow) );
218
- }
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-
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- protected:
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- const MappedSuperNodalMatrix& m_matrix; // Supernodal lower triangular matrix
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- const Index m_outer; // Current column
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- const Index m_supno; // Current SuperNode number
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- Index m_idval; // Index to browse the values in the current column
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- const Index m_startidval; // Start of the column value
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- const Index m_endidval; // End of the column value
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- Index m_idrow; // Index to browse the row indices
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- Index m_endidrow; // End index of row indices of the current column
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- };
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-
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- /**
232
- * \brief Solve with the supernode triangular matrix
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- *
234
- */
235
- template<typename Scalar, typename Index_>
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- template<typename Dest>
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- void MappedSuperNodalMatrix<Scalar,Index_>::solveInPlace( MatrixBase<Dest>&X) const
238
- {
239
- /* Explicit type conversion as the Index type of MatrixBase<Dest> may be wider than Index */
240
- // eigen_assert(X.rows() <= NumTraits<Index>::highest());
241
- // eigen_assert(X.cols() <= NumTraits<Index>::highest());
242
- Index n = int(X.rows());
243
- Index nrhs = Index(X.cols());
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- const Scalar * Lval = valuePtr(); // Nonzero values
245
- Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor> work(n, nrhs); // working vector
246
- work.setZero();
247
- for (Index k = 0; k <= nsuper(); k ++)
248
- {
249
- Index fsupc = supToCol()[k]; // First column of the current supernode
250
- Index istart = rowIndexPtr()[fsupc]; // Pointer index to the subscript of the current column
251
- Index nsupr = rowIndexPtr()[fsupc+1] - istart; // Number of rows in the current supernode
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- Index nsupc = supToCol()[k+1] - fsupc; // Number of columns in the current supernode
253
- Index nrow = nsupr - nsupc; // Number of rows in the non-diagonal part of the supernode
254
- Index irow; //Current index row
255
-
256
- if (nsupc == 1 )
257
- {
258
- for (Index j = 0; j < nrhs; j++)
259
- {
260
- InnerIterator it(*this, fsupc);
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- ++it; // Skip the diagonal element
262
- for (; it; ++it)
263
- {
264
- irow = it.row();
265
- X(irow, j) -= X(fsupc, j) * it.value();
266
- }
267
- }
268
- }
269
- else
270
- {
271
- // The supernode has more than one column
272
- Index luptr = colIndexPtr()[fsupc];
273
- Index lda = colIndexPtr()[fsupc+1] - luptr;
274
-
275
- // Triangular solve
276
- Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > A( &(Lval[luptr]), nsupc, nsupc, OuterStride<>(lda) );
277
- Map< Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
278
- U = A.template triangularView<UnitLower>().solve(U);
279
-
280
- // Matrix-vector product
281
- new (&A) Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > ( &(Lval[luptr+nsupc]), nrow, nsupc, OuterStride<>(lda) );
282
- work.topRows(nrow).noalias() = A * U;
283
-
284
- //Begin Scatter
285
- for (Index j = 0; j < nrhs; j++)
286
- {
287
- Index iptr = istart + nsupc;
288
- for (Index i = 0; i < nrow; i++)
289
- {
290
- irow = rowIndex()[iptr];
291
- X(irow, j) -= work(i, j); // Scatter operation
292
- work(i, j) = Scalar(0);
293
- iptr++;
294
- }
295
- }
296
- }
297
- }
298
- }
299
-
300
- template<typename Scalar, typename Index_>
301
- template<bool Conjugate, typename Dest>
302
- void MappedSuperNodalMatrix<Scalar,Index_>::solveTransposedInPlace( MatrixBase<Dest>&X) const
303
- {
304
- using numext::conj;
305
- Index n = int(X.rows());
306
- Index nrhs = Index(X.cols());
307
- const Scalar * Lval = valuePtr(); // Nonzero values
308
- Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor> work(n, nrhs); // working vector
309
- work.setZero();
310
- for (Index k = nsuper(); k >= 0; k--)
311
- {
312
- Index fsupc = supToCol()[k]; // First column of the current supernode
313
- Index istart = rowIndexPtr()[fsupc]; // Pointer index to the subscript of the current column
314
- Index nsupr = rowIndexPtr()[fsupc+1] - istart; // Number of rows in the current supernode
315
- Index nsupc = supToCol()[k+1] - fsupc; // Number of columns in the current supernode
316
- Index nrow = nsupr - nsupc; // Number of rows in the non-diagonal part of the supernode
317
- Index irow; //Current index row
318
-
319
- if (nsupc == 1 )
320
- {
321
- for (Index j = 0; j < nrhs; j++)
322
- {
323
- InnerIterator it(*this, fsupc);
324
- ++it; // Skip the diagonal element
325
- for (; it; ++it)
326
- {
327
- irow = it.row();
328
- X(fsupc,j) -= X(irow, j) * (Conjugate?conj(it.value()):it.value());
329
- }
330
- }
331
- }
332
- else
333
- {
334
- // The supernode has more than one column
335
- Index luptr = colIndexPtr()[fsupc];
336
- Index lda = colIndexPtr()[fsupc+1] - luptr;
337
-
338
- //Begin Gather
339
- for (Index j = 0; j < nrhs; j++)
340
- {
341
- Index iptr = istart + nsupc;
342
- for (Index i = 0; i < nrow; i++)
343
- {
344
- irow = rowIndex()[iptr];
345
- work.topRows(nrow)(i,j)= X(irow,j); // Gather operation
346
- iptr++;
347
- }
348
- }
349
-
350
- // Matrix-vector product with transposed submatrix
351
- Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > A( &(Lval[luptr+nsupc]), nrow, nsupc, OuterStride<>(lda) );
352
- Map< Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
353
- if(Conjugate)
354
- U = U - A.adjoint() * work.topRows(nrow);
355
- else
356
- U = U - A.transpose() * work.topRows(nrow);
357
-
358
- // Triangular solve (of transposed diagonal block)
359
- new (&A) Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > ( &(Lval[luptr]), nsupc, nsupc, OuterStride<>(lda) );
360
- if(Conjugate)
361
- U = A.adjoint().template triangularView<UnitUpper>().solve(U);
362
- else
363
- U = A.transpose().template triangularView<UnitUpper>().solve(U);
364
-
365
- }
366
-
367
- }
368
- }
369
-
370
-
371
- } // end namespace internal
372
-
373
- } // end namespace Eigen
374
-
375
- #endif // EIGEN_SPARSELU_MATRIX_H
@@ -1,80 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
5
- //
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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
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
-
11
- #ifndef EIGEN_SPARSELU_UTILS_H
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- #define EIGEN_SPARSELU_UTILS_H
13
-
14
- namespace Eigen {
15
- namespace internal {
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-
17
- /**
18
- * \brief Count Nonzero elements in the factors
19
- */
20
- template <typename Scalar, typename StorageIndex>
21
- void SparseLUImpl<Scalar,StorageIndex>::countnz(const Index n, Index& nnzL, Index& nnzU, GlobalLU_t& glu)
22
- {
23
- nnzL = 0;
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- nnzU = (glu.xusub)(n);
25
- Index nsuper = (glu.supno)(n);
26
- Index jlen;
27
- Index i, j, fsupc;
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- if (n <= 0 ) return;
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- // For each supernode
30
- for (i = 0; i <= nsuper; i++)
31
- {
32
- fsupc = glu.xsup(i);
33
- jlen = glu.xlsub(fsupc+1) - glu.xlsub(fsupc);
34
-
35
- for (j = fsupc; j < glu.xsup(i+1); j++)
36
- {
37
- nnzL += jlen;
38
- nnzU += j - fsupc + 1;
39
- jlen--;
40
- }
41
- }
42
- }
43
-
44
- /**
45
- * \brief Fix up the data storage lsub for L-subscripts.
46
- *
47
- * It removes the subscripts sets for structural pruning,
48
- * and applies permutation to the remaining subscripts
49
- *
50
- */
51
- template <typename Scalar, typename StorageIndex>
52
- void SparseLUImpl<Scalar,StorageIndex>::fixupL(const Index n, const IndexVector& perm_r, GlobalLU_t& glu)
53
- {
54
- Index fsupc, i, j, k, jstart;
55
-
56
- StorageIndex nextl = 0;
57
- Index nsuper = (glu.supno)(n);
58
-
59
- // For each supernode
60
- for (i = 0; i <= nsuper; i++)
61
- {
62
- fsupc = glu.xsup(i);
63
- jstart = glu.xlsub(fsupc);
64
- glu.xlsub(fsupc) = nextl;
65
- for (j = jstart; j < glu.xlsub(fsupc + 1); j++)
66
- {
67
- glu.lsub(nextl) = perm_r(glu.lsub(j)); // Now indexed into P*A
68
- nextl++;
69
- }
70
- for (k = fsupc+1; k < glu.xsup(i+1); k++)
71
- glu.xlsub(k) = nextl; // other columns in supernode i
72
- }
73
-
74
- glu.xlsub(n) = nextl;
75
- }
76
-
77
- } // end namespace internal
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-
79
- } // end namespace Eigen
80
- #endif // EIGEN_SPARSELU_UTILS_H
@@ -1,181 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
5
- // Copyright (C) 2012 Gael Guennebaud <gael.guennebaud@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
- /*
12
-
13
- * NOTE: This file is the modified version of xcolumn_bmod.c file in SuperLU
14
-
15
- * -- SuperLU routine (version 3.0) --
16
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
17
- * and Lawrence Berkeley National Lab.
18
- * October 15, 2003
19
- *
20
- * Copyright (c) 1994 by Xerox Corporation. All rights reserved.
21
- *
22
- * THIS MATERIAL IS PROVIDED AS IS, WITH ABSOLUTELY NO WARRANTY
23
- * EXPRESSED OR IMPLIED. ANY USE IS AT YOUR OWN RISK.
24
- *
25
- * Permission is hereby granted to use or copy this program for any
26
- * purpose, provided the above notices are retained on all copies.
27
- * Permission to modify the code and to distribute modified code is
28
- * granted, provided the above notices are retained, and a notice that
29
- * the code was modified is included with the above copyright notice.
30
- */
31
- #ifndef SPARSELU_COLUMN_BMOD_H
32
- #define SPARSELU_COLUMN_BMOD_H
33
-
34
- namespace Eigen {
35
-
36
- namespace internal {
37
- /**
38
- * \brief Performs numeric block updates (sup-col) in topological order
39
- *
40
- * \param jcol current column to update
41
- * \param nseg Number of segments in the U part
42
- * \param dense Store the full representation of the column
43
- * \param tempv working array
44
- * \param segrep segment representative ...
45
- * \param repfnz ??? First nonzero column in each row ??? ...
46
- * \param fpanelc First column in the current panel
47
- * \param glu Global LU data.
48
- * \return 0 - successful return
49
- * > 0 - number of bytes allocated when run out of space
50
- *
51
- */
52
- template <typename Scalar, typename StorageIndex>
53
- Index SparseLUImpl<Scalar,StorageIndex>::column_bmod(const Index jcol, const Index nseg, BlockScalarVector dense, ScalarVector& tempv,
54
- BlockIndexVector segrep, BlockIndexVector repfnz, Index fpanelc, GlobalLU_t& glu)
55
- {
56
- Index jsupno, k, ksub, krep, ksupno;
57
- Index lptr, nrow, isub, irow, nextlu, new_next, ufirst;
58
- Index fsupc, nsupc, nsupr, luptr, kfnz, no_zeros;
59
- /* krep = representative of current k-th supernode
60
- * fsupc = first supernodal column
61
- * nsupc = number of columns in a supernode
62
- * nsupr = number of rows in a supernode
63
- * luptr = location of supernodal LU-block in storage
64
- * kfnz = first nonz in the k-th supernodal segment
65
- * no_zeros = no lf leading zeros in a supernodal U-segment
66
- */
67
-
68
- jsupno = glu.supno(jcol);
69
- // For each nonzero supernode segment of U[*,j] in topological order
70
- k = nseg - 1;
71
- Index d_fsupc; // distance between the first column of the current panel and the
72
- // first column of the current snode
73
- Index fst_col; // First column within small LU update
74
- Index segsize;
75
- for (ksub = 0; ksub < nseg; ksub++)
76
- {
77
- krep = segrep(k); k--;
78
- ksupno = glu.supno(krep);
79
- if (jsupno != ksupno )
80
- {
81
- // outside the rectangular supernode
82
- fsupc = glu.xsup(ksupno);
83
- fst_col = (std::max)(fsupc, fpanelc);
84
-
85
- // Distance from the current supernode to the current panel;
86
- // d_fsupc = 0 if fsupc > fpanelc
87
- d_fsupc = fst_col - fsupc;
88
-
89
- luptr = glu.xlusup(fst_col) + d_fsupc;
90
- lptr = glu.xlsub(fsupc) + d_fsupc;
91
-
92
- kfnz = repfnz(krep);
93
- kfnz = (std::max)(kfnz, fpanelc);
94
-
95
- segsize = krep - kfnz + 1;
96
- nsupc = krep - fst_col + 1;
97
- nsupr = glu.xlsub(fsupc+1) - glu.xlsub(fsupc);
98
- nrow = nsupr - d_fsupc - nsupc;
99
- Index lda = glu.xlusup(fst_col+1) - glu.xlusup(fst_col);
100
-
101
-
102
- // Perform a triangular solver and block update,
103
- // then scatter the result of sup-col update to dense
104
- no_zeros = kfnz - fst_col;
105
- if(segsize==1)
106
- LU_kernel_bmod<1>::run(segsize, dense, tempv, glu.lusup, luptr, lda, nrow, glu.lsub, lptr, no_zeros);
107
- else
108
- LU_kernel_bmod<Dynamic>::run(segsize, dense, tempv, glu.lusup, luptr, lda, nrow, glu.lsub, lptr, no_zeros);
109
- } // end if jsupno
110
- } // end for each segment
111
-
112
- // Process the supernodal portion of L\U[*,j]
113
- nextlu = glu.xlusup(jcol);
114
- fsupc = glu.xsup(jsupno);
115
-
116
- // copy the SPA dense into L\U[*,j]
117
- Index mem;
118
- new_next = nextlu + glu.xlsub(fsupc + 1) - glu.xlsub(fsupc);
119
- Index offset = internal::first_multiple<Index>(new_next, internal::packet_traits<Scalar>::size) - new_next;
120
- if(offset)
121
- new_next += offset;
122
- while (new_next > glu.nzlumax )
123
- {
124
- mem = memXpand<ScalarVector>(glu.lusup, glu.nzlumax, nextlu, LUSUP, glu.num_expansions);
125
- if (mem) return mem;
126
- }
127
-
128
- for (isub = glu.xlsub(fsupc); isub < glu.xlsub(fsupc+1); isub++)
129
- {
130
- irow = glu.lsub(isub);
131
- glu.lusup(nextlu) = dense(irow);
132
- dense(irow) = Scalar(0.0);
133
- ++nextlu;
134
- }
135
-
136
- if(offset)
137
- {
138
- glu.lusup.segment(nextlu,offset).setZero();
139
- nextlu += offset;
140
- }
141
- glu.xlusup(jcol + 1) = StorageIndex(nextlu); // close L\U(*,jcol);
142
-
143
- /* For more updates within the panel (also within the current supernode),
144
- * should start from the first column of the panel, or the first column
145
- * of the supernode, whichever is bigger. There are two cases:
146
- * 1) fsupc < fpanelc, then fst_col <-- fpanelc
147
- * 2) fsupc >= fpanelc, then fst_col <-- fsupc
148
- */
149
- fst_col = (std::max)(fsupc, fpanelc);
150
-
151
- if (fst_col < jcol)
152
- {
153
- // Distance between the current supernode and the current panel
154
- // d_fsupc = 0 if fsupc >= fpanelc
155
- d_fsupc = fst_col - fsupc;
156
-
157
- lptr = glu.xlsub(fsupc) + d_fsupc;
158
- luptr = glu.xlusup(fst_col) + d_fsupc;
159
- nsupr = glu.xlsub(fsupc+1) - glu.xlsub(fsupc); // leading dimension
160
- nsupc = jcol - fst_col; // excluding jcol
161
- nrow = nsupr - d_fsupc - nsupc;
162
-
163
- // points to the beginning of jcol in snode L\U(jsupno)
164
- ufirst = glu.xlusup(jcol) + d_fsupc;
165
- Index lda = glu.xlusup(jcol+1) - glu.xlusup(jcol);
166
- MappedMatrixBlock A( &(glu.lusup.data()[luptr]), nsupc, nsupc, OuterStride<>(lda) );
167
- VectorBlock<ScalarVector> u(glu.lusup, ufirst, nsupc);
168
- u = A.template triangularView<UnitLower>().solve(u);
169
-
170
- new (&A) MappedMatrixBlock ( &(glu.lusup.data()[luptr+nsupc]), nrow, nsupc, OuterStride<>(lda) );
171
- VectorBlock<ScalarVector> l(glu.lusup, ufirst+nsupc, nrow);
172
- l.noalias() -= A * u;
173
-
174
- } // End if fst_col
175
- return 0;
176
- }
177
-
178
- } // end namespace internal
179
- } // end namespace Eigen
180
-
181
- #endif // SPARSELU_COLUMN_BMOD_H