sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.20__cp310-cp310-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +155 -155
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-310-darwin.so +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/hierarchical_clustering.py +108 -6
  6. sequenzo/define_sequence_data.py +10 -1
  7. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  8. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  9. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-310-darwin.so +0 -0
  11. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  12. sequenzo/dissimilarity_measures/utils/seqconc.cpython-310-darwin.so +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  14. sequenzo/dissimilarity_measures/utils/seqdss.cpython-310-darwin.so +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  16. sequenzo/dissimilarity_measures/utils/seqdur.cpython-310-darwin.so +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  18. sequenzo/dissimilarity_measures/utils/seqlength.cpython-310-darwin.so +0 -0
  19. sequenzo/multidomain/cat.py +0 -53
  20. sequenzo/multidomain/dat.py +11 -3
  21. sequenzo/multidomain/idcd.py +0 -3
  22. sequenzo/multidomain/linked_polyad.py +0 -1
  23. sequenzo/openmp_setup.py +233 -0
  24. sequenzo/visualization/plot_transition_matrix.py +21 -22
  25. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  26. sequenzo-0.1.20.dist-info/RECORD +215 -0
  27. sequenzo/dissimilarity_measures/setup.py +0 -35
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  171. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  172. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  173. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  174. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  175. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  176. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  177. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  178. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  179. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  180. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  181. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  182. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  183. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  184. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  185. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  186. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  187. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  188. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  189. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  190. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  191. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  192. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  193. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  194. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  195. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  196. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  197. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  198. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  199. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  200. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  201. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  202. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  203. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  204. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  205. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  206. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  207. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  208. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  209. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
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@@ -1,669 +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) 2013 Christian Seiler <christian@iwakd.de>
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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_CXX11_TENSORSYMMETRY_TEMPLATEGROUPTHEORY_H
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- #define EIGEN_CXX11_TENSORSYMMETRY_TEMPLATEGROUPTHEORY_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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- namespace group_theory {
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-
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- /** \internal
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- * \file CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h
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- * This file contains C++ templates that implement group theory algorithms.
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- *
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- * The algorithms allow for a compile-time analysis of finite groups.
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- *
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- * Currently only Dimino's algorithm is implemented, which returns a list
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- * of all elements in a group given a set of (possibly redundant) generators.
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- * (One could also do that with the so-called orbital algorithm, but that
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- * is much more expensive and usually has no advantages.)
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- */
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-
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- /**********************************************************************
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- * "Ok kid, here is where it gets complicated."
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- * - Amelia Pond in the "Doctor Who" episode
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- * "The Big Bang"
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- *
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- * Dimino's algorithm
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- * ==================
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- *
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- * The following is Dimino's algorithm in sequential form:
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- *
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- * Input: identity element, list of generators, equality check,
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- * multiplication operation
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- * Output: list of group elements
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- *
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- * 1. add identity element
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- * 2. remove identities from list of generators
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- * 3. add all powers of first generator that aren't the
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- * identity element
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- * 4. go through all remaining generators:
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- * a. if generator is already in the list of elements
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- * -> do nothing
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- * b. otherwise
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- * i. remember current # of elements
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- * (i.e. the size of the current subgroup)
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- * ii. add all current elements (which includes
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- * the identity) each multiplied from right
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- * with the current generator to the group
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- * iii. add all remaining cosets that are generated
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- * by products of the new generator with itself
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- * and all other generators seen so far
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- *
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- * In functional form, this is implemented as a long set of recursive
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- * templates that have a complicated relationship.
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- *
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- * The main interface for Dimino's algorithm is the template
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- * enumerate_group_elements. All lists are implemented as variadic
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- * type_list<typename...> and numeric_list<typename = int, int...>
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- * templates.
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- *
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- * 'Calling' templates is usually done via typedefs.
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- *
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- * This algorithm is an extended version of the basic version. The
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- * extension consists in the fact that each group element has a set
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- * of flags associated with it. Multiplication of two group elements
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- * with each other results in a group element whose flags are the
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- * XOR of the flags of the previous elements. Each time the algorithm
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- * notices that a group element it just calculated is already in the
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- * list of current elements, the flags of both will be compared and
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- * added to the so-called 'global flags' of the group.
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- *
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- * The rationale behind this extension is that this allows not only
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- * for the description of symmetries between tensor indices, but
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- * also allows for the description of hermiticity, antisymmetry and
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- * antihermiticity. Negation and conjugation each are specific bit
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- * in the flags value and if two different ways to reach a group
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- * element lead to two different flags, this poses a constraint on
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- * the allowed values of the resulting tensor. For example, if a
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- * group element is reach both with and without the conjugation
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- * flags, it is clear that the resulting tensor has to be real.
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- *
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- * Note that this flag mechanism is quite generic and may have other
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- * uses beyond tensor properties.
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- *
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- * IMPORTANT:
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- * This algorithm assumes the group to be finite. If you try to
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- * run it with a group that's infinite, the algorithm will only
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- * terminate once you hit a compiler limit (max template depth).
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- * Also note that trying to use this implementation to create a
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- * very large group will probably either make you hit the same
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- * limit, cause the compiler to segfault or at the very least
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- * take a *really* long time (hours, days, weeks - sic!) to
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- * compile. It is not recommended to plug in more than 4
103
- * generators, unless they are independent of each other.
104
- */
105
-
106
- /** \internal
107
- *
108
- * \class strip_identities
109
- * \ingroup CXX11_TensorSymmetry_Module
110
- *
111
- * \brief Cleanse a list of group elements of the identity element
112
- *
113
- * This template is used to make a first pass through all initial
114
- * generators of Dimino's algorithm and remove the identity
115
- * elements.
116
- *
117
- * \sa enumerate_group_elements
118
- */
119
- template<template<typename, typename> class Equality, typename id, typename L> struct strip_identities;
120
-
121
- template<
122
- template<typename, typename> class Equality,
123
- typename id,
124
- typename t,
125
- typename... ts
126
- >
127
- struct strip_identities<Equality, id, type_list<t, ts...>>
128
- {
129
- typedef typename conditional<
130
- Equality<id, t>::value,
131
- typename strip_identities<Equality, id, type_list<ts...>>::type,
132
- typename concat<type_list<t>, typename strip_identities<Equality, id, type_list<ts...>>::type>::type
133
- >::type type;
134
- constexpr static int global_flags = Equality<id, t>::global_flags | strip_identities<Equality, id, type_list<ts...>>::global_flags;
135
- };
136
-
137
- template<
138
- template<typename, typename> class Equality,
139
- typename id
140
- EIGEN_TPL_PP_SPEC_HACK_DEFC(typename, ts)
141
- >
142
- struct strip_identities<Equality, id, type_list<EIGEN_TPL_PP_SPEC_HACK_USE(ts)>>
143
- {
144
- typedef type_list<> type;
145
- constexpr static int global_flags = 0;
146
- };
147
-
148
- /** \internal
149
- *
150
- * \class dimino_first_step_elements_helper
151
- * \ingroup CXX11_TensorSymmetry_Module
152
- *
153
- * \brief Recursive template that adds powers of the first generator to the list of group elements
154
- *
155
- * This template calls itself recursively to add powers of the first
156
- * generator to the list of group elements. It stops if it reaches
157
- * the identity element again.
158
- *
159
- * \sa enumerate_group_elements, dimino_first_step_elements
160
- */
161
- template<
162
- template<typename, typename> class Multiply,
163
- template<typename, typename> class Equality,
164
- typename id,
165
- typename g,
166
- typename current_element,
167
- typename elements,
168
- bool dont_add_current_element // = false
169
- >
170
- struct dimino_first_step_elements_helper
171
- #ifndef EIGEN_PARSED_BY_DOXYGEN
172
- : // recursive inheritance is too difficult for Doxygen
173
- public dimino_first_step_elements_helper<
174
- Multiply,
175
- Equality,
176
- id,
177
- g,
178
- typename Multiply<current_element, g>::type,
179
- typename concat<elements, type_list<current_element>>::type,
180
- Equality<typename Multiply<current_element, g>::type, id>::value
181
- > {};
182
-
183
- template<
184
- template<typename, typename> class Multiply,
185
- template<typename, typename> class Equality,
186
- typename id,
187
- typename g,
188
- typename current_element,
189
- typename elements
190
- >
191
- struct dimino_first_step_elements_helper<Multiply, Equality, id, g, current_element, elements, true>
192
- #endif // EIGEN_PARSED_BY_DOXYGEN
193
- {
194
- typedef elements type;
195
- constexpr static int global_flags = Equality<current_element, id>::global_flags;
196
- };
197
-
198
- /** \internal
199
- *
200
- * \class dimino_first_step_elements
201
- * \ingroup CXX11_TensorSymmetry_Module
202
- *
203
- * \brief Add all powers of the first generator to the list of group elements
204
- *
205
- * This template takes the first non-identity generator and generates the initial
206
- * list of elements which consists of all powers of that generator. For a group
207
- * with just one generated, it would be enumerated after this.
208
- *
209
- * \sa enumerate_group_elements
210
- */
211
- template<
212
- template<typename, typename> class Multiply,
213
- template<typename, typename> class Equality,
214
- typename id,
215
- typename generators
216
- >
217
- struct dimino_first_step_elements
218
- {
219
- typedef typename get<0, generators>::type first_generator;
220
- typedef typename skip<1, generators>::type next_generators;
221
- typedef type_list<first_generator> generators_done;
222
-
223
- typedef dimino_first_step_elements_helper<
224
- Multiply,
225
- Equality,
226
- id,
227
- first_generator,
228
- first_generator,
229
- type_list<id>,
230
- false
231
- > helper;
232
- typedef typename helper::type type;
233
- constexpr static int global_flags = helper::global_flags;
234
- };
235
-
236
- /** \internal
237
- *
238
- * \class dimino_get_coset_elements
239
- * \ingroup CXX11_TensorSymmetry_Module
240
- *
241
- * \brief Generate all elements of a specific coset
242
- *
243
- * This template generates all the elements of a specific coset by
244
- * multiplying all elements in the given subgroup with the new
245
- * coset representative. Note that the first element of the
246
- * subgroup is always the identity element, so the first element of
247
- * the result of this template is going to be the coset
248
- * representative itself.
249
- *
250
- * Note that this template accepts an additional boolean parameter
251
- * that specifies whether to actually generate the coset (true) or
252
- * just return an empty list (false).
253
- *
254
- * \sa enumerate_group_elements, dimino_add_cosets_for_rep
255
- */
256
- template<
257
- template<typename, typename> class Multiply,
258
- typename sub_group_elements,
259
- typename new_coset_rep,
260
- bool generate_coset // = true
261
- >
262
- struct dimino_get_coset_elements
263
- {
264
- typedef typename apply_op_from_right<Multiply, new_coset_rep, sub_group_elements>::type type;
265
- };
266
-
267
- template<
268
- template<typename, typename> class Multiply,
269
- typename sub_group_elements,
270
- typename new_coset_rep
271
- >
272
- struct dimino_get_coset_elements<Multiply, sub_group_elements, new_coset_rep, false>
273
- {
274
- typedef type_list<> type;
275
- };
276
-
277
- /** \internal
278
- *
279
- * \class dimino_add_cosets_for_rep
280
- * \ingroup CXX11_TensorSymmetry_Module
281
- *
282
- * \brief Recursive template for adding coset spaces
283
- *
284
- * This template multiplies the coset representative with a generator
285
- * from the list of previous generators. If the new element is not in
286
- * the group already, it adds the corresponding coset. Finally it
287
- * proceeds to call itself with the next generator from the list.
288
- *
289
- * \sa enumerate_group_elements, dimino_add_all_coset_spaces
290
- */
291
- template<
292
- template<typename, typename> class Multiply,
293
- template<typename, typename> class Equality,
294
- typename id,
295
- typename sub_group_elements,
296
- typename elements,
297
- typename generators,
298
- typename rep_element,
299
- int sub_group_size
300
- >
301
- struct dimino_add_cosets_for_rep;
302
-
303
- template<
304
- template<typename, typename> class Multiply,
305
- template<typename, typename> class Equality,
306
- typename id,
307
- typename sub_group_elements,
308
- typename elements,
309
- typename g,
310
- typename... gs,
311
- typename rep_element,
312
- int sub_group_size
313
- >
314
- struct dimino_add_cosets_for_rep<Multiply, Equality, id, sub_group_elements, elements, type_list<g, gs...>, rep_element, sub_group_size>
315
- {
316
- typedef typename Multiply<rep_element, g>::type new_coset_rep;
317
- typedef contained_in_list_gf<Equality, new_coset_rep, elements> _cil;
318
- constexpr static bool add_coset = !_cil::value;
319
-
320
- typedef typename dimino_get_coset_elements<
321
- Multiply,
322
- sub_group_elements,
323
- new_coset_rep,
324
- add_coset
325
- >::type coset_elements;
326
-
327
- typedef dimino_add_cosets_for_rep<
328
- Multiply,
329
- Equality,
330
- id,
331
- sub_group_elements,
332
- typename concat<elements, coset_elements>::type,
333
- type_list<gs...>,
334
- rep_element,
335
- sub_group_size
336
- > _helper;
337
-
338
- typedef typename _helper::type type;
339
- constexpr static int global_flags = _cil::global_flags | _helper::global_flags;
340
-
341
- /* Note that we don't have to update global flags here, since
342
- * we will only add these elements if they are not part of
343
- * the group already. But that only happens if the coset rep
344
- * is not already in the group, so the check for the coset rep
345
- * will catch this.
346
- */
347
- };
348
-
349
- template<
350
- template<typename, typename> class Multiply,
351
- template<typename, typename> class Equality,
352
- typename id,
353
- typename sub_group_elements,
354
- typename elements
355
- EIGEN_TPL_PP_SPEC_HACK_DEFC(typename, empty),
356
- typename rep_element,
357
- int sub_group_size
358
- >
359
- struct dimino_add_cosets_for_rep<Multiply, Equality, id, sub_group_elements, elements, type_list<EIGEN_TPL_PP_SPEC_HACK_USE(empty)>, rep_element, sub_group_size>
360
- {
361
- typedef elements type;
362
- constexpr static int global_flags = 0;
363
- };
364
-
365
- /** \internal
366
- *
367
- * \class dimino_add_all_coset_spaces
368
- * \ingroup CXX11_TensorSymmetry_Module
369
- *
370
- * \brief Recursive template for adding all coset spaces for a new generator
371
- *
372
- * This template tries to go through the list of generators (with
373
- * the help of the dimino_add_cosets_for_rep template) as long as
374
- * it still finds elements that are not part of the group and add
375
- * the corresponding cosets.
376
- *
377
- * \sa enumerate_group_elements, dimino_add_cosets_for_rep
378
- */
379
- template<
380
- template<typename, typename> class Multiply,
381
- template<typename, typename> class Equality,
382
- typename id,
383
- typename sub_group_elements,
384
- typename elements,
385
- typename generators,
386
- int sub_group_size,
387
- int rep_pos,
388
- bool stop_condition // = false
389
- >
390
- struct dimino_add_all_coset_spaces
391
- {
392
- typedef typename get<rep_pos, elements>::type rep_element;
393
- typedef dimino_add_cosets_for_rep<
394
- Multiply,
395
- Equality,
396
- id,
397
- sub_group_elements,
398
- elements,
399
- generators,
400
- rep_element,
401
- sub_group_elements::count
402
- > _ac4r;
403
- typedef typename _ac4r::type new_elements;
404
-
405
- constexpr static int new_rep_pos = rep_pos + sub_group_elements::count;
406
- constexpr static bool new_stop_condition = new_rep_pos >= new_elements::count;
407
-
408
- typedef dimino_add_all_coset_spaces<
409
- Multiply,
410
- Equality,
411
- id,
412
- sub_group_elements,
413
- new_elements,
414
- generators,
415
- sub_group_size,
416
- new_rep_pos,
417
- new_stop_condition
418
- > _helper;
419
-
420
- typedef typename _helper::type type;
421
- constexpr static int global_flags = _helper::global_flags | _ac4r::global_flags;
422
- };
423
-
424
- template<
425
- template<typename, typename> class Multiply,
426
- template<typename, typename> class Equality,
427
- typename id,
428
- typename sub_group_elements,
429
- typename elements,
430
- typename generators,
431
- int sub_group_size,
432
- int rep_pos
433
- >
434
- struct dimino_add_all_coset_spaces<Multiply, Equality, id, sub_group_elements, elements, generators, sub_group_size, rep_pos, true>
435
- {
436
- typedef elements type;
437
- constexpr static int global_flags = 0;
438
- };
439
-
440
- /** \internal
441
- *
442
- * \class dimino_add_generator
443
- * \ingroup CXX11_TensorSymmetry_Module
444
- *
445
- * \brief Enlarge the group by adding a new generator.
446
- *
447
- * It accepts a boolean parameter that determines if the generator is redundant,
448
- * i.e. was already seen in the group. In that case, it reduces to a no-op.
449
- *
450
- * \sa enumerate_group_elements, dimino_add_all_coset_spaces
451
- */
452
- template<
453
- template<typename, typename> class Multiply,
454
- template<typename, typename> class Equality,
455
- typename id,
456
- typename elements,
457
- typename generators_done,
458
- typename current_generator,
459
- bool redundant // = false
460
- >
461
- struct dimino_add_generator
462
- {
463
- /* this template is only called if the generator is not redundant
464
- * => all elements of the group multiplied with the new generator
465
- * are going to be new elements of the most trivial coset space
466
- */
467
- typedef typename apply_op_from_right<Multiply, current_generator, elements>::type multiplied_elements;
468
- typedef typename concat<elements, multiplied_elements>::type new_elements;
469
-
470
- constexpr static int rep_pos = elements::count;
471
-
472
- typedef dimino_add_all_coset_spaces<
473
- Multiply,
474
- Equality,
475
- id,
476
- elements, // elements of previous subgroup
477
- new_elements,
478
- typename concat<generators_done, type_list<current_generator>>::type,
479
- elements::count, // size of previous subgroup
480
- rep_pos,
481
- false // don't stop (because rep_pos >= new_elements::count is always false at this point)
482
- > _helper;
483
- typedef typename _helper::type type;
484
- constexpr static int global_flags = _helper::global_flags;
485
- };
486
-
487
- template<
488
- template<typename, typename> class Multiply,
489
- template<typename, typename> class Equality,
490
- typename id,
491
- typename elements,
492
- typename generators_done,
493
- typename current_generator
494
- >
495
- struct dimino_add_generator<Multiply, Equality, id, elements, generators_done, current_generator, true>
496
- {
497
- // redundant case
498
- typedef elements type;
499
- constexpr static int global_flags = 0;
500
- };
501
-
502
- /** \internal
503
- *
504
- * \class dimino_add_remaining_generators
505
- * \ingroup CXX11_TensorSymmetry_Module
506
- *
507
- * \brief Recursive template that adds all remaining generators to a group
508
- *
509
- * Loop through the list of generators that remain and successively
510
- * add them to the group.
511
- *
512
- * \sa enumerate_group_elements, dimino_add_generator
513
- */
514
- template<
515
- template<typename, typename> class Multiply,
516
- template<typename, typename> class Equality,
517
- typename id,
518
- typename generators_done,
519
- typename remaining_generators,
520
- typename elements
521
- >
522
- struct dimino_add_remaining_generators
523
- {
524
- typedef typename get<0, remaining_generators>::type first_generator;
525
- typedef typename skip<1, remaining_generators>::type next_generators;
526
-
527
- typedef contained_in_list_gf<Equality, first_generator, elements> _cil;
528
-
529
- typedef dimino_add_generator<
530
- Multiply,
531
- Equality,
532
- id,
533
- elements,
534
- generators_done,
535
- first_generator,
536
- _cil::value
537
- > _helper;
538
-
539
- typedef typename _helper::type new_elements;
540
-
541
- typedef dimino_add_remaining_generators<
542
- Multiply,
543
- Equality,
544
- id,
545
- typename concat<generators_done, type_list<first_generator>>::type,
546
- next_generators,
547
- new_elements
548
- > _next_iter;
549
-
550
- typedef typename _next_iter::type type;
551
- constexpr static int global_flags =
552
- _cil::global_flags |
553
- _helper::global_flags |
554
- _next_iter::global_flags;
555
- };
556
-
557
- template<
558
- template<typename, typename> class Multiply,
559
- template<typename, typename> class Equality,
560
- typename id,
561
- typename generators_done,
562
- typename elements
563
- >
564
- struct dimino_add_remaining_generators<Multiply, Equality, id, generators_done, type_list<>, elements>
565
- {
566
- typedef elements type;
567
- constexpr static int global_flags = 0;
568
- };
569
-
570
- /** \internal
571
- *
572
- * \class enumerate_group_elements_noid
573
- * \ingroup CXX11_TensorSymmetry_Module
574
- *
575
- * \brief Helper template that implements group element enumeration
576
- *
577
- * This is a helper template that implements the actual enumeration
578
- * of group elements. This has been split so that the list of
579
- * generators can be cleansed of the identity element before
580
- * performing the actual operation.
581
- *
582
- * \sa enumerate_group_elements
583
- */
584
- template<
585
- template<typename, typename> class Multiply,
586
- template<typename, typename> class Equality,
587
- typename id,
588
- typename generators,
589
- int initial_global_flags = 0
590
- >
591
- struct enumerate_group_elements_noid
592
- {
593
- typedef dimino_first_step_elements<Multiply, Equality, id, generators> first_step;
594
- typedef typename first_step::type first_step_elements;
595
-
596
- typedef dimino_add_remaining_generators<
597
- Multiply,
598
- Equality,
599
- id,
600
- typename first_step::generators_done,
601
- typename first_step::next_generators, // remaining_generators
602
- typename first_step::type // first_step elements
603
- > _helper;
604
-
605
- typedef typename _helper::type type;
606
- constexpr static int global_flags =
607
- initial_global_flags |
608
- first_step::global_flags |
609
- _helper::global_flags;
610
- };
611
-
612
- // in case when no generators are specified
613
- template<
614
- template<typename, typename> class Multiply,
615
- template<typename, typename> class Equality,
616
- typename id,
617
- int initial_global_flags
618
- >
619
- struct enumerate_group_elements_noid<Multiply, Equality, id, type_list<>, initial_global_flags>
620
- {
621
- typedef type_list<id> type;
622
- constexpr static int global_flags = initial_global_flags;
623
- };
624
-
625
- /** \internal
626
- *
627
- * \class enumerate_group_elements
628
- * \ingroup CXX11_TensorSymmetry_Module
629
- *
630
- * \brief Enumerate all elements in a finite group
631
- *
632
- * This template enumerates all elements in a finite group. It accepts
633
- * the following template parameters:
634
- *
635
- * \tparam Multiply The multiplication operation that multiplies two group elements
636
- * with each other.
637
- * \tparam Equality The equality check operation that checks if two group elements
638
- * are equal to another.
639
- * \tparam id The identity element
640
- * \tparam _generators A list of (possibly redundant) generators of the group
641
- */
642
- template<
643
- template<typename, typename> class Multiply,
644
- template<typename, typename> class Equality,
645
- typename id,
646
- typename _generators
647
- >
648
- struct enumerate_group_elements
649
- : public enumerate_group_elements_noid<
650
- Multiply,
651
- Equality,
652
- id,
653
- typename strip_identities<Equality, id, _generators>::type,
654
- strip_identities<Equality, id, _generators>::global_flags
655
- >
656
- {
657
- };
658
-
659
- } // end namespace group_theory
660
-
661
- } // end namespace internal
662
-
663
- } // end namespace Eigen
664
-
665
- #endif // EIGEN_CXX11_TENSORSYMMETRY_TEMPLATEGROUPTHEORY_H
666
-
667
- /*
668
- * kate: space-indent on; indent-width 2; mixedindent off; indent-mode cstyle;
669
- */