sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.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 +157 -157
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/hierarchical_clustering.py +304 -8
  7. sequenzo/define_sequence_data.py +44 -3
  8. sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  14. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  15. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  60. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  70. sequenzo/multidomain/cat.py +0 -53
  71. sequenzo/multidomain/idcd.py +0 -1
  72. sequenzo/openmp_setup.py +233 -0
  73. sequenzo/sequence_characteristics/__init__.py +4 -0
  74. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  75. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  76. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  77. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  78. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  79. sequenzo/sequence_characteristics/turbulence.py +47 -67
  80. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  81. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  82. sequenzo/visualization/plot_sequence_index.py +58 -35
  83. sequenzo/visualization/plot_state_distribution.py +57 -36
  84. sequenzo/visualization/plot_transition_matrix.py +21 -22
  85. sequenzo/with_event_history_analysis/__init__.py +35 -0
  86. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  87. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  88. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  89. sequenzo-0.1.19.dist-info/RECORD +215 -0
  90. sequenzo/dissimilarity_measures/setup.py +0 -35
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
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  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  420. sequenzo-0.1.17.dist-info/RECORD +0 -537
  421. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  422. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  423. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,338 +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_SYMMETRY_H
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- #define EIGEN_CXX11_TENSORSYMMETRY_SYMMETRY_H
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-
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- namespace Eigen {
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-
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- enum {
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- NegationFlag = 0x01,
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- ConjugationFlag = 0x02
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- };
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-
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- enum {
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- GlobalRealFlag = 0x01,
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- GlobalImagFlag = 0x02,
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- GlobalZeroFlag = 0x03
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- };
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-
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- namespace internal {
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-
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- template<std::size_t NumIndices, typename... Sym> struct tensor_symmetry_pre_analysis;
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- template<std::size_t NumIndices, typename... Sym> struct tensor_static_symgroup;
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- template<bool instantiate, std::size_t NumIndices, typename... Sym> struct tensor_static_symgroup_if;
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- template<typename Tensor_> struct tensor_symmetry_calculate_flags;
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- template<typename Tensor_> struct tensor_symmetry_assign_value;
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- template<typename... Sym> struct tensor_symmetry_num_indices;
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-
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- } // end namespace internal
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-
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- template<int One_, int Two_>
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- struct Symmetry
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- {
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- static_assert(One_ != Two_, "Symmetries must cover distinct indices.");
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- constexpr static int One = One_;
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- constexpr static int Two = Two_;
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- constexpr static int Flags = 0;
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- };
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-
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- template<int One_, int Two_>
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- struct AntiSymmetry
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- {
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- static_assert(One_ != Two_, "Symmetries must cover distinct indices.");
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- constexpr static int One = One_;
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- constexpr static int Two = Two_;
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- constexpr static int Flags = NegationFlag;
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- };
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-
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- template<int One_, int Two_>
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- struct Hermiticity
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- {
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- static_assert(One_ != Two_, "Symmetries must cover distinct indices.");
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- constexpr static int One = One_;
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- constexpr static int Two = Two_;
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- constexpr static int Flags = ConjugationFlag;
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- };
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-
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- template<int One_, int Two_>
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- struct AntiHermiticity
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- {
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- static_assert(One_ != Two_, "Symmetries must cover distinct indices.");
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- constexpr static int One = One_;
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- constexpr static int Two = Two_;
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- constexpr static int Flags = ConjugationFlag | NegationFlag;
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- };
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-
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- /** \class DynamicSGroup
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- * \ingroup TensorSymmetry_Module
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- *
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- * \brief Dynamic symmetry group
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- *
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- * The %DynamicSGroup class represents a symmetry group that need not be known at
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- * compile time. It is useful if one wants to support arbitrary run-time defineable
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- * symmetries for tensors, but it is also instantiated if a symmetry group is defined
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- * at compile time that would be either too large for the compiler to reasonably
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- * generate (using templates to calculate this at compile time is very inefficient)
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- * or that the compiler could generate the group but that it wouldn't make sense to
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- * unroll the loop for setting coefficients anymore.
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- */
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- class DynamicSGroup;
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-
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- /** \internal
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- *
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- * \class DynamicSGroupFromTemplateArgs
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- * \ingroup TensorSymmetry_Module
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- *
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- * \brief Dynamic symmetry group, initialized from template arguments
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- *
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- * This class is a child class of DynamicSGroup. It uses the template arguments
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- * specified to initialize itself.
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- */
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- template<typename... Gen>
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- class DynamicSGroupFromTemplateArgs;
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-
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- /** \class StaticSGroup
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- * \ingroup TensorSymmetry_Module
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- *
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- * \brief Static symmetry group
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- *
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- * This class represents a symmetry group that is known and resolved completely
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- * at compile time. Ideally, no run-time penalty is incurred compared to the
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- * manual unrolling of the symmetry.
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- *
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- * <b><i>CAUTION:</i></b>
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- *
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- * Do not use this class directly for large symmetry groups. The compiler
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- * may run into a limit, or segfault or in the very least will take a very,
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- * very, very long time to compile the code. Use the SGroup class instead
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- * if you want a static group. That class contains logic that will
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- * automatically select the DynamicSGroup class instead if the symmetry
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- * group becomes too large. (In that case, unrolling may not even be
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- * beneficial.)
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- */
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- template<typename... Gen>
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- class StaticSGroup;
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-
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- /** \class SGroup
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- * \ingroup TensorSymmetry_Module
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- *
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- * \brief Symmetry group, initialized from template arguments
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- *
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- * This class represents a symmetry group whose generators are already
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- * known at compile time. It may or may not be resolved at compile time,
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- * depending on the estimated size of the group.
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- *
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- * \sa StaticSGroup
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- * \sa DynamicSGroup
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- */
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- template<typename... Gen>
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- class SGroup : public internal::tensor_symmetry_pre_analysis<internal::tensor_symmetry_num_indices<Gen...>::value, Gen...>::root_type
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- {
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- public:
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- constexpr static std::size_t NumIndices = internal::tensor_symmetry_num_indices<Gen...>::value;
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- typedef typename internal::tensor_symmetry_pre_analysis<NumIndices, Gen...>::root_type Base;
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-
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- // make standard constructors + assignment operators public
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- inline SGroup() : Base() { }
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- inline SGroup(const SGroup<Gen...>& other) : Base(other) { }
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- inline SGroup(SGroup<Gen...>&& other) : Base(other) { }
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- inline SGroup<Gen...>& operator=(const SGroup<Gen...>& other) { Base::operator=(other); return *this; }
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- inline SGroup<Gen...>& operator=(SGroup<Gen...>&& other) { Base::operator=(other); return *this; }
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-
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- // all else is defined in the base class
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- };
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-
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- namespace internal {
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-
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- template<typename... Sym> struct tensor_symmetry_num_indices
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- {
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- constexpr static std::size_t value = 1;
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- };
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-
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- template<int One_, int Two_, typename... Sym> struct tensor_symmetry_num_indices<Symmetry<One_, Two_>, Sym...>
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- {
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- private:
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- constexpr static std::size_t One = static_cast<std::size_t>(One_);
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- constexpr static std::size_t Two = static_cast<std::size_t>(Two_);
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- constexpr static std::size_t Three = tensor_symmetry_num_indices<Sym...>::value;
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-
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- // don't use std::max, since it's not constexpr until C++14...
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- constexpr static std::size_t maxOneTwoPlusOne = ((One > Two) ? One : Two) + 1;
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- public:
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- constexpr static std::size_t value = (maxOneTwoPlusOne > Three) ? maxOneTwoPlusOne : Three;
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- };
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-
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- template<int One_, int Two_, typename... Sym> struct tensor_symmetry_num_indices<AntiSymmetry<One_, Two_>, Sym...>
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- : public tensor_symmetry_num_indices<Symmetry<One_, Two_>, Sym...> {};
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- template<int One_, int Two_, typename... Sym> struct tensor_symmetry_num_indices<Hermiticity<One_, Two_>, Sym...>
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- : public tensor_symmetry_num_indices<Symmetry<One_, Two_>, Sym...> {};
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- template<int One_, int Two_, typename... Sym> struct tensor_symmetry_num_indices<AntiHermiticity<One_, Two_>, Sym...>
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- : public tensor_symmetry_num_indices<Symmetry<One_, Two_>, Sym...> {};
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-
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- /** \internal
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- *
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- * \class tensor_symmetry_pre_analysis
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- * \ingroup TensorSymmetry_Module
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- *
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- * \brief Pre-select whether to use a static or dynamic symmetry group
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- *
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- * When a symmetry group could in principle be determined at compile time,
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- * this template implements the logic whether to actually do that or whether
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- * to rather defer that to runtime.
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- *
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- * The logic is as follows:
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- * <dl>
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- * <dt><b>No generators (trivial symmetry):</b></dt>
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- * <dd>Use a trivial static group. Ideally, this has no performance impact
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- * compared to not using symmetry at all. In practice, this might not
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- * be the case.</dd>
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- * <dt><b>More than 4 generators:</b></dt>
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- * <dd>Calculate the group at run time, it is likely far too large for the
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- * compiler to be able to properly generate it in a realistic time.</dd>
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- * <dt><b>Up to and including 4 generators:</b></dt>
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- * <dd>Actually enumerate all group elements, but then check how many there
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- * are. If there are more than 16, it is unlikely that unrolling the
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- * loop (as is done in the static compile-time case) is sensible, so
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- * use a dynamic group instead. If there are at most 16 elements, actually
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- * use that static group. Note that the largest group with 4 generators
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- * still compiles with reasonable resources.</dd>
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- * </dl>
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- *
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- * Note: Example compile time performance with g++-4.6 on an Intenl Core i5-3470
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- * with 16 GiB RAM (all generators non-redundant and the subgroups don't
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- * factorize):
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- *
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- * # Generators -O0 -ggdb -O2
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- * -------------------------------------------------------------------
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- * 1 0.5 s / 250 MiB 0.45s / 230 MiB
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- * 2 0.5 s / 260 MiB 0.5 s / 250 MiB
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- * 3 0.65s / 310 MiB 0.62s / 310 MiB
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- * 4 2.2 s / 860 MiB 1.7 s / 770 MiB
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- * 5 130 s / 13000 MiB 120 s / 11000 MiB
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- *
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- * It is clear that everything is still very efficient up to 4 generators, then
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- * the memory and CPU requirements become unreasonable. Thus we only instantiate
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- * the template group theory logic if the number of generators supplied is 4 or
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- * lower, otherwise this will be forced to be done during runtime, where the
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- * algorithm is reasonably fast.
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- */
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- template<std::size_t NumIndices>
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- struct tensor_symmetry_pre_analysis<NumIndices>
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- {
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- typedef StaticSGroup<> root_type;
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- };
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-
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- template<std::size_t NumIndices, typename Gen_, typename... Gens_>
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- struct tensor_symmetry_pre_analysis<NumIndices, Gen_, Gens_...>
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- {
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- constexpr static std::size_t max_static_generators = 4;
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- constexpr static std::size_t max_static_elements = 16;
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- typedef tensor_static_symgroup_if<(sizeof...(Gens_) + 1 <= max_static_generators), NumIndices, Gen_, Gens_...> helper;
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- constexpr static std::size_t possible_size = helper::size;
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-
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- typedef typename conditional<
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- possible_size == 0 || possible_size >= max_static_elements,
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- DynamicSGroupFromTemplateArgs<Gen_, Gens_...>,
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- typename helper::type
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- >::type root_type;
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- };
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-
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- template<bool instantiate, std::size_t NumIndices, typename... Gens>
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- struct tensor_static_symgroup_if
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- {
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- constexpr static std::size_t size = 0;
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- typedef void type;
252
- };
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-
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- template<std::size_t NumIndices, typename... Gens>
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- struct tensor_static_symgroup_if<true, NumIndices, Gens...> : tensor_static_symgroup<NumIndices, Gens...> {};
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-
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- template<typename Tensor_>
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- struct tensor_symmetry_assign_value
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- {
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- typedef typename Tensor_::Index Index;
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- typedef typename Tensor_::Scalar Scalar;
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- constexpr static std::size_t NumIndices = Tensor_::NumIndices;
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-
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- static inline int run(const std::array<Index, NumIndices>& transformed_indices, int transformation_flags, int dummy, Tensor_& tensor, const Scalar& value_)
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- {
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- Scalar value(value_);
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- if (transformation_flags & ConjugationFlag)
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- value = numext::conj(value);
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- if (transformation_flags & NegationFlag)
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- value = -value;
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- tensor.coeffRef(transformed_indices) = value;
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- return dummy;
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- }
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- };
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-
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- template<typename Tensor_>
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- struct tensor_symmetry_calculate_flags
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- {
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- typedef typename Tensor_::Index Index;
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- constexpr static std::size_t NumIndices = Tensor_::NumIndices;
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-
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- static inline int run(const std::array<Index, NumIndices>& transformed_indices, int transform_flags, int current_flags, const std::array<Index, NumIndices>& orig_indices)
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- {
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- if (transformed_indices == orig_indices) {
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- if (transform_flags & (ConjugationFlag | NegationFlag))
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- return current_flags | GlobalImagFlag; // anti-hermitian diagonal
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- else if (transform_flags & ConjugationFlag)
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- return current_flags | GlobalRealFlag; // hermitian diagonal
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- else if (transform_flags & NegationFlag)
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- return current_flags | GlobalZeroFlag; // anti-symmetric diagonal
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- }
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- return current_flags;
293
- }
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- };
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-
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- template<typename Tensor_, typename Symmetry_, int Flags = 0>
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- class tensor_symmetry_value_setter
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- {
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- public:
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- typedef typename Tensor_::Index Index;
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- typedef typename Tensor_::Scalar Scalar;
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- constexpr static std::size_t NumIndices = Tensor_::NumIndices;
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-
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- inline tensor_symmetry_value_setter(Tensor_& tensor, Symmetry_ const& symmetry, std::array<Index, NumIndices> const& indices)
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- : m_tensor(tensor), m_symmetry(symmetry), m_indices(indices) { }
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-
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- inline tensor_symmetry_value_setter<Tensor_, Symmetry_, Flags>& operator=(Scalar const& value)
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- {
309
- doAssign(value);
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- return *this;
311
- }
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- private:
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- Tensor_& m_tensor;
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- Symmetry_ m_symmetry;
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- std::array<Index, NumIndices> m_indices;
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-
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- inline void doAssign(Scalar const& value)
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- {
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- #ifdef EIGEN_TENSOR_SYMMETRY_CHECK_VALUES
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- int value_flags = m_symmetry.template apply<internal::tensor_symmetry_calculate_flags<Tensor_>, int>(m_indices, m_symmetry.globalFlags(), m_indices);
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- if (value_flags & GlobalRealFlag)
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- eigen_assert(numext::imag(value) == 0);
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- if (value_flags & GlobalImagFlag)
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- eigen_assert(numext::real(value) == 0);
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- #endif
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- m_symmetry.template apply<internal::tensor_symmetry_assign_value<Tensor_>, int>(m_indices, 0, m_tensor, value);
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- }
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- };
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-
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- } // end namespace internal
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-
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- } // end namespace Eigen
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-
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- #endif // EIGEN_CXX11_TENSORSYMMETRY_SYMMETRY_H
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-
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- /*
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- * kate: space-indent on; indent-width 2; mixedindent off; indent-mode cstyle;
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- */