├── .github └── workflows │ ├── test.yml │ └── wheels.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── pyproject.toml ├── scripts ├── setup.sh └── test.sh ├── setup.py ├── src ├── CHECKLIST_B4_RELEASE.txt ├── Docs │ ├── Visualizing_pore_size_distribution_files_in_VisIt.ppt │ └── Zeo_tutorial_word.ppt ├── Eigen │ ├── Array │ ├── CMakeLists.txt │ ├── Cholesky │ ├── CholmodSupport │ ├── Core │ ├── Dense │ ├── Eigen │ ├── Eigen2Support │ ├── Eigenvalues │ ├── Geometry │ ├── Householder │ ├── IterativeLinearSolvers │ ├── Jacobi │ ├── LU │ ├── LeastSquares │ ├── MetisSupport │ ├── OrderingMethods │ ├── PaStiXSupport │ ├── PardisoSupport │ ├── QR │ ├── QtAlignedMalloc │ ├── SPQRSupport │ ├── SVD │ ├── Sparse │ ├── SparseCholesky │ ├── SparseCore │ ├── SparseLU │ ├── SparseQR │ ├── StdDeque │ ├── StdList │ ├── StdVector │ ├── SuperLUSupport │ ├── UmfPackSupport │ └── src │ │ ├── CMakeLists.txt │ │ ├── Cholesky │ │ ├── CMakeLists.txt │ │ ├── LDLT.h │ │ ├── LLT.h │ │ └── LLT_MKL.h │ │ ├── CholmodSupport │ │ ├── CMakeLists.txt │ │ └── CholmodSupport.h │ │ ├── Core │ │ ├── Array.h │ │ ├── ArrayBase.h │ │ ├── ArrayWrapper.h │ │ ├── Assign.h │ │ ├── Assign_MKL.h │ │ ├── BandMatrix.h │ │ ├── Block.h │ │ ├── BooleanRedux.h │ │ ├── CMakeLists.txt │ │ ├── CommaInitializer.h │ │ ├── CoreIterators.h │ │ ├── CwiseBinaryOp.h │ │ ├── CwiseNullaryOp.h │ │ ├── CwiseUnaryOp.h │ │ ├── CwiseUnaryView.h │ │ ├── DenseBase.h │ │ ├── DenseCoeffsBase.h │ │ ├── DenseStorage.h │ │ ├── Diagonal.h │ │ ├── DiagonalMatrix.h │ │ ├── DiagonalProduct.h │ │ ├── Dot.h │ │ ├── EigenBase.h │ │ ├── Flagged.h │ │ ├── ForceAlignedAccess.h │ │ ├── Functors.h │ │ ├── Fuzzy.h │ │ ├── GeneralProduct.h │ │ ├── GenericPacketMath.h │ │ ├── GlobalFunctions.h │ │ ├── IO.h │ │ ├── Map.h │ │ ├── MapBase.h │ │ ├── MathFunctions.h │ │ ├── Matrix.h │ │ ├── MatrixBase.h │ │ ├── NestByValue.h │ │ ├── NoAlias.h │ │ ├── NumTraits.h │ │ ├── PermutationMatrix.h │ │ ├── PlainObjectBase.h │ │ ├── ProductBase.h │ │ ├── Random.h │ │ ├── Redux.h │ │ ├── Ref.h │ │ ├── Replicate.h │ │ ├── ReturnByValue.h │ │ ├── Reverse.h │ │ ├── Select.h │ │ ├── SelfAdjointView.h │ │ ├── SelfCwiseBinaryOp.h │ │ ├── SolveTriangular.h │ │ ├── StableNorm.h │ │ ├── Stride.h │ │ ├── Swap.h │ │ ├── Transpose.h │ │ ├── Transpositions.h │ │ ├── TriangularMatrix.h │ │ ├── VectorBlock.h │ │ ├── VectorwiseOp.h │ │ ├── Visitor.h │ │ ├── arch │ │ │ ├── AltiVec │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── Complex.h │ │ │ │ └── PacketMath.h │ │ │ ├── CMakeLists.txt │ │ │ ├── Default │ │ │ │ ├── CMakeLists.txt │ │ │ │ └── Settings.h │ │ │ ├── NEON │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── Complex.h │ │ │ │ └── PacketMath.h │ │ │ └── SSE │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ ├── products │ │ │ ├── CMakeLists.txt │ │ │ ├── CoeffBasedProduct.h │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ ├── GeneralMatrixMatrix.h │ │ │ ├── GeneralMatrixMatrixTriangular.h │ │ │ ├── GeneralMatrixMatrixTriangular_MKL.h │ │ │ ├── GeneralMatrixMatrix_MKL.h │ │ │ ├── GeneralMatrixVector.h │ │ │ ├── GeneralMatrixVector_MKL.h │ │ │ ├── Parallelizer.h │ │ │ ├── SelfadjointMatrixMatrix.h │ │ │ ├── SelfadjointMatrixMatrix_MKL.h │ │ │ ├── SelfadjointMatrixVector.h │ │ │ ├── SelfadjointMatrixVector_MKL.h │ │ │ ├── SelfadjointProduct.h │ │ │ ├── SelfadjointRank2Update.h │ │ │ ├── TriangularMatrixMatrix.h │ │ │ ├── TriangularMatrixMatrix_MKL.h │ │ │ ├── TriangularMatrixVector.h │ │ │ ├── TriangularMatrixVector_MKL.h │ │ │ ├── TriangularSolverMatrix.h │ │ │ ├── TriangularSolverMatrix_MKL.h │ │ │ └── TriangularSolverVector.h │ │ └── util │ │ │ ├── BlasUtil.h │ │ │ ├── CMakeLists.txt │ │ │ ├── Constants.h │ │ │ ├── DisableStupidWarnings.h │ │ │ ├── ForwardDeclarations.h │ │ │ ├── MKL_support.h │ │ │ ├── Macros.h │ │ │ ├── Memory.h │ │ │ ├── Meta.h │ │ │ ├── NonMPL2.h │ │ │ ├── ReenableStupidWarnings.h │ │ │ ├── StaticAssert.h │ │ │ └── XprHelper.h │ │ ├── Eigen2Support │ │ ├── Block.h │ │ ├── CMakeLists.txt │ │ ├── Cwise.h │ │ ├── CwiseOperators.h │ │ ├── Geometry │ │ │ ├── AlignedBox.h │ │ │ ├── All.h │ │ │ ├── AngleAxis.h │ │ │ ├── CMakeLists.txt │ │ │ ├── Hyperplane.h │ │ │ ├── ParametrizedLine.h │ │ │ ├── Quaternion.h │ │ │ ├── Rotation2D.h │ │ │ ├── RotationBase.h │ │ │ ├── Scaling.h │ │ │ ├── Transform.h │ │ │ └── Translation.h │ │ ├── LU.h │ │ ├── Lazy.h │ │ ├── LeastSquares.h │ │ ├── Macros.h │ │ ├── MathFunctions.h │ │ ├── Memory.h │ │ ├── Meta.h │ │ ├── Minor.h │ │ ├── QR.h │ │ ├── SVD.h │ │ ├── TriangularSolver.h │ │ └── VectorBlock.h │ │ ├── Eigenvalues │ │ ├── CMakeLists.txt │ │ ├── ComplexEigenSolver.h │ │ ├── ComplexSchur.h │ │ ├── ComplexSchur_MKL.h │ │ ├── EigenSolver.h │ │ ├── GeneralizedEigenSolver.h │ │ ├── GeneralizedSelfAdjointEigenSolver.h │ │ ├── HessenbergDecomposition.h │ │ ├── MatrixBaseEigenvalues.h │ │ ├── RealQZ.h │ │ ├── RealSchur.h │ │ ├── RealSchur_MKL.h │ │ ├── SelfAdjointEigenSolver.h │ │ ├── SelfAdjointEigenSolver_MKL.h │ │ └── Tridiagonalization.h │ │ ├── Geometry │ │ ├── AlignedBox.h │ │ ├── AngleAxis.h │ │ ├── CMakeLists.txt │ │ ├── EulerAngles.h │ │ ├── Homogeneous.h │ │ ├── Hyperplane.h │ │ ├── OrthoMethods.h │ │ ├── ParametrizedLine.h │ │ ├── Quaternion.h │ │ ├── Rotation2D.h │ │ ├── RotationBase.h │ │ ├── Scaling.h │ │ ├── Transform.h │ │ ├── Translation.h │ │ ├── Umeyama.h │ │ └── arch │ │ │ ├── CMakeLists.txt │ │ │ └── Geometry_SSE.h │ │ ├── Householder │ │ ├── BlockHouseholder.h │ │ ├── CMakeLists.txt │ │ ├── Householder.h │ │ └── HouseholderSequence.h │ │ ├── IterativeLinearSolvers │ │ ├── BasicPreconditioners.h │ │ ├── BiCGSTAB.h │ │ ├── CMakeLists.txt │ │ ├── ConjugateGradient.h │ │ ├── IncompleteLUT.h │ │ └── IterativeSolverBase.h │ │ ├── Jacobi │ │ ├── CMakeLists.txt │ │ └── Jacobi.h │ │ ├── LU │ │ ├── CMakeLists.txt │ │ ├── Determinant.h │ │ ├── FullPivLU.h │ │ ├── Inverse.h │ │ ├── PartialPivLU.h │ │ ├── PartialPivLU_MKL.h │ │ └── arch │ │ │ ├── CMakeLists.txt │ │ │ └── Inverse_SSE.h │ │ ├── MetisSupport │ │ ├── CMakeLists.txt │ │ └── MetisSupport.h │ │ ├── OrderingMethods │ │ ├── Amd.h │ │ ├── CMakeLists.txt │ │ ├── Eigen_Colamd.h │ │ └── Ordering.h │ │ ├── PaStiXSupport │ │ ├── CMakeLists.txt │ │ └── PaStiXSupport.h │ │ ├── PardisoSupport │ │ ├── CMakeLists.txt │ │ └── PardisoSupport.h │ │ ├── QR │ │ ├── CMakeLists.txt │ │ ├── ColPivHouseholderQR.h │ │ ├── ColPivHouseholderQR_MKL.h │ │ ├── FullPivHouseholderQR.h │ │ ├── HouseholderQR.h │ │ └── HouseholderQR_MKL.h │ │ ├── SPQRSupport │ │ ├── CMakeLists.txt │ │ └── SuiteSparseQRSupport.h │ │ ├── SVD │ │ ├── CMakeLists.txt │ │ ├── JacobiSVD.h │ │ ├── JacobiSVD_MKL.h │ │ └── UpperBidiagonalization.h │ │ ├── SparseCholesky │ │ ├── CMakeLists.txt │ │ ├── SimplicialCholesky.h │ │ └── SimplicialCholesky_impl.h │ │ ├── SparseCore │ │ ├── AmbiVector.h │ │ ├── CMakeLists.txt │ │ ├── CompressedStorage.h │ │ ├── ConservativeSparseSparseProduct.h │ │ ├── MappedSparseMatrix.h │ │ ├── SparseBlock.h │ │ ├── SparseColEtree.h │ │ ├── SparseCwiseBinaryOp.h │ │ ├── SparseCwiseUnaryOp.h │ │ ├── SparseDenseProduct.h │ │ ├── SparseDiagonalProduct.h │ │ ├── SparseDot.h │ │ ├── SparseFuzzy.h │ │ ├── SparseMatrix.h │ │ ├── SparseMatrixBase.h │ │ ├── SparsePermutation.h │ │ ├── SparseProduct.h │ │ ├── SparseRedux.h │ │ ├── SparseSelfAdjointView.h │ │ ├── SparseSparseProductWithPruning.h │ │ ├── SparseTranspose.h │ │ ├── SparseTriangularView.h │ │ ├── SparseUtil.h │ │ ├── SparseVector.h │ │ ├── SparseView.h │ │ └── TriangularSolver.h │ │ ├── SparseLU │ │ ├── CMakeLists.txt │ │ ├── SparseLU.h │ │ ├── SparseLUImpl.h │ │ ├── SparseLU_Memory.h │ │ ├── SparseLU_Structs.h │ │ ├── SparseLU_SupernodalMatrix.h │ │ ├── SparseLU_Utils.h │ │ ├── SparseLU_column_bmod.h │ │ ├── SparseLU_column_dfs.h │ │ ├── SparseLU_copy_to_ucol.h │ │ ├── SparseLU_gemm_kernel.h │ │ ├── SparseLU_heap_relax_snode.h │ │ ├── SparseLU_kernel_bmod.h │ │ ├── SparseLU_panel_bmod.h │ │ ├── SparseLU_panel_dfs.h │ │ ├── SparseLU_pivotL.h │ │ ├── SparseLU_pruneL.h │ │ └── SparseLU_relax_snode.h │ │ ├── SparseQR │ │ ├── CMakeLists.txt │ │ └── SparseQR.h │ │ ├── StlSupport │ │ ├── CMakeLists.txt │ │ ├── StdDeque.h │ │ ├── StdList.h │ │ ├── StdVector.h │ │ └── details.h │ │ ├── SuperLUSupport │ │ ├── CMakeLists.txt │ │ └── SuperLUSupport.h │ │ ├── UmfPackSupport │ │ ├── CMakeLists.txt │ │ └── UmfPackSupport.h │ │ ├── misc │ │ ├── CMakeLists.txt │ │ ├── Image.h │ │ ├── Kernel.h │ │ ├── Solve.h │ │ ├── SparseSolve.h │ │ └── blas.h │ │ └── plugins │ │ ├── ArrayCwiseBinaryOps.h │ │ ├── ArrayCwiseUnaryOps.h │ │ ├── BlockMethods.h │ │ ├── CMakeLists.txt │ │ ├── CommonCwiseBinaryOps.h │ │ ├── CommonCwiseUnaryOps.h │ │ ├── MatrixCwiseBinaryOps.h │ │ └── MatrixCwiseUnaryOps.h ├── HELP.txt ├── LICENSE ├── Makefile ├── Makefile.dep ├── NEWS ├── OMS.cc ├── OMS.h ├── OVERVIEW.txt ├── R │ ├── R_PSD_shell_plot.pdf │ ├── noninteractive_graph_functions.R │ ├── noninteractive_graph_shell.R │ └── parameters.R ├── README ├── UNITTEST │ ├── COMMANDS.txt │ ├── EDI.chan │ ├── EDI.cssr │ ├── EDI.psd_histo │ ├── EDI.res │ ├── EDI.sa │ ├── EDI.vol │ ├── history_1000.cssr │ ├── history_1000.res │ ├── history_1000.sa │ └── history_1000.vol ├── area_and_volume.cc ├── area_and_volume.h ├── arguments.cc ├── arguments.h ├── builder_examples │ ├── building_blocks │ │ ├── C.xyz │ │ ├── Cu2.xyz │ │ ├── Zn4O.xyz │ │ ├── linear.xyz │ │ ├── linear_nonsym_without_sites.xyz │ │ ├── molecule3.xyz │ │ ├── moleculeC.xyz │ │ ├── molecule_without_sites.xyz │ │ ├── pyr_linker_without_sites.xyz │ │ ├── qom_linker_without_sites.xyz │ │ ├── tetrahedral.xyz │ │ └── trigonal.xyz │ └── nets │ │ ├── dia-c5.cgd │ │ ├── dia.cgd │ │ ├── hcb.cgd │ │ ├── ntt_simple.cgd │ │ ├── pts.cgd │ │ ├── pyr.cgd │ │ ├── qom.cgd │ │ ├── rhr.cgd │ │ └── tbo.cgd ├── channel.cc ├── channel.h ├── cluster.cc ├── cluster.h ├── config.mk ├── cycle.cc ├── cycle.h ├── default_bin_bounds.tar ├── diversity_selection_holos.c ├── documentation │ ├── README │ ├── README_rich_test │ ├── example.mass │ └── example.rad ├── feature.cc ├── feature.h ├── framework_builder.cc ├── general.h ├── geometry.cc ├── geometry.h ├── get_holo_similarity.c ├── gpu_energy.cc ├── gpu_energy.h ├── graphstorage.cc ├── graphstorage.h ├── grid.cc ├── grid.h ├── heap.h ├── holo_similarity.h ├── holograms.cc ├── holograms.h ├── instructions.cc ├── instructions.h ├── main.cc ├── material.cc ├── material.h ├── mindist.cc ├── mindist.h ├── molecule_to_abstract.cc ├── net.cc ├── net.h ├── nets │ ├── dia-c5.cgd │ ├── dia.cgd │ ├── hcb.cgd │ ├── ntt_simple.cgd │ ├── pts.cgd │ ├── pyr.cgd │ ├── qom.cgd │ ├── rhr.cgd │ └── tbo.cgd ├── network.cc ├── network.h ├── networkaccessibility.cc ├── networkaccessibility.h ├── networkanalysis.cc ├── networkanalysis.h ├── networkinfo.cc ├── networkinfo.h ├── networkio.cc ├── networkio.h ├── networkstorage.cc ├── networkstorage.h ├── octree.cpp ├── octree.hpp ├── poreinfo.cc ├── poreinfo.h ├── psd.cc ├── psd.h ├── pyzeo │ ├── __init__.py │ ├── area_volume │ │ └── __init__.py │ ├── cluster │ │ └── __init__.py │ ├── cycle │ │ └── __init__.py │ ├── extension.cpp │ ├── extension.pxd │ ├── extension.pyx │ ├── high_accuracy │ │ └── __init__.py │ ├── netstorage │ │ └── __init__.py │ └── psd │ │ └── __init__.py ├── ray.cc ├── ray.h ├── rmsd.cc ├── rmsd.h ├── segment.cc ├── segment.h ├── sphere_approx.cc ├── sphere_approx.h ├── string_additions.cc ├── string_additions.h ├── symbcalc.cc ├── symbcalc.h ├── symmetry.cc ├── symmetry.h ├── tdpldhistogram.cc ├── v_network.cc ├── v_network.h ├── voro++ │ ├── LICENSE │ ├── Makefile │ ├── NEWS │ ├── README │ ├── config.mk │ ├── examples │ │ ├── Makefile │ │ ├── README │ │ ├── basic │ │ │ ├── Makefile │ │ │ ├── README │ │ │ ├── convex_test.cc │ │ │ ├── import.cc │ │ │ ├── import.pov │ │ │ ├── pack_ten_cube │ │ │ ├── platonic.cc │ │ │ ├── random_points.cc │ │ │ └── single_cell.cc │ │ ├── custom │ │ │ ├── Makefile │ │ │ ├── README │ │ │ ├── cell_statistics.cc │ │ │ ├── custom_output.cc │ │ │ ├── custom_output.pl │ │ │ ├── custom_output.pov │ │ │ ├── pack_six_cube │ │ │ ├── pack_six_cube.pov │ │ │ ├── pack_six_cube_poly │ │ │ ├── pack_six_cube_poly.pov │ │ │ └── radical.cc │ │ ├── degenerate │ │ │ ├── Makefile │ │ │ ├── README │ │ │ ├── degenerate.cc │ │ │ ├── degenerate.pov │ │ │ ├── degenerate2.cc │ │ │ └── degenerate2.pov │ │ ├── extra │ │ │ ├── Makefile │ │ │ ├── README │ │ │ ├── box_cut.cc │ │ │ ├── cut_region.cc │ │ │ ├── irregular.cc │ │ │ ├── irregular.pov │ │ │ ├── l_shape.cc │ │ │ ├── pack_irregular │ │ │ ├── superellipsoid.cc │ │ │ └── superellipsoid.pov │ │ ├── interface │ │ │ ├── Makefile │ │ │ ├── README │ │ │ ├── find_voro_cell.cc │ │ │ ├── loops.cc │ │ │ ├── loops.pov │ │ │ ├── odd_even.cc │ │ │ ├── odd_even.pov │ │ │ ├── pack_six_cube │ │ │ ├── polygons.cc │ │ │ ├── polygons4.pov │ │ │ ├── polygons5.pov │ │ │ └── polygons6.pov │ │ ├── no_release │ │ │ ├── Makefile │ │ │ ├── cylinder_inv.cc │ │ │ ├── cylinder_inv.pov │ │ │ ├── ellipsoid.cc │ │ │ ├── finite_sys.cc │ │ │ ├── finite_sys.pov │ │ │ ├── ghost_test.cc │ │ │ ├── import_freeman.cc │ │ │ ├── import_nguyen.cc │ │ │ ├── import_rahman.cc │ │ │ ├── liq-900K.dat │ │ │ ├── lloyd_box.cc │ │ │ ├── minkowski.cc │ │ │ ├── neigh_test.cc │ │ │ ├── pack_semicircle │ │ │ ├── period.cc │ │ │ ├── polycry.gnuplot │ │ │ ├── polycrystal_rahman.cc │ │ │ ├── r_pts_interface.cc │ │ │ ├── rad_test.cc │ │ │ ├── rad_test.pl │ │ │ ├── rad_test.pov │ │ │ ├── random_points_10.cc │ │ │ ├── random_points_200.cc │ │ │ ├── single_cell_2d.cc │ │ │ ├── sphere.cc │ │ │ ├── sphere_mesh.cc │ │ │ ├── split_cell.cc │ │ │ ├── tri_mesh.cc │ │ │ └── voro_lf.cc │ │ ├── timing │ │ │ ├── README │ │ │ ├── timing_test.cc │ │ │ └── timing_test.pl │ │ └── walls │ │ │ ├── Makefile │ │ │ ├── README │ │ │ ├── cylinder.cc │ │ │ ├── cylinder.pov │ │ │ ├── frustum.cc │ │ │ ├── frustum.pov │ │ │ ├── pack_cylinder │ │ │ ├── pack_torus │ │ │ ├── tetrahedron.cc │ │ │ ├── tetrahedron.pov │ │ │ ├── torus.cc │ │ │ └── torus.pov │ ├── man │ │ └── voro++.1 │ ├── scripts │ │ ├── README │ │ ├── network.pl │ │ ├── random.pl │ │ └── sum.pl │ ├── src │ │ ├── Doxyfile │ │ ├── Makefile │ │ ├── Makefile.dep │ │ ├── README │ │ ├── c_loops.cc │ │ ├── c_loops.hh │ │ ├── cell.cc │ │ ├── cell.hh │ │ ├── cmd_line.cc │ │ ├── common.cc │ │ ├── common.hh │ │ ├── config.hh │ │ ├── container.cc │ │ ├── container.hh │ │ ├── container_prd.cc │ │ ├── container_prd.hh │ │ ├── pre_container.cc │ │ ├── pre_container.hh │ │ ├── rad_option.hh │ │ ├── unitcell.cc │ │ ├── unitcell.hh │ │ ├── v_base.cc │ │ ├── v_base.hh │ │ ├── v_base_wl.cc │ │ ├── v_compute.cc │ │ ├── v_compute.hh │ │ ├── voro++.cc │ │ ├── voro++.hh │ │ ├── wall.cc │ │ ├── wall.hh │ │ ├── worklist.hh │ │ └── worklist_gen.pl │ └── zeo │ │ ├── Makefile │ │ ├── cp_test.cc │ │ ├── cp_test.gnuplot │ │ ├── examples │ │ ├── AFX.v1 │ │ ├── BIK.v1 │ │ ├── EDI.v1 │ │ ├── EMT.v1 │ │ ├── HEU.v1 │ │ ├── HV.v1 │ │ ├── IFR.v1 │ │ ├── JBW.v1 │ │ ├── P1.v1 │ │ ├── P2.v1 │ │ ├── P3.v1 │ │ ├── P4.v1 │ │ ├── YUG.v1 │ │ └── test.v1 │ │ 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