From f11e9390fd9ffee6af9cc5202dabb17a7e946d99 Mon Sep 17 00:00:00 2001 From: Magdalena Schreter Date: Wed, 21 Sep 2022 22:59:01 +0200 Subject: [PATCH] add MCA algorithm for 1d --- doc/news/changes/minor/20220923SchreterMunch | 3 + include/deal.II/grid/grid_tools.h | 97 ++- source/grid/grid_tools.cc | 206 +++-- source/grid/grid_tools.inst.in | 2 - ...id_generator_marching_cube_algorithm_01.cc | 8 +- ...id_generator_marching_cube_algorithm_02.cc | 124 +++ ...gorithm_02.with_p4est=true.mpirun=1.output | 791 ++++++++++++++++++ 7 files changed, 1147 insertions(+), 84 deletions(-) create mode 100644 doc/news/changes/minor/20220923SchreterMunch create mode 100644 tests/grid/grid_generator_marching_cube_algorithm_02.cc create mode 100644 tests/grid/grid_generator_marching_cube_algorithm_02.with_p4est=true.mpirun=1.output diff --git a/doc/news/changes/minor/20220923SchreterMunch b/doc/news/changes/minor/20220923SchreterMunch new file mode 100644 index 0000000000..a3c21aa4c8 --- /dev/null +++ b/doc/news/changes/minor/20220923SchreterMunch @@ -0,0 +1,3 @@ +New: The GridTools::MarchingCubeAlgorithm supports now also 1D. +
+(Magdalena Schreter, Peter Munch, 2022/09/23) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index b04f3265c3..25aa2220ce 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -3440,26 +3440,53 @@ namespace GridTools /** * Process all locally-owned cells and fill @p vertices and @p cells for all * cells that are cut. + * + * @note: This function is only implemented for dim>1. Use + * process(background_dof_handler, ls_vector, iso_level, vertices) for + * dim==1. + */ + void + process(const DoFHandler & background_dof_handler, + const VectorType & ls_vector, + const double iso_level, + std::vector> &vertices, + std::vector> &cells) const; + + /** + * Process all locally-owned cells and fill @p vertices for all cells that + * are cut. */ void - process(const DoFHandler & background_dof_handler, - const VectorType & ls_vector, - const double iso_level, - std::vector> & vertices, - std::vector> &cells) const; + process(const DoFHandler & background_dof_handler, + const VectorType & ls_vector, + const double iso_level, + std::vector> &vertices) const; /** * Process the provided cell and fill @p vertices and @p cells for all cells * that are cut. * * @note The resulting vectors are empty if the cell is not cut. + * + * @note: This function is only implemented for dim>1. Use + * process_cell(cell, ls_vector, iso_level, vertices) for dim==1. */ void process_cell(const typename DoFHandler::active_cell_iterator &cell, - const VectorType & ls_vector, - const double iso_level, - std::vector> & vertices, - std::vector> &cells) const; + const VectorType & ls_vector, + const double iso_level, + std::vector> & vertices, + std::vector> &cells) const; + /** + * Process the provided cell and fill @p vertices for all cells that are cut. + * + * @note The resulting vector is empty if the cell is not cut. + */ + void + process_cell(const typename DoFHandler::active_cell_iterator &cell, + const VectorType & ls_vector, + const double iso_level, + std::vector> &vertices) const; private: /** @@ -3473,11 +3500,27 @@ namespace GridTools * Process a cell. */ void - process_cell(std::vector & ls_values, - const std::vector> & points, - const double iso_level, - std::vector> & vertices, - std::vector> &cells) const; + process_cell(std::vector & ls_values, + const std::vector> & points, + const double iso_level, + std::vector> & vertices, + std::vector> &cells, + const bool write_back_cell_data = true) const; + + /** + * Dummy function for 1D processing a sub-cell. + */ + void + process_sub_cell(const std::vector &, + const std::vector> &, + const std::vector &, + const double, + std::vector> &, + std::vector> &, + const bool) const + { + AssertThrow(false, ExcNotImplemented()); + } /** * Process a sub-cell (2D). @@ -3486,23 +3529,25 @@ namespace GridTools * of subdivisions in this case. */ void - process_sub_cell(const std::vector & ls_values, - const std::vector> & points, - const std::vector mask, - const double iso_level, - std::vector> & vertices, - std::vector> & cells) const; + process_sub_cell(const std::vector & ls_values, + const std::vector> & points, + const std::vector &mask, + const double iso_level, + std::vector> & vertices, + std::vector> & cells, + const bool write_back_cell_data) const; /** * Process a sub-cell (3D). */ void - process_sub_cell(const std::vector & ls_values, - const std::vector> & points, - const std::vector mask, - const double iso_level, - std::vector> & vertices, - std::vector> & cells) const; + process_sub_cell(const std::vector & ls_values, + const std::vector> & points, + const std::vector &mask, + const double iso_level, + std::vector> & vertices, + std::vector> & cells, + const bool write_back_cell_data) const; /** * Number of subdivisions each cell is subdivided into in each direction to diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index fba8c7ac48..60327d834f 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -6670,7 +6670,12 @@ namespace GridTools { std::vector> quadrature_points; - if (dim == 2) + if (dim == 1) + { + for (unsigned int i = 0; i <= n_subdivisions; ++i) + quadrature_points.emplace_back(1.0 / n_subdivisions * i); + } + else if (dim == 2) { for (unsigned int j = 0; j <= n_subdivisions; ++j) for (unsigned int i = 0; i <= n_subdivisions; ++i) @@ -6696,17 +6701,35 @@ namespace GridTools template void MarchingCubeAlgorithm::process( - const DoFHandler & background_dof_handler, - const VectorType & ls_vector, - const double iso_level, - std::vector> & vertices, - std::vector> &cells) const + const DoFHandler & background_dof_handler, + const VectorType & ls_vector, + const double iso_level, + std::vector> & vertices, + std::vector> &cells) const { + AssertThrow( + dim > 1, + ExcMessage( + "Not implemented for dim==1. Use the alternative process()-function " + "not returning a vector of CellData objects.")); + for (const auto &cell : background_dof_handler.active_cell_iterators() | IteratorFilters::LocallyOwnedCell()) process_cell(cell, ls_vector, iso_level, vertices, cells); } + template + void + MarchingCubeAlgorithm::process( + const DoFHandler & background_dof_handler, + const VectorType & ls_vector, + const double iso_level, + std::vector> &vertices) const + { + for (const auto &cell : background_dof_handler.active_cell_iterators() | + IteratorFilters::LocallyOwnedCell()) + process_cell(cell, ls_vector, iso_level, vertices); + } template @@ -6716,8 +6739,14 @@ namespace GridTools const VectorType & ls_vector, const double iso_level, std::vector> & vertices, - std::vector> & cells) const + std::vector> & cells) const { + AssertThrow( + dim > 1, + ExcMessage( + "Not implemented for dim==1. Use the alternative process_cell()-function " + "not returning a vector of CellData objects.")); + std::vector ls_values; fe_values.reinit(cell); @@ -6727,20 +6756,81 @@ namespace GridTools ls_values, fe_values.get_quadrature_points(), iso_level, vertices, cells); } + template + void + MarchingCubeAlgorithm::process_cell( + const typename DoFHandler::active_cell_iterator &cell, + const VectorType & ls_vector, + const double iso_level, + std::vector> & vertices) const + { + // This vector is just a placeholder to reuse the process_cell function. + std::vector> dummy_cells; + + std::vector ls_values; + + fe_values.reinit(cell); + ls_values.resize(fe_values.n_quadrature_points); + fe_values.get_function_values(ls_vector, ls_values); + + process_cell(ls_values, + fe_values.get_quadrature_points(), + iso_level, + vertices, + dummy_cells, + false /*don't write back cell data*/); + } template void MarchingCubeAlgorithm::process_cell( - std::vector & ls_values, - const std::vector> & points, - const double iso_level, - std::vector> & vertices, - std::vector> &cells) const + std::vector & ls_values, + const std::vector> & points, + const double iso_level, + std::vector> & vertices, + std::vector> &cells, + const bool write_back_cell_data) const { const unsigned p = n_subdivisions + 1; - if (dim == 2) + if (dim == 1) + { + for (unsigned int i = 0; i < n_subdivisions; ++i) + { + std::vector mask{i + 0, i + 1}; + + // check if a corner node is cut + if (std::abs(iso_level - ls_values[mask[0]]) < tolerance) + vertices.emplace_back(points[mask[0]]); + else if (std::abs(iso_level - ls_values[mask[1]]) < tolerance) + { + if (i + 1 == n_subdivisions) + vertices.emplace_back(points[mask[1]]); + } + // check for a saddle point, if iso_level values of the two + // corner nodes are identical + else if ((std::abs(ls_values[mask[0]] - ls_values[mask[1]]) < + tolerance) && + (ls_values[mask[0]] >= iso_level)) + vertices.emplace_back(0.5 * (points[mask[0]] + points[mask[1]])); + // check if the edge is cut + else if (((ls_values[mask[0]] > iso_level) && + (ls_values[mask[1]] < iso_level)) || + ((ls_values[mask[0]] < iso_level) && + (ls_values[mask[1]] > iso_level))) + { + // determine the interpolation weight (0 & cut_line_table, const ndarray &new_line_table, - const ndarray &line_to_vertex_table, - const std::vector & ls_values, - const std::vector> & points, - const std::vector & mask, - const double iso_level, - const double tolerance, - std::vector> & vertices, - std::vector> & cells) + const ndarray & line_to_vertex_table, + const std::vector & ls_values, + const std::vector> & points, + const std::vector & mask, + const double iso_level, + const double tolerance, + std::vector> & vertices, + std::vector> &cells, + const bool write_back_cell_data) { // inspired by https://graphics.stanford.edu/~mdfisher/MarchingCubes.html @@ -6858,16 +6959,19 @@ namespace GridTools vertices.push_back(vertex_list_reduced[i]); // write back cells - for (unsigned int i = 0; new_line_table[configuration][i] != X; - i += n_sub_vertices) + if (write_back_cell_data && dim > 1) { - cells.resize(cells.size() + 1); - cells.back().vertices.resize(n_sub_vertices); + for (unsigned int i = 0; new_line_table[configuration][i] != X; + i += n_sub_vertices) + { + cells.resize(cells.size() + 1); + cells.back().vertices.resize(n_sub_vertices); - for (unsigned int v = 0; v < n_sub_vertices; ++v) - cells.back().vertices[v] = - local_remap[new_line_table[configuration][i + v]] + - n_vertices_old; + for (unsigned int v = 0; v < n_sub_vertices; ++v) + cells.back().vertices[v] = + local_remap[new_line_table[configuration][i + v]] + + n_vertices_old; + } } } } // namespace internal @@ -6877,12 +6981,13 @@ namespace GridTools template void MarchingCubeAlgorithm::process_sub_cell( - const std::vector & ls_values, - const std::vector> & points, - const std::vector mask, - const double iso_level, - std::vector> & vertices, - std::vector> & cells) const + const std::vector & ls_values, + const std::vector> & points, + const std::vector &mask, + const double iso_level, + std::vector> & vertices, + std::vector> & cells, + const bool write_back_cell_data) const { // set up dimension-dependent sizes and tables constexpr unsigned int n_vertices = 4; @@ -6891,7 +6996,7 @@ namespace GridTools constexpr unsigned int n_configurations = Utilities::pow(2, n_vertices); constexpr unsigned int X = static_cast(-1); - // table that indicates if an edge is cut (it the i-th bit is set the i-th + // table that indicates if an edge is cut (if the i-th bit is set the i-th // line is cut) constexpr std::array cut_line_table = { {0b0000, @@ -6950,7 +7055,8 @@ namespace GridTools iso_level, tolerance, vertices, - cells); + cells, + write_back_cell_data); } @@ -6958,12 +7064,13 @@ namespace GridTools template void MarchingCubeAlgorithm::process_sub_cell( - const std::vector & ls_values, - const std::vector> & points, - const std::vector mask, - const double iso_level, - std::vector> & vertices, - std::vector> & cells) const + const std::vector & ls_values, + const std::vector> & points, + const std::vector &mask, + const double iso_level, + std::vector> & vertices, + std::vector> & cells, + const bool write_back_cell_data) const { // set up dimension-dependent sizes and tables constexpr unsigned int n_vertices = 8; @@ -6973,7 +7080,7 @@ namespace GridTools constexpr unsigned int X = static_cast(-1); // clang-format off - // table that indicates if an edge is cut (it the i-th bit is set the i-th + // table that indicates if an edge is cut (if the i-th bit is set the i-th // line is cut) constexpr std::array cut_line_table = {{ 0x0, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c, 0x80c, 0x905, @@ -7294,7 +7401,8 @@ namespace GridTools iso_level, tolerance, vertices, - cells); + cells, + write_back_cell_data); } } /* namespace GridTools */ diff --git a/source/grid/grid_tools.inst.in b/source/grid/grid_tools.inst.in index b91bd63eec..1b709413fa 100644 --- a/source/grid/grid_tools.inst.in +++ b/source/grid/grid_tools.inst.in @@ -511,8 +511,6 @@ for (deal_II_dimension : DIMENSIONS) for (deal_II_vec : REAL_NONBLOCK_VECTORS; deal_II_dimension : DIMENSIONS) { -#if deal_II_dimension > 1 template class GridTools::MarchingCubeAlgorithm; -#endif } diff --git a/tests/grid/grid_generator_marching_cube_algorithm_01.cc b/tests/grid/grid_generator_marching_cube_algorithm_01.cc index 5f83685f3f..88595adb1f 100644 --- a/tests/grid/grid_generator_marching_cube_algorithm_01.cc +++ b/tests/grid/grid_generator_marching_cube_algorithm_01.cc @@ -145,13 +145,7 @@ template void test(const unsigned int n_subdivisions, const double iso_level) { - const unsigned int spacedim = dim + 1; - - const unsigned int fe_degree = 3; - const unsigned int mapping_degree = fe_degree; - const unsigned int n_refinements = 5; - - + const unsigned int spacedim = dim + 1; const unsigned int background_fe_degree = 3; parallel::shared::Triangulation background_tria( diff --git a/tests/grid/grid_generator_marching_cube_algorithm_02.cc b/tests/grid/grid_generator_marching_cube_algorithm_02.cc new file mode 100644 index 0000000000..019573f842 --- /dev/null +++ b/tests/grid/grid_generator_marching_cube_algorithm_02.cc @@ -0,0 +1,124 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2021 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Test GridTools::MarchingCubeAlgorithm::process() + +#include + +#include + +#include + +#include +#include + +#include +#include + +#include + +#include + +#include +#include + +#include + +#include "../tests.h" + +using namespace dealii; + +using VectorType = LinearAlgebra::distributed::Vector; + +template +void +test(const unsigned int n_subdivisions, const double iso_level) +{ + deallog << "dim=" << dim << " iso level: " << iso_level << std::endl; + const int degree = 3; + const int n_refinements = 5; + + parallel::shared::Triangulation triangulation(MPI_COMM_WORLD); + + GridGenerator::hyper_cube(triangulation, -1.5, 1.5); + + triangulation.refine_global(n_refinements); + + FE_Q fe(degree); + MappingQ1 mapping; + + DoFHandler background_dof_handler; + background_dof_handler.reinit(triangulation); + background_dof_handler.distribute_dofs(fe); + + VectorType ls_vector; + IndexSet locally_relevant_dofs; + DoFTools::extract_locally_relevant_dofs(background_dof_handler, + locally_relevant_dofs); + + + ls_vector.reinit(background_dof_handler.locally_owned_dofs(), + locally_relevant_dofs, + MPI_COMM_WORLD); + + dealii::VectorTools::interpolate( + mapping, + background_dof_handler, + Functions::SignedDistance::Sphere(Point(), 0.75), + ls_vector); + + std::vector> vertices; + + const GridTools::MarchingCubeAlgorithm mc( + mapping, background_dof_handler.get_fe(), n_subdivisions); + + ls_vector.update_ghost_values(); + mc.process(background_dof_handler, ls_vector, iso_level, vertices); + + for (const auto &v : vertices) + deallog << "point found: " << v << std::endl; + + if (false /*write background mesh*/) + { + DataOut data_out; + data_out.attach_dof_handler(background_dof_handler); + data_out.add_data_vector(ls_vector, "level_set"); + data_out.build_patches(2); + data_out.write_vtu_with_pvtu_record("./", + "data_background_" + + std::to_string(n_subdivisions), + 0, + triangulation.get_communicator()); + } +} + +int +main(int argc, char *argv[]) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1); + MPILogInitAll all; + + deallog << std::scientific << std::setprecision(6); + + // dim==1 + for (unsigned int i = 1; i <= 3; ++i) + test<1>(i, -0.1 + i * 0.05); + + // dim==2 + for (unsigned int i = 1; i <= 3; ++i) + test<2>(i, -0.1 + i * 0.05); + + return 0; +} diff --git a/tests/grid/grid_generator_marching_cube_algorithm_02.with_p4est=true.mpirun=1.output b/tests/grid/grid_generator_marching_cube_algorithm_02.with_p4est=true.mpirun=1.output new file mode 100644 index 0000000000..a02ac59bf0 --- /dev/null +++ b/tests/grid/grid_generator_marching_cube_algorithm_02.with_p4est=true.mpirun=1.output @@ -0,0 +1,791 @@ + +DEAL:0::dim=1 iso level: -5.000000e-02 +DEAL:0::point found: -7.000000e-01 +DEAL:0::point found: 7.000000e-01 +DEAL:0::dim=1 iso level: 0.000000e+00 +DEAL:0::point found: -7.500000e-01 +DEAL:0::point found: -7.500000e-01 +DEAL:0::point found: 7.500000e-01 +DEAL:0::point found: 7.500000e-01 +DEAL:0::dim=1 iso level: 5.000000e-02 +DEAL:0::point found: -8.000000e-01 +DEAL:0::point found: 8.000000e-01 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