From: Peter Munch Date: Tue, 8 Jun 2021 12:09:29 +0000 (+0200) Subject: Add DataOutResample X-Git-Tag: v9.4.0-rc1~1170^2 X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=refs%2Fpull%2F12408%2Fhead;p=dealii.git Add DataOutResample Review comments --- diff --git a/doc/news/changes/major/20210608Munch b/doc/news/changes/major/20210608Munch new file mode 100644 index 0000000000..8dba487306 --- /dev/null +++ b/doc/news/changes/major/20210608Munch @@ -0,0 +1,5 @@ +New: The new postprocessing class DataOutResample is similar to +DataOut but allows to interpolate the result onto a second +triangulation. +
+(Peter Munch, Martin Kronbichler, Magdalena Schreter, 2021/06/08) diff --git a/include/deal.II/numerics/data_out_dof_data.h b/include/deal.II/numerics/data_out_dof_data.h index 7ab9a7764a..e66bc5208c 100644 --- a/include/deal.II/numerics/data_out_dof_data.h +++ b/include/deal.II/numerics/data_out_dof_data.h @@ -1001,6 +1001,7 @@ public: virtual const std::vector & get_patches() const override; +protected: /** * Virtual function through which the names of data sets are obtained by the * output functions of the base class. diff --git a/include/deal.II/numerics/data_out_resample.h b/include/deal.II/numerics/data_out_resample.h new file mode 100644 index 0000000000..b87305191d --- /dev/null +++ b/include/deal.II/numerics/data_out_resample.h @@ -0,0 +1,168 @@ +// --------------------------------------------------------------------- +// +// 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. +// +// --------------------------------------------------------------------- + +#ifndef dealii_data_out_resample_h +#define dealii_data_out_resample_h + + + +#include + +#include + +#include +#include + +#include + +DEAL_II_NAMESPACE_OPEN + +/** + * A DataOut-like class that does not output a numerical solution on + * the cells of the original triangulation but interpolates the result onto a + * second triangulation (that can be completely unrelated). + * By using this class, one can output the result obtained on an unstructured + * mesh onto a structured one or one can create a slice in 3D. + * + * The following code snippet shows the steps how to use the class when the + * solution is given for a three dimensional triangulation and the result + * should be outputted on a (2D) slice: + * @code + * // setup and first usage + * DataOutResample<3, 2, 3> data_out(patch_tria,patch_mapping); + * data_out.add_data_vector(dof_handler, vector, "solution"); + * data_out.build_patches(mapping); + * + * // ... no changes in triangulation and mapping -> reuse internal data + * structures data_out.build_patches(); + * + * // ... changes in triangulation or mapping -> reinitialize internal data + * structures data_out.build_patches(mapping); + * @endcode + * + * @note While the dimension of the two triangulations might differ, their + * space dimension need to coincide. + */ +template +class DataOutResample + : public DataOut_DoFData +{ +public: + /** + * Constructor taking the triangulation and mapping for which the patches + * should be generated. + */ + DataOutResample(const Triangulation &patch_tria, + const Mapping & patch_mapping); + + /** + * Update the @p mapping of original triangulation. One needs to call this + * function if the mapping has changed. Just like in the DataOut context, + * @p n_subdivisions determines how many "patches" this function will build + * out of every cell. + * + * This function involves an expensive setup: evaluation points are generated + * and their owners are determined, which is used to set up the communication + * pattern. + * + * @note If you use the version of build_patches() that does not take a + * mapping, this function has to be called before its first usage. + */ + void + update_mapping(const Mapping &mapping, + const unsigned int n_subdivisions = 0); + + /** + * This is the central function of this class since it builds the list of + * patches to be written by the low-level functions of the base class. A + * patch is, in essence, some intermediate representation of the data on + * each cell of a triangulation and DoFHandler object that can then be used + * to write files in some format that is readable by visualization programs. + * + * Since this function calls internally at the beginning update_mapping(), + * this function also involves an expensive setup. + * + * Just like in the DataOut::build_patches() context, @p n_subdivisions + * determines how many "patches" this function will build out of every cell. + */ + void + build_patches( + const Mapping &mapping, + const unsigned int n_subdivisions = 0, + const typename DataOut::CurvedCellRegion + curved_region = + DataOut::CurvedCellRegion::curved_boundary); + + /** + * Just like the above function, this function builds a list of + * patches to be written by the low-level functions of the base class. + * However it skips the update of the mapping and reuses the one registered + * via update_mapping(). This allows to skip the expensive setup of the + * internal communication routines. + * + * @note This function can be only used if a mapping has been registered via + * update_mapping() or the other build_patches() function. The same + * n_subdivisions previously passed to these functions is used. + */ + void + build_patches( + const typename DataOut::CurvedCellRegion + curved_region = + DataOut::CurvedCellRegion::curved_boundary); + +protected: + virtual const std::vector> & + get_patches() const override; + +private: + /** + * Intermediate DoFHandler + */ + DoFHandler patch_dof_handler; + + /** + * Mapping used in connection with patch_tria. + */ + const SmartPointer> patch_mapping; + + /** + * DataOut object that does the actual building of the patches. + */ + DataOut patch_data_out; + + /** + * Object to evaluate + */ + Utilities::MPI::RemotePointEvaluation rpe; + + /** + * Partitioner to create internally distributed vectors. + */ + std::shared_ptr partitioner; + + /** + * Process local indices to access efficiently internal distributed vectors. + */ + std::vector point_to_local_vector_indices; + + /** + * Mapping of the original triangulation provided in update_mapping(). + */ + SmartPointer> mapping; +}; + +DEAL_II_NAMESPACE_CLOSE + +#endif diff --git a/source/numerics/CMakeLists.txt b/source/numerics/CMakeLists.txt index 513ace04d7..9b0031d40a 100644 --- a/source/numerics/CMakeLists.txt +++ b/source/numerics/CMakeLists.txt @@ -18,8 +18,8 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}) SET(_unity_include_src data_out.cc data_out_faces.cc - data_out_stack.cc data_out_rotation.cc + data_out_stack.cc data_postprocessor.cc dof_output_operator.cc histogram.cc @@ -38,6 +38,7 @@ SET(_separate_src data_out_dof_data.cc data_out_dof_data_inst2.cc data_out_dof_data_codim.cc + data_out_resample.cc derivative_approximation.cc error_estimator_1d.cc error_estimator.cc @@ -77,6 +78,7 @@ SET(_inst data_out_dof_data_codim.inst.in data_out_faces.inst.in data_out.inst.in + data_out_resample.inst.in data_out_rotation.inst.in data_out_stack.inst.in data_postprocessor.inst.in diff --git a/source/numerics/data_out_resample.cc b/source/numerics/data_out_resample.cc new file mode 100644 index 0000000000..a2d564a86e --- /dev/null +++ b/source/numerics/data_out_resample.cc @@ -0,0 +1,202 @@ +// --------------------------------------------------------------------- +// +// 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. +// +// --------------------------------------------------------------------- + +#include + +#include +#include + +#include +#include + +#include +#include +#include + +#include + +DEAL_II_NAMESPACE_OPEN + + +template +DataOutResample::DataOutResample( + const Triangulation &patch_tria, + const Mapping & patch_mapping) + : patch_dof_handler(patch_tria) + , patch_mapping(&patch_mapping) +{} + + + +template +void +DataOutResample::update_mapping( + const Mapping &mapping, + const unsigned int n_subdivisions) +{ + this->mapping = &mapping; + this->point_to_local_vector_indices.clear(); + + FE_Q_iso_Q1 fe( + std::max(1, n_subdivisions)); + patch_dof_handler.distribute_dofs(fe); + + std::vector>> points_all; + + Quadrature quadrature(fe.get_unit_support_points()); + + FEValues fe_values(*patch_mapping, + fe, + quadrature, + update_quadrature_points); + + std::vector dof_indices(fe.n_dofs_per_cell()); + + IndexSet active_dofs; + DoFTools::extract_locally_active_dofs(patch_dof_handler, active_dofs); + partitioner = std::make_shared( + patch_dof_handler.locally_owned_dofs(), active_dofs, MPI_COMM_WORLD); + + for (const auto &cell : patch_dof_handler.active_cell_iterators()) + { + if (cell->is_locally_owned() == false) + continue; + + fe_values.reinit(cell); + + cell->get_dof_indices(dof_indices); + + for (unsigned int i = 0; i < dof_indices.size(); ++i) + points_all.emplace_back(partitioner->global_to_local(dof_indices[i]), + fe_values.quadrature_point(i)); + } + + std::sort(points_all.begin(), + points_all.end(), + [](const auto &a, const auto &b) { return a.first < b.first; }); + points_all.erase(std::unique(points_all.begin(), + points_all.end(), + [](const auto &a, const auto &b) { + return a.first == b.first; + }), + points_all.end()); + + std::vector> points; + + for (const auto &i : points_all) + { + point_to_local_vector_indices.push_back(i.first); + points.push_back(i.second); + } + + rpe.reinit(points, *this->triangulation, *this->mapping); +} + + + +template +void +DataOutResample::build_patches( + const Mapping & mapping, + const unsigned int n_subdivisions, + const typename DataOut::CurvedCellRegion curved_region) +{ + this->update_mapping(mapping, n_subdivisions); + this->build_patches(curved_region); +} + + + +template +void +DataOutResample::build_patches( + const typename DataOut::CurvedCellRegion curved_region) +{ + patch_data_out.clear(); + + if (rpe.is_ready() == false) + { + Assert( + this->mapping, + ExcMessage( + "Mapping is not valid anymore! Please register a new mapping via " + "update_mapping() or the other build_patches() function.")); + update_mapping(*this->mapping, patch_dof_handler.get_fe().degree); + } + + std::vector>> + vectors; + + patch_data_out.attach_dof_handler(patch_dof_handler); + + unsigned int counter = 0; + + for (const auto &data : this->dof_data) + { + const auto data_ptr = dynamic_cast< + internal::DataOutImplementation::DataEntry *>( + data.get()); + + Assert(data_ptr, ExcNotImplemented()); + + const auto &dh = *data_ptr->dof_handler; + + // TODO: enable more components + AssertDimension(dh.get_fe_collection().n_components(), 1); + + const auto values = + VectorTools::point_values<1>(rpe, dh, data_ptr->vector); + + vectors.emplace_back( + std::make_shared>( + partitioner)); + + for (unsigned int j = 0; j < values.size(); ++j) + vectors.back()->local_element(point_to_local_vector_indices[j]) = + values[j]; + + vectors.back()->set_ghost_state(true); + + // we can give the vectors arbitrary names ("temp_*") here, since these + // are only used internally (by patch_data_out) but not later on during + // the actual output to file + patch_data_out.add_data_vector( + *vectors.back(), + std::string("temp_" + std::to_string(counter)), + DataOut_DoFData:: + DataVectorType::type_dof_data); + + counter++; + } + + patch_data_out.build_patches(*patch_mapping, + patch_dof_handler.get_fe().degree, + curved_region); +} + + + +template +const std::vector> & +DataOutResample::get_patches() const +{ + return patch_data_out.get_patches(); +} + + +// explicit instantiations +#include "data_out_resample.inst" + +DEAL_II_NAMESPACE_CLOSE diff --git a/source/numerics/data_out_resample.inst.in b/source/numerics/data_out_resample.inst.in new file mode 100644 index 0000000000..853119f471 --- /dev/null +++ b/source/numerics/data_out_resample.inst.in @@ -0,0 +1,26 @@ +// --------------------------------------------------------------------- +// +// 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. +// +// --------------------------------------------------------------------- + + +for (deal_II_dimension : DIMENSIONS; deal_II_patch_dimension : DIMENSIONS; + deal_II_space_dimension : DIMENSIONS) + { +#if deal_II_dimension == deal_II_space_dimension && \ + deal_II_patch_dimension <= deal_II_space_dimension + template class DataOutResample; +#endif + } diff --git a/tests/remote_point_evaluation/data_out_resample_01.cc b/tests/remote_point_evaluation/data_out_resample_01.cc new file mode 100644 index 0000000000..7d55c87597 --- /dev/null +++ b/tests/remote_point_evaluation/data_out_resample_01.cc @@ -0,0 +1,121 @@ +// --------------------------------------------------------------------- +// +// 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 DataOutResample to create a slice. + +#include +#include + +#include + +#include +#include + +#include + +#include + +#include +#include + +#include "../tests.h" + +using namespace dealii; + +template +class AnalyticalFunction : public Function +{ +public: + AnalyticalFunction() + : Function(1) + {} + + virtual double + value(const Point &p, const unsigned int component = 0) const + { + (void)component; + + return p[0] * p[0] + p[1] * p[1] + p[2] * p[2]; + } +}; + + +template +std::shared_ptr +create_partitioner(const DoFHandler &dof_handler) +{ + IndexSet locally_relevant_dofs; + + DoFTools::extract_locally_relevant_dofs(dof_handler, locally_relevant_dofs); + + return std::make_shared( + dof_handler.locally_owned_dofs(), + locally_relevant_dofs, + dof_handler.get_communicator()); +} + + + +int +main(int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi(argc, argv, 1); + MPILogInitAll all; + + const int dim = 3; + const int patch_dim = 2; + const int spacedim = 3; + + const unsigned int n_refinements_1 = 3; + const unsigned int n_refinements_2 = 3; + const MPI_Comm comm = MPI_COMM_WORLD; + + parallel::distributed::Triangulation tria_slice(comm); + GridGenerator::hyper_cube(tria_slice, -1.0, +1.0); + tria_slice.refine_global(n_refinements_2); + + MappingQ1 mapping_slice; + + parallel::distributed::Triangulation tria_backround(comm); + GridGenerator::hyper_cube(tria_backround, -1.0, +1.0); + tria_backround.refine_global(n_refinements_1); + + DoFHandler dof_handler(tria_backround); + dof_handler.distribute_dofs(FE_Q{1}); + + MappingQ1 mapping; + + LinearAlgebra::distributed::Vector vector( + create_partitioner(dof_handler)); + + VectorTools::interpolate(mapping, + dof_handler, + AnalyticalFunction(), + vector); + + vector.update_ghost_values(); + + DataOutResample data_out(tria_slice, mapping_slice); + data_out.add_data_vector(dof_handler, vector, "solution_0"); + data_out.add_data_vector(dof_handler, vector, "solution_1"); + data_out.update_mapping(mapping); + data_out.build_patches(); + +#if 1 + data_out.write_vtk(deallog.get_file_stream()); +#else + data_out.write_vtu_with_pvtu_record("./", "data_out_01", 0, comm, 1, 1); +#endif +} diff --git 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