diff --git a/snap_tessellated_mesh/.clang-format b/snap_tessellated_mesh/.clang-format new file mode 100644 index 0000000..41be722 --- /dev/null +++ b/snap_tessellated_mesh/.clang-format @@ -0,0 +1,22 @@ +BasedOnStyle: LLVM +--- +Language: Cpp +AlwaysBreakTemplateDeclarations: true +BreakBeforeBraces: Allman +IncludeBlocks: Regroup +IncludeCategories: + - Regex: "[a-z]*.hh" + Priority: 100 + - Regex: "deal.II*" + Priority: 200 + - Regex: "boost*" + Priority: 300 + - Regex: "adiak*" + Priority: 400 + - Regex: "caliper*" + Priority: 500 + - Regex: "Kokkos*" + Priority: 600 + - Regex: "<[a-z_]+>" + Priority: 1000 +... diff --git a/snap_tessellated_mesh/CMakeLists.txt b/snap_tessellated_mesh/CMakeLists.txt new file mode 100644 index 0000000..de0d78d --- /dev/null +++ b/snap_tessellated_mesh/CMakeLists.txt @@ -0,0 +1,15 @@ +cmake_minimum_required(VERSION 3.13.4) +project(snap_tessellated_mesh) + +find_package(deal.II 9.5.0 REQUIRED HINTS ${DEAL_II_DIR}) + +if(NOT DEAL_II_WITH_OPENCASCADE) + message(FATAL_ERROR "This tool requires deal.II to be built with OpenCASCADE support!") +endif() + +add_executable(snap_to_tessellated_mesh.exe snap_to_tessellated_mesh.cpp) + +target_link_libraries(snap_to_tessellated_mesh.exe dealii::dealii) + +enable_testing() +add_subdirectory(tests) diff --git a/snap_tessellated_mesh/README.md b/snap_tessellated_mesh/README.md new file mode 100755 index 0000000..52a2de0 --- /dev/null +++ b/snap_tessellated_mesh/README.md @@ -0,0 +1,34 @@ +# snap\_to\_tessellated\_mesh +`snap_to_tesselated_mesh` snaps a tessellated vtk mesh to the geometries surface given by an iges file. + +## Installation +Installing `snap_to_tessellated_mesh` requires: +* deal.II: 9.5 or later +* OpenCASCADE (compatible with deal.II) + +You need to compile deal.II with OpenCASCADE support. + +To configure `snap_to_tessellated_mesh` use: +```CMake +cmake \ + -D CMAKE_BUILD_TYPE=Release \ + -D DEAL_II_DIR=/path/to/dealii \ +/path/to/source/dir +``` +Then simply use `make`. This will compile `snap_to_tessellated_mesh` and create an executable +called `snap_to_tessellated_mesh.exe` in the build directory + +## Run +After compiling `snap_to_tessellated_mesh`, you can create a snapped vtk mesh file via +```bash +./snap_to_tessellated_mesh input.vtk input.iges output.vtk +``` +Note that the name of the input and output files is totally arbitrary, `input.vtk` is as +valid as `input_vtk`. + +## License +`snap_to_tessellated_mesh` is distributed under the 3-Clause BSD License. + +## Questions +If you have any question, find a bug, or have feature request please open an +issue. diff --git a/snap_tessellated_mesh/ci/Dockerfile b/snap_tessellated_mesh/ci/Dockerfile new file mode 100644 index 0000000..e401612 --- /dev/null +++ b/snap_tessellated_mesh/ci/Dockerfile @@ -0,0 +1,108 @@ +ARG BASE=ubuntu:24.04 +FROM $BASE + +ARG N_PROCS=8 + +ENV DEBIAN_FRONTEND=noninteractive +RUN apt-get update && apt-get upgrade -y && apt-get install -y \ + gcc \ + gfortran \ + build-essential \ + wget \ + curl \ + libcurl4-gnutls-dev \ + bison \ + python3-dev \ + git \ + lcov \ + zlib1g-dev \ + libopenblas-dev \ + libdw-dev \ + libpfm4-dev \ + libunwind-dev \ + libgl1-mesa-dev \ + libgmp-dev \ + libxi-dev \ + libxmu-dev \ + tk-dev \ + tcl-dev \ + libfreetype6-dev \ + && \ + apt-get clean && rm -rf /var/lib/apt/lists/* + +ENV PREFIX=/scratch +ENV ARCHIVE_DIR=${PREFIX}/archive +ENV SOURCE_DIR=${PREFIX}/source +ENV BUILD_DIR=${PREFIX}/build +ENV INSTALL_DIR=/opt + +RUN mkdir -p ${PREFIX} && \ + cd ${PREFIX} && \ + mkdir archive && \ + mkdir source && \ + mkdir build + +# Install CMake +RUN export CMAKE_VERSION=3.27.8 && \ + export CMAKE_SHA256=dfedc30abe69dcabe326a4de632210bb52004185bd2c0b096c21924f4510681f && \ + export CMAKE_URL=https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cmake-${CMAKE_VERSION}-linux-x86_64.tar.gz && \ + export CMAKE_ARCHIVE=${ARCHIVE_DIR}/cmake.tar.gz && \ + export CMAKE_BUILD_DIR=${BUILD_DIR}/cmake && \ + wget --quiet ${CMAKE_URL} --output-document=${CMAKE_ARCHIVE} && \ + echo "${CMAKE_SHA256} ${CMAKE_ARCHIVE}" | sha256sum -c && \ + mkdir -p ${CMAKE_BUILD_DIR} && \ + tar xf ${CMAKE_ARCHIVE} -C ${CMAKE_BUILD_DIR} --strip-components=1 && \ + mv ${CMAKE_BUILD_DIR} ${INSTALL_DIR} && \ + rm -rf ${CMAKE_ARCHIVE} && \ + rm -rf ${CMAKE_BUILD_DIR} +ENV PATH=${INSTALL_DIR}/cmake/bin:$PATH + +# Install OpenCascade 7.5.0 +RUN export OPENCASCADE_HASH=29cf1a701ca269df10f2d1c4037e2826cf704355 && \ + export OPENCASCADE_URL=https://github.com/tpaviot/oce/archive/${OPENCASCADE_HASH}.tar.gz && \ + export OPENCASCADE_ARCHIVE=${ARCHIVE_DIR}/opencascade.tar.gz && \ + export OPENCASCADE_SOURCE_DIR=${SOURCE_DIR}/opencascade && \ + export OPENCASCADE_BUILD_DIR=${BUILD_DIR}/opencascade && \ + export OPENCASCADE_INSTALL_DIR=${INSTALL_DIR}/opencascade && \ + wget --quiet ${OPENCASCADE_URL} --output-document=${OPENCASCADE_ARCHIVE} && \ + mkdir -p ${OPENCASCADE_SOURCE_DIR} && \ + tar -xf ${OPENCASCADE_ARCHIVE} -C ${OPENCASCADE_SOURCE_DIR} --strip-components=1 && \ + mkdir -p ${OPENCASCADE_INSTALL_DIR} && \ + mkdir ${OPENCASCADE_BUILD_DIR} && \ + cd ${OPENCASCADE_BUILD_DIR} && \ + cmake -D OCE_INSTALL_PREFIX=${OPENCASCADE_INSTALL_DIR} \ + -D OCE_TESTING=OFF \ + -D OCE_VISUALISATION=OFF \ + -D OCE_DISABLE_X11=ON \ + ${OPENCASCADE_SOURCE_DIR} && \ + make -j${N_PROCS} install && \ + rm -rf ${OPENCASCADE_ARCHIVE} && \ + rm -rf ${OPENCASCADE_BUILD_DIR} && \ + rm -rf ${OPENCASCADE_SOURCE_DIR} +ENV OPENCASCADE_DIR=${INSTALL_DIR}/opencascade + +# Install deal.II 9.5.1 +RUN export DEAL_II_HASH=9e847302b21355f355c87890477f4dd485da26b1 && \ + export DEAL_II_URL=https://github.com/dealii/dealii/archive/${DEAL_II_HASH}.tar.gz && \ + export DEAL_II_ARCHIVE=${ARCHIVE_DIR}/dealii.tar.gz && \ + export DEAL_II_SOURCE_DIR=${SOURCE_DIR}/dealii && \ + export DEAL_II_BUILD_DIR=${BUILD_DIR}/dealii && \ + export DEAL_II_INSTALL_DIR=${INSTALL_DIR}/dealii && \ + wget --quiet ${DEAL_II_URL} --output-document=${DEAL_II_ARCHIVE} && \ + mkdir -p ${DEAL_II_SOURCE_DIR} && \ + tar -xf ${DEAL_II_ARCHIVE} -C ${DEAL_II_SOURCE_DIR} --strip-components=1 && \ + mkdir -p ${DEAL_II_BUILD_DIR} && cd ${DEAL_II_BUILD_DIR} && \ + cmake -D CMAKE_BUILD_TYPE=DebugRelease \ + -D CMAKE_CXX_STANDARD=17 \ + -D DEAL_II_ALLOW_AUTODETECTION=OFF \ + -D DEAL_II_WITH_COMPLEX_VALUES=OFF \ + -D DEAL_II_WITH_OPENCASCADE=ON \ + -D OPENCASCADE_DIR=${OPENCASCADE_DIR} \ + -D DEAL_II_COMPONENT_EXAMPLES=OFF \ + -D CMAKE_INSTALL_PREFIX=${DEAL_II_INSTALL_DIR} \ + ${DEAL_II_SOURCE_DIR} && \ + make -j${N_PROCS} install && \ + rm -rf ${DEAL_II_ARCHIVE} && \ + rm -rf ${DEAL_II_BUILD_DIR} +# We keep the source file for debugging purpose +ENV DEAL_II_DIR=${INSTALL_DIR}/dealii diff --git a/snap_tessellated_mesh/snap_to_tessellated_mesh.cpp b/snap_tessellated_mesh/snap_to_tessellated_mesh.cpp new file mode 100644 index 0000000..1dc5a09 --- /dev/null +++ b/snap_tessellated_mesh/snap_to_tessellated_mesh.cpp @@ -0,0 +1,255 @@ +/* Copyright (c) 2023 - 2024, the adamantine authors. + * + * This file is subject to the Modified BSD License and may not be distributed + * without copyright and license information. Please refer to the file LICENSE + * for the text and further information on this license. + */ + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +// This is basically the same as dealii::OpenCASCADE closest_point +// but simplified for our needs. The interface also allows passing in +// a std::vector of faces instead of the whole shape. +dealii::Point<3> closest_point(const std::vector &faces, + const dealii::Point<3> &origin, + const double tolerance) +{ + gp_Pnt Pproj = dealii::OpenCASCADE::point(origin); + + double minDistance = std::numeric_limits::max(); + gp_Pnt tmp_proj(0.0, 0.0, 0.0); + + for (const auto &face : faces) + { + // the projection function needs a surface, so we obtain the + // surface upon which the face is defined + Handle(Geom_Surface) SurfToProj = BRep_Tool::Surface(face); + + ShapeAnalysis_Surface projector(SurfToProj); + gp_Pnt2d proj_params = + projector.ValueOfUV(dealii::OpenCASCADE::point(origin), tolerance); + + SurfToProj->D0(proj_params.X(), proj_params.Y(), tmp_proj); + + double distance = dealii::OpenCASCADE::point<3>(tmp_proj).distance(origin); + if (distance < minDistance) + { + minDistance = distance; + Pproj = tmp_proj; + } + } + + return dealii::OpenCASCADE::point<3>(Pproj); +} + +// Try to move every boundary point to the surface described by the TopoDS_Faces +// passed in as argument. Optionally, ignore faces in z-direction. +void snap_to_iges( + dealii::Triangulation<3> &tria, const std::vector &faces, + dealii::OpenCASCADE::NormalProjectionManifold<3, 3> &projector, + bool exclude_z_faces) +{ + + // Store for every boundary point all its normal vectors. If all of these + // point in the same direction, replace its x- and y-coordinates with the + // respective coordinates of the closest point on the surface. Otherwise, the + // point is a corner point and projecting it would collapse vertices. Instead + // take the average of the old and new point. + std::map>, + std::vector>>> + vertex_map; + std::array, dealii::GeometryInfo<3>::vertices_per_face> + normal_at_vertex; + for (const auto &cell : tria.active_cell_iterators()) + { + for (const unsigned int i : cell->face_indices()) + { + const auto &face = cell->face(i); + if (face->at_boundary()) + { + projector.get_normals_at_vertices(face, normal_at_vertex); + for (unsigned j = 0; j < face->n_vertices(); ++j) + { + const unsigned int vertex_index = face->vertex_index(j); + const auto &vertex_map_iterator = vertex_map.find(vertex_index); + auto normal = normal_at_vertex[j] / normal_at_vertex[j].norm(); + + if (!(exclude_z_faces && + std::abs(normal * dealii::Tensor<1, 3>{{0, 0, 1}}) > 0.1)) + { + if (vertex_map_iterator == vertex_map.end()) + { + std::pair>, + std::vector>> + pair(face->vertex(j), {normal}); + vertex_map.emplace(vertex_index, pair); + } + else + { + std::get<1>(vertex_map_iterator->second).push_back(normal); + } + } + } + } + } + } + + for (const auto &boundary_vertex_iterator : vertex_map) + { + const auto &normals = std::get<1>(boundary_vertex_iterator.second); + double minimum_product = 1; + for (unsigned int i = 0; i < normals.size(); ++i) + { + for (unsigned int j = i + 1; j < normals.size(); ++j) + { + auto product = normals[i] * normals[j]; + minimum_product = std::min(product, minimum_product); + } + } + auto &vertex = std::get<0>(boundary_vertex_iterator.second).get(); + auto proj = closest_point(faces, vertex, 1.e-10); + // For tessellated meshes the minimal product between normal vectors can + // only be -1,0, or 1. + if (minimum_product > .5) + { + vertex(0) = proj(0); + vertex(1) = proj(1); + } + else + { + vertex(0) = (vertex(0) + proj(0)) / 2; + vertex(1) = (vertex(1) + proj(1)) / 2; + } + } +} + +int main(int argc, char *argv[]) +{ + if (argc < 4 || argc > 5) + { + std::cerr << "ERROR: The tool requires three runtime arguments for the " + "tessellated input vtk file, the IGES file, and the output " + "vtk file! Optionally, excluding z-facses can be requested. " + "However, the number of runtime arguments is " + << argc - 1 << std::endl; + std::abort(); + } + std::cout << "Input VTK file: " << argv[1] << '\n' + << "Input IGES file: " << argv[2] << '\n' + << "Output VTK file: " << argv[3] << '\n'; + + TopoDS_Shape surface = dealii::OpenCASCADE::read_IGES(argv[2]); + + double minima[3]; + double maxima[3]; + Bnd_Box B; + BRepBndLib::Add(surface, B); + B.Get(minima[0], minima[1], minima[2], maxima[0], maxima[1], maxima[2]); + + std::cout << "Bounding Box: (" << minima[0] << ',' << minima[1] << ',' + << minima[2] << "), (" << maxima[0] << ',' << maxima[1] << ',' + << maxima[2] << ")\n"; + + dealii::OpenCASCADE::write_STL(surface, "debug.STL", 1.e-3); + + TopExp_Explorer exp; + gp_Pnt tmp_proj; + + // Ignore TopoDS::Faces that are planes with z-normal. This might or might not + // be a good choice depending on the input files. It should not be detrimental + // if the face is indeed planar but might be problematic if we wrongly detect + // it to be planar. Excluding those faces should mostly help with the edges at + // the top and bottom of the mesh (assuming thet are planar). + bool const exclude_z_faces = argc == 5 ? std::stoi(argv[4]) : false; + + std::vector faces; + { + for (exp.Init(surface, TopAbs_FACE); exp.More(); exp.Next()) + { + TopoDS_Face face = TopoDS::Face(exp.Current()); + if (exclude_z_faces) + { + Handle(Geom_Surface) SurfToProj = BRep_Tool::Surface(face); + double aXmin, aYmin, aZmin, aXmax, aYmax, aZmax; + + Bnd_Box box; + BRepBndLib::Add(face, box); + box.Get(aXmin, aYmin, aZmin, aXmax, aYmax, aZmax); + + // Obtain the four corners of the face and check if they are lying in + // the same plane with z-normal + double u1, u2, v1, v2; + SurfToProj->Bounds(u1, u2, v1, v2); + auto point_0 = dealii::OpenCASCADE::point<3>(SurfToProj->Value(u1, v1)); + auto point_1 = dealii::OpenCASCADE::point<3>(SurfToProj->Value(u1, v2)); + auto point_2 = dealii::OpenCASCADE::point<3>(SurfToProj->Value(u2, v1)); + auto point_3 = dealii::OpenCASCADE::point<3>(SurfToProj->Value(u2, v2)); + auto vector_0 = point_1 - point_0; + auto vector_1 = point_2 - point_0; + auto vector_2 = point_3 - point_0; + auto normal = cross_product_3d(vector_0, vector_1); + double deviation = normal / normal.norm() * vector_2 / vector_2.norm(); + double deviation_from_z = + normal / normal.norm() * dealii::Tensor<1, 3>({0, 0, 1}); + + // TODO find better tolerances to decide if a face is planar with + // z-normal or not. + if (std::abs(deviation) > .1 || std::abs(deviation_from_z) < .9) + faces.push_back(face); + } + else + faces.push_back(face); + } + } + + std::ifstream in; + in.open(argv[1]); + dealii::GridIn<3, 3> gi; + dealii::Triangulation<3> tria; + gi.attach_triangulation(tria); + gi.read_vtk(in); + + dealii::BoundingBox vtk_bounding_box = tria.begin_active()->bounding_box(); + for (const auto &cell : tria.active_cell_iterators()) + vtk_bounding_box.merge_with(cell->bounding_box()); + std::cout << "Bounding Box (VTK): (" + << vtk_bounding_box.get_boundary_points().first << ") (" + << vtk_bounding_box.get_boundary_points().second << ")\n"; + + // Compute shift and scaling to transform bouding boxes for debugging. + for (int i = 0; i < 3; ++i) + { + double new_1 = vtk_bounding_box.get_boundary_points().first(i); + double new_2 = vtk_bounding_box.get_boundary_points().second(i); + double old_1 = minima[i]; + double old_2 = maxima[i]; + double shift = (old_2 * new_1 - new_2 * old_1) / (new_2 - new_1); + double scale = new_1 / (old_1 + shift); + std::cout << "shift[" << i << "]: " << shift << ", scale[" << i + << "]: " << scale << '\n'; + } + + dealii::GridOut grid_out; + { + std::ofstream logfile("debug.vtk"); + grid_out.write_vtk(tria, logfile); + } + dealii::OpenCASCADE::NormalProjectionManifold<3, 3> normal_projector(surface); + snap_to_iges(tria, faces, normal_projector, exclude_z_faces); + + const std::string filename = argv[3]; + std::ofstream logfile(filename); + grid_out.write_vtk(tria, logfile); +} diff --git a/snap_tessellated_mesh/tests/CMakeLists.txt b/snap_tessellated_mesh/tests/CMakeLists.txt new file mode 100644 index 0000000..a0d41b8 --- /dev/null +++ b/snap_tessellated_mesh/tests/CMakeLists.txt @@ -0,0 +1,19 @@ +include(CTest) +add_test(NAME RunCurvedWall COMMAND + snap_to_tessellated_mesh.exe + ${CMAKE_CURRENT_SOURCE_DIR}/curved_wall_input.vtk + ${CMAKE_CURRENT_SOURCE_DIR}/curved_wall_input.igs + test_output.vtk) +add_test(NAME CompareCurvedWall COMMAND + ${CMAKE_COMMAND} -E compare_files + test_output.vtk ${CMAKE_CURRENT_SOURCE_DIR}/curved_wall_output.vtk) + +add_test(NAME RunCurvedWallNoZFaces COMMAND + snap_to_tessellated_mesh.exe + ${CMAKE_CURRENT_SOURCE_DIR}/curved_wall_input.vtk + ${CMAKE_CURRENT_SOURCE_DIR}/curved_wall_input.igs + test_output_z.vtk + 1) +add_test(NAME CompareCurvedWallNoZFaces COMMAND + ${CMAKE_COMMAND} -E compare_files + test_output_z.vtk ${CMAKE_CURRENT_SOURCE_DIR}/curved_wall_output_z.vtk) diff --git a/snap_tessellated_mesh/tests/curved_wall_input.igs b/snap_tessellated_mesh/tests/curved_wall_input.igs new file mode 100644 index 0000000..1f1655f --- /dev/null +++ b/snap_tessellated_mesh/tests/curved_wall_input.igs @@ -0,0 +1,419 @@ +SolidWorks IGES file using analytic representation for surfaces S 1 +1H,,1H;,19HCurved Wall - Solid,43HC:\Users\4q4\Downloads\CurvedWall_TakeG 1 +2.IGS,15HSolidWorks 2023,15HSolidWorks 2023,32,308,15,308,15,19HCurved WG 2 +all - Solid,1.,10,2HCM,50,0.125,13H240405.114830,1E-08,49999.,3H4q4,, G 3 +11,0,13H240405.114830; G 4 + 314 1 0 0 0 00000200D 1 + 314 0 8 1 0 0D 2 + 110 2 0 0 0 01010000D 3 + 110 0 0 2 0 0D 4 + 110 4 0 0 0 01010000D 5 + 110 0 0 2 0 0D 6 + 120 6 0 0 0 01010000D 7 + 120 0 0 1 0 0D 8 + 126 7 0 0 0 01010500D 9 + 126 0 0 2 0 0D 10 + 100 9 0 0 0 01010000D 11 + 100 0 0 2 0 0D 12 + 126 11 0 0 0 01010500D 13 + 126 0 0 2 0 0D 14 + 110 13 0 0 0 01010000D 15 + 110 0 0 2 0 0D 16 + 126 15 0 0 0 01010500D 17 + 126 0 0 2 0 0D 18 + 124 17 0 0 0 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143P 172 +144,119,1,0,143; 145P 173 +128,1,1,1,1,0,0,1,0,0,0.,0.,1.,1.,0.,0.,1.,1.,1.,1.,1.,1., 147P 174 +-69.414320346,-4.002457456,0.,67.187674715,-4.002457456,0., 147P 175 +-69.414320346,28.60973671,0.,67.187674715,28.60973671,0.,0.,1., 147P 176 +0.,1.; 147P 177 +126,1,1,1,0,1,0,0.,0.,1.,1.,1.,1.,0.005928854,0.240821205,0., 149P 178 +0.052984545,0.005930056,0.,0.,1.,0.,0.,1.; 149P 179 +110,-68.604427095,3.851250437,0.,-62.176525851,-3.809065325,0.; 151P 180 +126,32,2,1,0,1,0,0.,0.,0.,0.0625,0.0625,0.125,0.125,0.1875, 153P 181 +0.1875,0.25,0.25,0.3125,0.3125,0.375,0.375,0.4375,0.4375,0.5, 153P 182 +0.5,0.5625,0.5625,0.625,0.625,0.6875,0.6875,0.75,0.75,0.8125, 153P 183 +0.8125,0.875,0.875,0.9375,0.9375,1.,1.,1.,1.,1.,1.,1.,1.,1.,1., 153P 184 +1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1., 153P 185 +1.,1.,1.,1.,1.,0.052984545,0.005930056,0.,0.076243997, 153P 186 +0.087682179,0.,0.101116018,0.160631806,0.,0.125988038, 153P 187 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