Merge pull request #2144 from endJunction/ConvertGeometriesToMeshesUtility

[A/U] Add CLI to construct meshes from geometries.

Applications/Utils/MeshGeoTools/CMakeLists.txt

-ADD_EXECUTABLE( ComputeSurfaceNodeIDsInPolygonalRegion ComputeSurfaceNodeIDsInPolygonalRegion.cpp )
-SET_TARGET_PROPERTIES( ComputeSurfaceNodeIDsInPolygonalRegion PROPERTIES FOLDER Utilities)
-TARGET_LINK_LIBRARIES( ComputeSurfaceNodeIDsInPolygonalRegion
+add_executable( ComputeSurfaceNodeIDsInPolygonalRegion ComputeSurfaceNodeIDsInPolygonalRegion.cpp )
+set_target_properties( ComputeSurfaceNodeIDsInPolygonalRegion PROPERTIES FOLDER Utilities)
+target_link_libraries( ComputeSurfaceNodeIDsInPolygonalRegion
     MeshLib
     GeoLib
     MathLib
@@ -8,3 +8,10 @@ TARGET_LINK_LIBRARIES( ComputeSurfaceNodeIDsInPolygonalRegion
     ${OGS_VTK_REQUIRED_LIBS}
 )
 
+add_executable(constructMeshesFromGeometry ConstructMeshesFromGeometry.cpp )
+set_target_properties(constructMeshesFromGeometry PROPERTIES FOLDER Utilities)
+target_link_libraries(constructMeshesFromGeometry
+    MeshGeoToolsLib
+    ApplicationsFileIO
+    ${OGS_VTK_REQUIRED_LIBS}
+)

Applications/Utils/MeshGeoTools/ConstructMeshesFromGeometry.cpp

+/**
+ * \copyright
+ * Copyright (c) 2012-2018, OpenGeoSys Community (http://www.opengeosys.org)
+ *            Distributed under a Modified BSD License.
+ *              See accompanying file LICENSE.txt or
+ *              http://www.opengeosys.org/project/license
+ *
+ */
+
+#include <tclap/CmdLine.h>
+
+#include "Applications/ApplicationsLib/LogogSetup.h"
+#include "GeoLib/GEOObjects.h"
+#include "GeoLib/IO/XmlIO/Boost/BoostXmlGmlInterface.h"
+#include "MeshGeoToolsLib/ConstructMeshesFromGeometries.h"
+#include "MeshGeoToolsLib/SearchLength.h"
+#include "MeshLib/IO/readMeshFromFile.h"
+#include "MeshLib/IO/writeMeshToFile.h"
+#include "MeshLib/Mesh.h"
+
+std::unique_ptr<GeoLib::GEOObjects> readGeometry(std::string const& filename)
+{
+    auto geo_objects = std::make_unique<GeoLib::GEOObjects>();
+    GeoLib::IO::BoostXmlGmlInterface gml_reader(*geo_objects);
+
+    DBUG("Reading geometry file \'%s\'.", filename.c_str());
+    gml_reader.readFile(filename);
+    return geo_objects;
+}
+
+int main(int argc, char* argv[])
+{
+    ApplicationsLib::LogogSetup logo_setup;
+
+    TCLAP::CmdLine cmd(
+        "Converts a geometry defined on a given mesh to distinct meshes.",
+        ' ',
+        "0.1");
+
+    TCLAP::ValueArg<std::string> geometry_arg("g",
+                                              "geometry",
+                                              "the file name the geometry",
+                                              true,
+                                              "",
+                                              "geometry file name");
+    cmd.add(geometry_arg);
+
+    TCLAP::ValueArg<std::string> mesh_arg(
+        "m",
+        "mesh",
+        "the file name of the mesh where the geometry is defined",
+        true,
+        "",
+        "mesh file name");
+    cmd.add(mesh_arg);
+    cmd.parse(argc, argv);
+
+    std::unique_ptr<MeshLib::Mesh> mesh{
+        MeshLib::IO::readMeshFromFile(mesh_arg.getValue())};
+
+    auto const geo_objects = readGeometry(geometry_arg.getValue());
+
+    auto const extracted_meshes = constructAdditionalMeshesFromGeoObjects(
+        *geo_objects, *mesh, std::make_unique<MeshGeoToolsLib::SearchLength>());
+
+    for (auto const& m_ptr : extracted_meshes)
+    {
+        MeshLib::IO::writeMeshToFile(*m_ptr, m_ptr->getName() + ".vtu");
+    }
+
+    return EXIT_SUCCESS;
+}

netlify.toml

@@ -2,9 +2,13 @@
 [build]
   base    = "web"
   publish = "web/public"
-  command = "git lfs fetch && yarn --ignore-engines --ignore-optional --non-interactive && yarn prod"
+  command = """
+    git lfs fetch
+    yarn --ignore-engines --ignore-optional --non-interactive &&
+    node_modules/.bin/webpack -p --mode=production &&
+    hugo -b $DEPLOY_PRIME_URL"""
 
 [context.production.environment]
-  HUGO_VERSION = "0.41"
+  HUGO_VERSION = "0.42.1"
 [context.deploy-preview.environment]
-  HUGO_VERSION = "0.41"
+  HUGO_VERSION = "0.42.1"

web/config.toml

@@ -3,6 +3,7 @@ title = "OpenGeoSys"
 theme = "ogs"
 baseURL = "https://www.opengeosys.org"
 buildDrafts = false
+buildFuture = true
 pygmentsstyle = 'friendly'
 enableGitInfo = true
 canonifyURLs = true

web/content/docs/tools/model-preparation/constructMeshesFromGeometry/index.pandoc

++++
+date = "2018-06-19T15:56:57+01:00"
+title = "Construct meshes from bulk mesh and geometries"
+author = "Dmitri Naumov"
+
+[menu]
+  [menu.tools]
+    parent = "model-preparation"
++++
+
+## General
+
+`constructMeshesFromGeometry` is a conversion tool for the `gml` files.  Given a
+"bulk" mesh and the `gml` geometry file the tool generates meshes for all named
+geometries.
+
+The meshes are used for the boundary conditions and provide node ids and element
+ids mappings to the bulk mesh.
+
+## Example
+
+For example a conversion of a mesh from `Tests/Data/LIE/Hydromechanics` single
+fracture 3D project:
+```
+constructMeshesFromGeometry -m single_fracture_3D.vtu -g single_fracture_3D.gml
+
+debug: Reading geometry file '../s/Tests/Data/LIE/HydroMechanics/single_fracture_3D.gml'.
+debug: Project configuration from file '../s/Tests/Data/LIE/HydroMechanics/single_fracture_3D.gml' read.
+debug: The search length for mesh "single_fracture_3D" is 1.000000e-09.
+debug: Creating mesh from geometry single_fracture_3D inlet.
+debug: Found 3 elements in the mesh
+debug: Creating mesh from geometry single_fracture_3D outlet.
+debug: Found 3 elements in the mesh
+debug: Creating mesh from geometry single_fracture_3D left.
+debug: Found 46 elements in the mesh
+debug: Creating mesh from geometry single_fracture_3D right.
+debug: Found 46 elements in the mesh
+debug: Creating mesh from geometry single_fracture_3D front.
+debug: Found 1150 elements in the mesh
+debug: Creating mesh from geometry single_fracture_3D back.
+debug: Found 1150 elements in the mesh
+debug: Creating mesh from geometry single_fracture_3D bottom.
+debug: Found 25 elements in the mesh
+debug: Creating mesh from geometry single_fracture_3D top.
+debug: Found 25 elements in the mesh
+```
+yields new meshes for each named geometry: `single_fracture_3D_inlet.vtu`,
+`single_fracture_3D_right.vtu`, `single_fracture_3D_outlet.vtu`,
+`single_fracture_3D_left.vtu`, `single_fracture_3D_front.vtu`,
+`single_fracture_3D_top.vtu`, `single_fracture_3D_bottom.vtu`, and
+`single_fracture_3D_back.vtu`.
+
+![](single_fracture_3D_geometries.png)
+The figure shows the front part of the mesh with the extracted geometries. Note,
+the lower dimensional inlet boundary, shown as a line.