Merge branch 'trm-bentonite-tests-prep' into 'master'

Preparations to add tests of a bentonite material model to OGS See merge request ogs/ogs!5063
ufz · Aug 22, 2024 · d6bb24a · d6bb24a
2 parents 24d62b4 + a9635ea
commit d6bb24a
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Showing 23 changed files with 118 additions and 91 deletions.
diff --git a/Applications/ApplicationsLib/ProjectData.cpp b/Applications/ApplicationsLib/ProjectData.cpp
@@ -157,11 +157,11 @@ void readGeometry(std::string const& fname, GeoLib::GEOObjects& geo_objects,
 {
     DBUG("Reading geometry file '{:s}'.", fname);
     GeoLib::IO::BoostXmlGmlInterface gml_reader(geo_objects);
-    std::string geometry_file = BaseLib::copyPathToFileName(fname, dir_first);
+    std::string geometry_file = BaseLib::joinPaths(dir_first, fname);
     if (!BaseLib::IsFileExisting(geometry_file))
     {
         // Fallback to reading gml from prj-file directory
-        geometry_file = BaseLib::copyPathToFileName(fname, dir_second);
+        geometry_file = BaseLib::joinPaths(dir_second, fname);
         WARN("File {:s} not found in {:s}! Trying reading from {:s}.", fname,
              dir_first, dir_second);
         if (!BaseLib::IsFileExisting(geometry_file))
@@ -177,16 +177,27 @@ std::unique_ptr<MeshLib::Mesh> readSingleMesh(
     BaseLib::ConfigTree const& mesh_config_parameter,
     std::string const& directory)
 {
-    std::string const mesh_file = BaseLib::copyPathToFileName(
-        mesh_config_parameter.getValue<std::string>(), directory);
+    std::string const mesh_file = BaseLib::joinPaths(
+        directory, mesh_config_parameter.getValue<std::string>());
     DBUG("Reading mesh file '{:s}'.", mesh_file);
 
     auto mesh = std::unique_ptr<MeshLib::Mesh>(MeshLib::IO::readMeshFromFile(
         mesh_file, true /* compute_element_neighbors */));
     if (!mesh)
     {
+        std::filesystem::path abspath{mesh_file};
+        try
+        {
+            abspath = std::filesystem::absolute(mesh_file);
+        }
+        catch (std::filesystem::filesystem_error const& e)
+        {
+            ERR("Determining the absolute path of '{}' failed: {}", mesh_file,
+                e.what());
+        }
+
         OGS_FATAL("Could not read mesh from '{:s}' file. No mesh added.",
-                  mesh_file);
+                  abspath.string());
     }
 
 #ifdef DOXYGEN_DOCU_ONLY
@@ -369,7 +380,7 @@ ProjectData::ProjectData(BaseLib::ConfigTree const& project_config,
         py_path.attr("append")(script_directory);  // .prj or -s directory
 
         auto const script_path =
-            BaseLib::copyPathToFileName(*python_script, script_directory);
+            BaseLib::joinPaths(script_directory, *python_script);
 
         // Evaluate in scope of main module
         py::object scope = py::module::import("__main__").attr("__dict__");

diff --git a/BaseLib/FileTools.cpp b/BaseLib/FileTools.cpp
@@ -200,17 +200,6 @@ bool hasFileExtension(std::string const& extension, std::string const& filename)
     return boost::iequals(extension, getFileExtension(filename));
 }
 
-std::string copyPathToFileName(const std::string& file_name,
-                               const std::string& source)
-{
-    auto filePath = std::filesystem::path(file_name);
-    if (filePath.has_parent_path())
-    {
-        return filePath.string();
-    }
-    return (std::filesystem::path(source) /= filePath).string();
-}
-
 std::string extractPath(std::string const& pathname)
 {
     return std::filesystem::path(pathname).parent_path().string();

diff --git a/BaseLib/FileTools.h b/BaseLib/FileTools.h
@@ -120,13 +120,6 @@ std::string getFileExtension(std::string const& path);
 bool hasFileExtension(std::string const& extension,
                       std::string const& filename);
 
-/**
- * Checks if file_name already contains a qualified path and if not copies the
- * path from source.
- */
-std::string copyPathToFileName(const std::string& file_name,
-                               const std::string& source);
-
 /** Returns a string with file extension as found by getFileExtension()
  * dropped.
  */

diff --git a/...al/solid/constitutive_relation/MFront/library/a_path_is_relative_to_prj_file.md b/...al/solid/constitutive_relation/MFront/library/a_path_is_relative_to_prj_file.md
@@ -0,0 +1,5 @@
+This setting modifies where the shared library containing the MFront behaviour will be looked for.
+
+The default setting of `true` should work for almost all use cases. `false` is used for some special tests in OGS's test suite.
+
+See also the documentation of the \ref ogs_file_param__material__solid__constitutive_relation__MFront__library "<code>&lt;library&gt;</code>" tag.
diff --git a/...on/ProjectFile/material/solid/constitutive_relation/MFront/library/i_library.md b/...on/ProjectFile/material/solid/constitutive_relation/MFront/library/i_library.md
@@ -0,0 +1,3 @@
+Path of the shared library containing the material model.
+
+Relative paths are interpreted relative to the project directory unless \ref ogs_file_attr__material__solid__constitutive_relation__MFront__library__path_is_relative_to_prj_file "<code>path_is_relative_to_prj_file</code>" is set to `false`, in which case the library path/name is used verbatim and will be searched based on the operating system's library lookup rules.
diff --git a/Documentation/ProjectFile/material/solid/constitutive_relation/MFront/t_library.md b/Documentation/ProjectFile/material/solid/constitutive_relation/MFront/t_library.md
diff --git a/GeoLib/IO/XmlIO/Qt/XmlStnInterface.cpp b/GeoLib/IO/XmlIO/Qt/XmlStnInterface.cpp
@@ -149,8 +149,8 @@ void XmlStnInterface::readStations(const QDomNode& stationsRoot,
                 s->setStationValue(stationValue);
                 if (!sensor_data_file_name.empty())
                 {
-                    s->addSensorDataFromCSV(BaseLib::copyPathToFileName(
-                        sensor_data_file_name, station_file_name));
+                    s->addSensorDataFromCSV(BaseLib::joinPaths(
+                        station_file_name, sensor_data_file_name));
                 }
                 stations.push_back(s);
             }

diff --git a/MaterialLib/SolidModels/MFront/CreateMFront.cpp b/MaterialLib/SolidModels/MFront/CreateMFront.cpp
@@ -29,9 +29,7 @@ std::unique_ptr<MechanicsBase<DisplacementDim>> createMFront(
         local_coordinate_system,
     BaseLib::ConfigTree const& config)
 {
-    bool const library_path_is_relative_to_prj_file = true;
-    auto conf = createMFrontConfig(DisplacementDim, parameters, config,
-                                   library_path_is_relative_to_prj_file);
+    auto conf = createMFrontConfig(DisplacementDim, parameters, config);
 
     return std::make_unique<MFront<DisplacementDim>>(
         std::move(conf.behaviour), std::move(conf.material_properties),

diff --git a/MaterialLib/SolidModels/MFront/CreateMFrontGeneric.cpp b/MaterialLib/SolidModels/MFront/CreateMFrontGeneric.cpp
@@ -324,23 +324,31 @@ namespace MaterialLib::Solids::MFront
 MFrontConfig createMFrontConfig(
     int const displacement_dim,
     std::vector<std::unique_ptr<ParameterLib::ParameterBase>> const& parameters,
-    BaseLib::ConfigTree const& config,
-    bool const library_path_is_relative_to_prj_file)
+    BaseLib::ConfigTree const& config)
 {
     INFO("### MFRONT ########################################################");
 
     //! \ogs_file_param{material__solid__constitutive_relation__type}
     config.checkConfigParameter("type", "MFront");
 
-    auto const library_name =
-        //! \ogs_file_param{material__solid__constitutive_relation__MFront__library}
-        config.getConfigParameterOptional<std::string>("library");
+    //! \ogs_file_param{material__solid__constitutive_relation__MFront__library}
+    auto const library = config.getConfigSubtreeOptional("library");
+
+    bool const library_path_is_relative_to_prj_file =
+        library /* If no library tag is specified in the prj file, the lib
+                   shipped with OGS is used, whose path is not relative to the
+                   project file. */
+        &&
+        //! \ogs_file_attr{material__solid__constitutive_relation__MFront__library__path_is_relative_to_prj_file}
+        library->getConfigAttribute("path_is_relative_to_prj_file", true);
+
+    std::string const library_name =
+        library ? library->getValue<std::string>() : "libOgsMFrontBehaviour";
+
     auto const lib_path =
-        library_name ? (library_path_is_relative_to_prj_file
-                            ? BaseLib::joinPaths(BaseLib::getProjectDirectory(),
-                                                 *library_name)
-                            : *library_name)
-                     : "libOgsMFrontBehaviour";
+        library_path_is_relative_to_prj_file
+            ? BaseLib::joinPaths(BaseLib::getProjectDirectory(), library_name)
+            : library_name;
 
     mgis::behaviour::Hypothesis hypothesis;
     if (displacement_dim == 2)

diff --git a/MaterialLib/SolidModels/MFront/CreateMFrontGeneric.h b/MaterialLib/SolidModels/MFront/CreateMFrontGeneric.h
@@ -26,8 +26,7 @@ struct MFrontConfig
 MFrontConfig createMFrontConfig(
     int const displacement_dim,
     std::vector<std::unique_ptr<ParameterLib::ParameterBase>> const& parameters,
-    BaseLib::ConfigTree const& config,
-    bool const library_path_is_relative_to_prj_file);
+    BaseLib::ConfigTree const& config);
 
 template <int DisplacementDim, typename Gradients, typename TDynForces,
           typename ExtStateVars>
@@ -37,11 +36,9 @@ createMFrontGeneric(
     std::vector<std::unique_ptr<ParameterLib::ParameterBase>> const& parameters,
     std::optional<ParameterLib::CoordinateSystem> const&
         local_coordinate_system,
-    BaseLib::ConfigTree const& config,
-    bool const library_path_is_relative_to_prj_file)
+    BaseLib::ConfigTree const& config)
 {
-    auto conf = createMFrontConfig(DisplacementDim, parameters, config,
-                                   library_path_is_relative_to_prj_file);
+    auto conf = createMFrontConfig(DisplacementDim, parameters, config);
 
     return std::make_unique<
         MFrontGeneric<DisplacementDim, Gradients, TDynForces, ExtStateVars>>(

diff --git a/MeshLib/IO/readMeshFromFile.cpp b/MeshLib/IO/readMeshFromFile.cpp
@@ -85,6 +85,12 @@ MeshLib::Mesh* readMeshFromFile(const std::string& file_name,
         {
             std::unique_ptr<Mesh> mesh{
                 readMeshFromFileSerial(file_name, compute_element_neighbors)};
+
+            if (!mesh)
+            {
+                return nullptr;
+            }
+
             return new MeshLib::NodePartitionedMesh(*mesh);
         }
         return nullptr;

diff --git a/ProcessLib/HeatConduction/Tests.cmake b/ProcessLib/HeatConduction/Tests.cmake
@@ -452,6 +452,15 @@ AddTest(
     line_1_line_1e2_ts_500_t_39062500.000000_reference.vtu line_1_line_1e2_ts_500_t_39062500.000000.vtu temperature temperature 1e-10 0.0
 )
 
+# failing test - mesh not found
+AddTest(
+    NAME 1D_HeatConduction_dirichlet_SourceTerm_fail_mesh_not_found
+    PATH Parabolic/T/1D_dirichlet_source-term
+    EXECUTABLE ogs
+    EXECUTABLE_ARGS line_1_line_1e2_source_term_fail_mesh_not_found.xml
+    PROPERTIES PASS_REGULAR_EXPRESSION "Could not read mesh from '.*' file[.] No mesh added[.]"
+)
+
 AddTest(
         NAME HeatConduction_t1_1Dsource
         PATH Parabolic/T/t1_1Dsource

diff --git a/ProcessLib/LargeDeformation/ConstitutiveRelations/CreateConstitutiveSetting.cpp b/ProcessLib/LargeDeformation/ConstitutiveRelations/CreateConstitutiveSetting.cpp
@@ -26,13 +26,10 @@ std::unique_ptr<SolidConstitutiveRelation<DisplacementDim>> createMFrontGeneric(
     namespace MSM = MaterialLib::Solids::MFront;
     using namespace boost::mp11;
 
-    bool const library_path_is_relative_to_prj_file = true;
-
     return MSM::createMFrontGeneric<
         DisplacementDim, mp_list<MSM::DeformationGradient>,
         mp_list<MSM::SecondPiolaKirchhoffStress>, mp_list<MSM::Temperature>>(
-        parameters, local_coordinate_system, config,
-        library_path_is_relative_to_prj_file);
+        parameters, local_coordinate_system, config);
 }
 
 template <int DisplacementDim>

diff --git a/...nics/ConstitutiveStressSaturation_StrainPressureTemperature/CreateConstitutiveSetting.cpp b/...nics/ConstitutiveStressSaturation_StrainPressureTemperature/CreateConstitutiveSetting.cpp
@@ -27,13 +27,10 @@ std::unique_ptr<SolidConstitutiveRelation<DisplacementDim>> createMFrontGeneric(
     namespace MSM = MaterialLib::Solids::MFront;
     using namespace boost::mp11;
 
-    bool const library_path_is_relative_to_prj_file = true;
-
     return MSM::createMFrontGeneric<
         DisplacementDim, mp_list<MSM::Strain, MSM::LiquidPressure>,
         mp_list<MSM::Stress, MSM::Saturation>, mp_list<MSM::Temperature>>(
-        parameters, local_coordinate_system, config,
-        library_path_is_relative_to_prj_file);
+        parameters, local_coordinate_system, config);
 }
 
 template <int DisplacementDim>

diff --git a/Tests/BaseLib/TestFilePathStringManipulation.cpp b/Tests/BaseLib/TestFilePathStringManipulation.cpp
@@ -13,30 +13,27 @@
 #include "BaseLib/FileTools.h"
 
 #ifdef WIN32
-TEST(BaseLib, CopyPathToFileNameWin)
+TEST(BaseLib, JoinPathsWin)
 {
-    ASSERT_EQ("extend\\file", BaseLib::copyPathToFileName("file", "extend"));
-    ASSERT_EQ("path\\file",
-              BaseLib::copyPathToFileName("path\\file", "extend"));
-    ASSERT_EQ("extend\\file", BaseLib::copyPathToFileName("file", "extend\\"));
-    ASSERT_EQ("path\\file",
-              BaseLib::copyPathToFileName("path\\file", "extend\\"));
-    ASSERT_EQ("extend\\smth\\file",
-              BaseLib::copyPathToFileName("file", "extend\\smth"));
-    ASSERT_EQ("path\\file",
-              BaseLib::copyPathToFileName("path\\file", "extend\\smth"));
+    ASSERT_EQ("extend\\file", BaseLib::joinPaths("extend", "file"));
+    ASSERT_EQ("extend\\path\\file", BaseLib::joinPaths("extend", "path\\file"));
+    ASSERT_EQ("extend\\file", BaseLib::joinPaths("extend\\", "file"));
+    ASSERT_EQ("extend\\path\\file",
+              BaseLib::joinPaths("extend\\", "path\\file"));
+    ASSERT_EQ("extend\\smth\\file", BaseLib::joinPaths("extend\\smth", "file"));
+    ASSERT_EQ("extend\\smth\\path\\file",
+              BaseLib::joinPaths("extend\\smth", "path\\file"));
 }
 #else
-TEST(BaseLib, CopyPathToFileNameUnix)
+TEST(BaseLib, JoinPathsUnix)
 {
-    ASSERT_EQ("extend/file", BaseLib::copyPathToFileName("file", "extend"));
-    ASSERT_EQ("path/file", BaseLib::copyPathToFileName("path/file", "extend"));
-    ASSERT_EQ("extend/file", BaseLib::copyPathToFileName("file", "extend/"));
-    ASSERT_EQ("path/file", BaseLib::copyPathToFileName("path/file", "extend/"));
+    ASSERT_EQ("extend/file", BaseLib::joinPaths("extend", "file"));
+    ASSERT_EQ("extend/path/file", BaseLib::joinPaths("extend", "path/file"));
+    ASSERT_EQ("extend/file", BaseLib::joinPaths("extend/", "file"));
+    ASSERT_EQ("extend/path/file", BaseLib::joinPaths("extend/", "path/file"));
 
-    ASSERT_EQ("extend/smth/file",
-              BaseLib::copyPathToFileName("file", "extend/smth"));
-    ASSERT_EQ("path/file",
-              BaseLib::copyPathToFileName("path/file", "extend/smth"));
+    ASSERT_EQ("extend/smth/file", BaseLib::joinPaths("extend/smth", "file"));
+    ASSERT_EQ("extend/smth/path/file",
+              BaseLib::joinPaths("extend/smth", "path/file"));
 }
 #endif
diff --git a/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb b/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb
@@ -171,7 +171,9 @@
     ")\n",
     "try:\n",
     "    model.write_input()\n",
-    "    model.run_model(logfile=(out_dir / f\"{prj_name}.txt\"), args=f\"-o {out_dir}\")\n",
+    "    model.run_model(\n",
+    "        logfile=(out_dir / f\"{prj_name}-out.txt\"), args=f\"-o {out_dir} -m .\"\n",
+    "    )\n",
     "except Exception as inst:\n",
     "    print(f\"{type(inst)}: {inst.args[0]}\")\n",
     "\n",

diff --git a/.../Parabolic/T/1D_dirichlet_source-term/line_1_line_1e2_source_term_fail_mesh_not_found.xml b/.../Parabolic/T/1D_dirichlet_source-term/line_1_line_1e2_source_term_fail_mesh_not_found.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<OpenGeoSysProjectDiff base_file="line_1_line_1e2_source_term.prj">
+    <replace msel="/*/meshes/mesh[1]/text()">
+        NON_EXISTENT_MESH.vtu
+    </replace>
+</OpenGeoSysProjectDiff>
+
diff --git a/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.ipynb b/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.ipynb
@@ -67,8 +67,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data_dir = os.environ.get(\"OGS_DATA_DIR\", \"../../..\")\n",
-    "\n",
     "from pathlib import Path\n",
     "\n",
     "out_dir = Path(os.environ.get(\"OGS_TESTRUNNER_OUT_DIR\", \"_out\"))\n",
@@ -147,7 +145,9 @@
     "    print(\n",
     "        f\"> Running single edge notched shear test {phasefield_model} - {energy_split_model} ... <\"\n",
     "    )\n",
-    "    logfile = f\"{out_dir}/log_{phasefield_model}_{energy_split_model}.txt\"  # noqa: F841\n",
+    "    # fmt: off\n",
+    "    logfile = f\"{out_dir}/log_{phasefield_model}_{energy_split_model}_out.txt\"  # noqa: F841\n",
+    "    # fmt: on\n",
     "    model = ogs.OGS(INPUT_FILE=prj_name, PROJECT_FILE=f\"{out_dir}/{prj_name}\", MKL=True)\n",
     "\n",
     "    # generate prefix from properties\n",
@@ -201,16 +201,18 @@
     "            xpath=\"./linear_solvers/linear_solver/petsc/parameters\",\n",
     "            occurrence=1,\n",
     "        )\n",
-    "    model.replace_text(\"./shear.gml\", xpath=\"./geometry\")\n",
+    "    model.replace_text(Path(\"./shear.gml\").resolve(), xpath=\"./geometry\")\n",
     "    model.write_input()\n",
     "    # run ogs\n",
     "    t0 = time.time()\n",
     "    if MPI:\n",
     "        print(f\"  > OGS started execution with MPI - {ncores} cores...\")\n",
     "        ! mpirun --bind-to none -np {ncores} ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}\n",
+    "        assert _exit_code == 0  # noqa: F821\n",
     "    else:\n",
     "        print(\"  > OGS started execution - \")\n",
     "        ! ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}\n",
+    "        assert _exit_code == 0  # noqa: F821\n",
     "    tf = time.time()\n",
     "    print(\"  > OGS terminated execution. Elapsed time: \", round(tf - t0, 2), \" s.\")"
    ]

diff --git a/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.ipynb b/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.ipynb
@@ -317,14 +317,19 @@
     "        MKL=True,\n",
     "        args=f\"-o {out_dir}\",\n",
     "    )\n",
+    "\n",
+    "    gml_file = Path(\"./Kregime_Static.gml\").resolve()\n",
+    "\n",
     "    model.replace_parameter_value(name=\"ls\", value=ls)\n",
-    "    model.replace_text(\"./Kregime_Static.gml\", xpath=\"./geometry\")\n",
+    "    model.replace_text(gml_file, xpath=\"./geometry\")\n",
     "    model.replace_text(filename, xpath=\"./time_loop/output/prefix\")\n",
     "    model.write_input()\n",
     "    # run simulation with ogs\n",
     "    t0 = time.time()\n",
     "    print(\">>> OGS started execution ... <<<\")\n",
-    "    !ogs {out_dir}/{prj_name} -o {out_dir} > {out_dir}/log.txt\n",
+    "\n",
+    "    !ogs {out_dir}/{prj_name} -o {out_dir} -m {out_dir} > {out_dir}/ogs-out.txt\n",
+    "    assert _exit_code == 0  # noqa: F821\n",
     "    tf = time.time()\n",
     "    print(\">>> OGS terminated execution  <<< Elapsed time: \", round(tf - t0, 2), \" s.\")"
    ]