CreateBoundaryConditionsAlongPolylines.cpp

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/*
 * \file
 * \date 2014-09-30
 * \brief Create BoundaryConditions from a polylines.
 *
 * \copyright
 * Copyright (c) 2012-2024, 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>
 
#ifdef USE_PETSC
#include <mpi.h>
#endif
 
#include <fstream>
#include <map>
#include <string>
#include <vector>
 
#include "Applications/FileIO/readGeometryFromFile.h"
#include "Applications/FileIO/writeGeometryToFile.h"
#include "BaseLib/FileTools.h"
#include "GeoLib/GEOObjects.h"
#include "GeoLib/Point.h"
#include "InfoLib/GitInfo.h"
#include "MeshGeoToolsLib/MeshNodeSearcher.h"
#include "MeshLib/IO/readMeshFromFile.h"
#include "MeshLib/IO/writeMeshToFile.h"
#include "MeshLib/Mesh.h"
#include "MeshLib/Node.h"
#include "MeshToolsLib/MeshSurfaceExtraction.h"
 
void convertMeshNodesToGeometry(std::vector<MeshLib::Node*> const& nodes,
                                std::vector<std::size_t> const& node_ids,
                                std::string& geo_name,
                                GeoLib::GEOObjects& geometry_sets)
{
    // copy data
    std::vector<GeoLib::Point*> pnts;
    GeoLib::PointVec::NameIdMap pnt_names;
    std::size_t cnt(0);
    for (std::size_t id : node_ids)
    {
        pnts.push_back(new GeoLib::Point(*(nodes[id]), cnt));
        pnt_names[geo_name + "-PNT-" + std::to_string(cnt)] = cnt;
        cnt++;
    }
 
    // create data structures for geometry
    geometry_sets.addPointVec(std::move(pnts), geo_name, std::move(pnt_names));
}
 
void writeGroundwaterFlowPointBC(std::ostream& bc_out,
                                 std::string const& pnt_name, double head_value)
{
    bc_out << "#BOUNDARY_CONDITION\n";
    bc_out << "  $PCS_TYPE\n";
    bc_out << "    GROUNDWATER_FLOW\n";
    bc_out << "  $PRIMARY_VARIABLE\n";
    bc_out << "    HEAD\n";
    bc_out << "  $GEO_TYPE\n";
    bc_out << "    POINT " << pnt_name << "\n";
    bc_out << "  $DIS_TYPE\n";
    bc_out << "    CONSTANT " << head_value << "\n";
}
 
void writeLiquidFlowPointBC(std::ostream& bc_out, std::string const& pnt_name)
{
    bc_out << "#BOUNDARY_CONDITION\n";
    bc_out << "  $PCS_TYPE\n";
    bc_out << "    LIQUID_FLOW\n";
    bc_out << "  $PRIMARY_VARIABLE\n";
    bc_out << "    PRESSURE1\n";
    bc_out << "  $GEO_TYPE\n";
    bc_out << "    POINT " << pnt_name << "\n";
    bc_out << "  $DIS_TYPE\n";
    bc_out << "    CONSTANT 0.0\n";
}
 
// geometry_sets contains the geometric points the boundary conditions will be
// set on, geo_name is the name the geometry can be accessed with, out_fname is
// the base file name the gli and bc as well as the gml file will be written to.
void writeBCsAndGeometry(GeoLib::GEOObjects& geometry_sets,
                         std::string const& geo_name,
                         std::string const& out_fname,
                         std::string const& bc_type, bool const write_gml)
{
    if (write_gml)
    {
        INFO("write points to '{:s}.gml'.", geo_name);
        FileIO::writeGeometryToFile(geo_name, geometry_sets,
                                    out_fname + ".gml");
    }
    FileIO::writeGeometryToFile(geo_name, geometry_sets, out_fname + ".gli");
 
    bool liquid_flow(false);
    if (bc_type == "LIQUID_FLOW")
    {
        liquid_flow = true;
    }
 
    GeoLib::PointVec const* pnt_vec_objs(
        geometry_sets.getPointVecObj(geo_name));
    auto const& pnts(pnt_vec_objs->getVector());
    std::ofstream bc_out(out_fname + ".bc");
    for (std::size_t k(0); k < pnts.size(); k++)
    {
        std::string const& pnt_name(pnt_vec_objs->getItemNameByID(k));
        if (!pnt_name.empty())
        {
            if (liquid_flow)
            {
                writeLiquidFlowPointBC(bc_out, pnt_name);
            }
            else
            {
                writeGroundwaterFlowPointBC(bc_out, pnt_name, (*pnts[k])[2]);
            }
        }
    }
    bc_out << "#STOP\n";
    bc_out.close();
}
 
int main(int argc, char* argv[])
{
    TCLAP::CmdLine cmd(
        "Creates boundary conditions for mesh nodes along polylines."
        "The documentation is available at "
        "https://docs.opengeosys.org/docs/tools/model-preparation/"
        "create-boundary-conditions-along-a-polyline.\n\n"
        "OpenGeoSys-6 software, version " +
            GitInfoLib::GitInfo::ogs_version +
            ".\n"
            "Copyright (c) 2012-2024, OpenGeoSys Community "
            "(http://www.opengeosys.org)",
        ' ', GitInfoLib::GitInfo::ogs_version);
    TCLAP::SwitchArg gml_arg("", "gml", "Write found nodes to gml file.");
    cmd.add(gml_arg);
 
    TCLAP::ValueArg<std::string> output_base_fname(
        "o", "output-base-file-name",
        "the base name of the file the output (geometry (gli) and boundary "
        "condition (bc)) will be written to",
        true, "", "file name");
    cmd.add(output_base_fname);
 
    TCLAP::ValueArg<std::string> bc_type(
        "t", "type",
        "the process type the boundary condition will be written for currently "
        "LIQUID_FLOW (primary variable PRESSURE1) and GROUNDWATER_FLOW "
        "(primary variable HEAD, default) are supported",
        true, "",
        "process type as string (LIQUID_FLOW or GROUNDWATER_FLOW (default))");
    cmd.add(bc_type);
 
    TCLAP::ValueArg<double> search_length_arg(
        "s", "search-length",
        "The size of the search length. The default value is "
        "std::numeric_limits<double>::epsilon()",
        false, std::numeric_limits<double>::epsilon(), "floating point number");
    cmd.add(search_length_arg);
 
    TCLAP::ValueArg<std::string> geometry_fname(
        "i", "input-geometry",
        "the name of the file containing the input geometry", true, "",
        "file name");
    cmd.add(geometry_fname);
 
    TCLAP::ValueArg<std::string> mesh_arg(
        "m", "mesh-file", "the name of the file containing the mesh", true, "",
        "file name");
    cmd.add(mesh_arg);
 
    TCLAP::ValueArg<std::string> gmsh_path_arg("g", "gmsh-path",
                                               "the path to the gmsh binary",
                                               false, "", "path as string");
    cmd.add(gmsh_path_arg);
 
    cmd.parse(argc, argv);
 
#ifdef USE_PETSC
    MPI_Init(&argc, &argv);
#endif
 
    // *** read mesh
    INFO("Reading mesh '{:s}' ... ", mesh_arg.getValue());
    std::unique_ptr<MeshLib::Mesh> subsurface_mesh(
        MeshLib::IO::readMeshFromFile(mesh_arg.getValue()));
    INFO("done.");
    INFO("Extracting top surface of mesh '{:s}' ... ", mesh_arg.getValue());
    Eigen::Vector3d const dir({0, 0, -1});
    double const angle(90);
    std::unique_ptr<MeshLib::Mesh> surface_mesh(
        MeshToolsLib::MeshSurfaceExtraction::getMeshSurface(*subsurface_mesh,
                                                            dir, angle));
    INFO("done.");
    subsurface_mesh.reset(nullptr);
 
    // *** read geometry
    GeoLib::GEOObjects geometries;
    FileIO::readGeometryFromFile(geometry_fname.getValue(), geometries,
                                 gmsh_path_arg.getValue());
 
    auto const geo_name = geometries.getGeometryNames()[0];
 
    // *** check if the data is usable
    // *** get vector of polylines
    std::vector<GeoLib::Polyline*> const* plys(
        geometries.getPolylineVec(geo_name));
    if (!plys)
    {
        ERR("Could not get vector of polylines out of geometry '{:s}'.",
            geo_name);
#ifdef USE_PETSC
        MPI_Finalize();
#endif
        return EXIT_FAILURE;
    }
 
    auto search_length_strategy =
        std::make_unique<MeshGeoToolsLib::SearchLength>();
    if (search_length_arg.isSet())
    {
        search_length_strategy.reset(
            new MeshGeoToolsLib::SearchLength(search_length_arg.getValue()));
    }
 
    GeoLib::GEOObjects geometry_sets;
    MeshGeoToolsLib::MeshNodeSearcher mesh_searcher(
        *surface_mesh, std::move(search_length_strategy),
        MeshGeoToolsLib::SearchAllNodes::Yes);
    for (std::size_t k(0); k < plys->size(); k++)
    {
        auto const& ids = mesh_searcher.getMeshNodeIDs(*((*plys)[k]));
        if (ids.empty())
        {
            continue;
        }
        std::string polyline_name("Polyline-" + std::to_string(k));
        convertMeshNodesToGeometry(surface_mesh->getNodes(), ids, polyline_name,
                                   geometry_sets);
    }
 
    // merge all together
    auto const geo_names = geometry_sets.getGeometryNames();
    if (geo_names.empty())
    {
        ERR("Did not find mesh nodes along polylines.");
#ifdef USE_PETSC
        MPI_Finalize();
#endif
        return EXIT_FAILURE;
    }
 
    std::string merge_name("AllMeshNodesAlongPolylines");
    if (geometry_sets.mergeGeometries(geo_names, merge_name) == 2)
    {
        merge_name = geo_names[0];
    }
 
    GeoLib::PointVec const* pnt_vec(geometry_sets.getPointVecObj(merge_name));
    auto const& merged_pnts(pnt_vec->getVector());
 
    std::vector<GeoLib::Point> pnts_with_id;
    const std::size_t n_merged_pnts(merged_pnts.size());
    for (std::size_t k(0); k < n_merged_pnts; ++k)
    {
        pnts_with_id.emplace_back(*(merged_pnts[k]), k);
    }
 
    std::sort(pnts_with_id.begin(), pnts_with_id.end(),
              [](GeoLib::Point const& p0, GeoLib::Point const& p1)
              { return p0 < p1; });
 
    double const eps(std::numeric_limits<double>::epsilon());
    std::vector<GeoLib::Point*> surface_pnts;
    GeoLib::PointVec::NameIdMap name_id_map;
 
    // insert first point
    surface_pnts.push_back(
        new GeoLib::Point(pnts_with_id[0], surface_pnts.size()));
    {
        std::string element_name;
        pnt_vec->getNameOfElementByID(0, element_name);
        name_id_map[element_name] = 0;
    }
    for (std::size_t k(1); k < n_merged_pnts; ++k)
    {
        const GeoLib::Point& p0(pnts_with_id[k - 1]);
        const GeoLib::Point& p1(pnts_with_id[k]);
        if (std::abs(p0[0] - p1[0]) > eps || std::abs(p0[1] - p1[1]) > eps)
        {
            surface_pnts.push_back(
                new GeoLib::Point(pnts_with_id[k], surface_pnts.size()));
            std::string element_name;
            pnt_vec->getNameOfElementByID(k, element_name);
            name_id_map[element_name] = surface_pnts.size() - 1;
        }
    }
 
    std::string surface_name(BaseLib::dropFileExtension(mesh_arg.getValue()) +
                             "-MeshNodesAlongPolylines");
    geometry_sets.addPointVec(std::move(surface_pnts), surface_name,
                              std::move(name_id_map), 1e-6);
 
    // write the BCs and the merged geometry set to file
    std::string const base_fname(
        BaseLib::dropFileExtension(output_base_fname.getValue()));
    writeBCsAndGeometry(geometry_sets, surface_name, base_fname,
                        bc_type.getValue(), gml_arg.getValue());
#ifdef USE_PETSC
    MPI_Finalize();
#endif
    return EXIT_SUCCESS;
}