CreateAnchors.cpp File Reference

#include <tclap/CmdLine.h>
#include <vtkXMLUnstructuredGridWriter.h>
#include <fstream>
#include <nlohmann/json.hpp>
#include "BaseLib/FileTools.h"
#include "BaseLib/Logging.h"
#include "BaseLib/MPI.h"
#include "BaseLib/TCLAPArguments.h"
#include "ComputeIntersections.h"
#include "ComputeNaturalCoordsAlgorithm.h"
#include "InfoLib/GitInfo.h"
#include "MeshLib/IO/VtkIO/VtuInterface.h"

Include dependency graph for CreateAnchors.cpp:

Go to the source code of this file.

Functions
vtkSmartPointer< vtkUnstructuredGrid >	readGrid (std::string const &input_filename)
void	writeGrid (vtkUnstructuredGrid *grid, std::string const &output_filename)
void	checkJSONEntries (nlohmann::json const &data, size_t number_of_anchors)
std::tuple< AU::ComputeNaturalCoordsResult, Eigen::VectorXd >	readJSON (TCLAP::ValueArg< std::string > const &input_filename)
int	main (int argc, char **argv)

Function Documentation

checkJSONEntries()

void checkJSONEntries	(	nlohmann::json const &	data,
		size_t	number_of_anchors )

Definition at line 45 of file CreateAnchors.cpp.

{
    std::vector<std::string> required_keys = {"anchor_stiffness",
                                              "anchor_cross_sectional_area"};
    std::vector<std::string> optional_keys = {
        "maximum_anchor_stress", "initial_anchor_stress",
        "residual_anchor_stress", "free_fraction"};
    if (number_of_anchors == 0)
    {
        OGS_FATAL("No anchors found in the json.");
    }
    for (const auto& key : required_keys)
    {
        if (!data.contains(key))
        {
            OGS_FATAL("JSON file does not contain required key '{:s}'", key);
        }
        if (number_of_anchors != data[key].size())
        {
            OGS_FATAL(
                "Number of anchor start points does not match the number of {} "
                "entries.",
                key);
        }
        for (size_t i = 0; i < number_of_anchors; ++i)
        {
            if (!data[key][i].is_number())
            {
                OGS_FATAL("Non-numeric element in JSON array for key {}!", key);
            }
        }
    }
    for (const auto& key : optional_keys)
    {
        if (data.contains(key))
        {
            if (number_of_anchors != data[key].size())
            {
                OGS_FATAL(
                    "Number of anchor start points does not match the number "
                    "of {} "
                    "entries.",
                    key);
            }
            for (size_t i = 0; i < number_of_anchors; ++i)
            {
                if (!data[key][i].is_number())
                {
                    OGS_FATAL("Non-numeric element in JSON array for key {}!",
                              key);
                }
                if (key == "free_fraction")
                {
                    double const free_fraction_number =
                        data["free_fraction"][i].get<double>();
                    if (free_fraction_number < 0.0 ||
                        free_fraction_number > 1.0)
                    {
                        OGS_FATAL(
                            "Free fraction must be in the range [0, 1] but is "
                            "{} for anchor #{}.",
                            free_fraction_number, i);
                    }
                }
            }
        }
    }
}

References OGS_FATAL.

Referenced by readJSON().

main()

int main	(	int	argc,
		char **	argv )

Definition at line 233 of file CreateAnchors.cpp.

{
    // parse cmdline -----------------------------------------------------------
 
    TCLAP::CmdLine cmd(
        "Computes natual coordinates from given real coordinates\n\n"
 
        "OpenGeoSys-6 software, version " +
            GitInfoLib::GitInfo::ogs_version +
            ".\n"
            "Copyright (c) 2012-2026, OpenGeoSys Community "
            "(http://www.opengeosys.org)",
        ' ', GitInfoLib::GitInfo::ogs_version);
 
    auto log_level_arg = BaseLib::makeLogLevelArg();
    cmd.add(log_level_arg);
 
    TCLAP::ValueArg<std::string> input_filename_arg(
        "i", "input", "Input (.vtu) bulk mesh file", true, "", "INPUT_FILE",
        cmd);
 
    TCLAP::ValueArg<std::string> output_filename_arg(
        "o", "output", "Output (.vtu). Anchor mesh file", true, "",
        "OUTPUT_FILE", cmd);
 
    TCLAP::ValueArg<std::string> json_filename_arg(
        "f", "json-file",
        "Input (.json) JSON file containing anchor start and end points", true,
        "", "INPUT_FILE", cmd);
 
    TCLAP::ValueArg<double> tolerance_arg(
        "", "tolerance", "Tolerance/Search length", false,
        std::numeric_limits<double>::epsilon(), "float", cmd);
 
    TCLAP::ValueArg<unsigned> max_iter_arg(
        "", "max-iter",
        "maximum number of iterations of the internal root-finding "
        "algorithm, (min = 0)",
        false, 5, "MAX_ITER", cmd);
 
    cmd.parse(argc, argv);
 
    BaseLib::MPI::Setup mpi_setup(argc, argv);
    BaseLib::initOGSLogger(log_level_arg.getValue());
 
    auto const& [json_data, free_fraction] = readJSON(json_filename_arg);
    auto const bulk_mesh = readGrid(input_filename_arg.getValue());
 
    auto split_anchor_coords =
        getOrderedAnchorCoords(bulk_mesh, json_data.real_coords, free_fraction,
                               tolerance_arg.getValue());
 
    AU::ComputeNaturalCoordsResult const anchor_data =
        setPhysicalPropertiesForIntersectionPoints(split_anchor_coords,
                                                   json_data);
 
    // Compute natural coordinates
    AU::ComputeNaturalCoordsResult const result = AU::computeNaturalCoords(
        bulk_mesh, anchor_data, tolerance_arg.getValue(),
        max_iter_arg.getValue());
    // Write output
    auto const output_mesh = AU::toVTKGrid(result);
    writeGrid(output_mesh, output_filename_arg.getValue());
 
    if (!result.success)
    {
        OGS_FATAL("Failed to compute natural coordinates.");
    }
 
    return EXIT_SUCCESS;
}

References ApplicationUtils::computeNaturalCoords(), getOrderedAnchorCoords(), BaseLib::initOGSLogger(), BaseLib::makeLogLevelArg(), OGS_FATAL, GitInfoLib::GitInfo::ogs_version, readGrid(), readJSON(), setPhysicalPropertiesForIntersectionPoints(), ApplicationUtils::ComputeNaturalCoordsResult::success, ApplicationUtils::toVTKGrid(), and writeGrid().

readGrid()

vtkSmartPointer< vtkUnstructuredGrid > readGrid

(

std::string const &

input_filename

)

Definition at line 21 of file CreateAnchors.cpp.

{
    vtkSmartPointer<vtkUnstructuredGrid> grid =
        MeshLib::IO::VtuInterface::readVtuFileToVtkUnstructuredGrid(
            input_filename);
    if (grid == nullptr)
    {
        OGS_FATAL("Could not open file '{}'", input_filename);
    }
    if (grid->GetNumberOfCells() == 0)
    {
        OGS_FATAL("Mesh file '{}' contains no cells.", input_filename);
    }
    return grid;
}

References OGS_FATAL, and MeshLib::IO::VtuInterface::readVtuFileToVtkUnstructuredGrid().

Referenced by main().

readJSON()

std::tuple< AU::ComputeNaturalCoordsResult, Eigen::VectorXd > readJSON

(

TCLAP::ValueArg< std::string > const &

input_filename

)

Reads a JSON file containing anchor start and end points and physical properties of the anchors. Also returns the free fraction of each anchor. If the free fraction is not given, it is set to 1.0 for all anchors.

Definition at line 117 of file CreateAnchors.cpp.

{
    using json = nlohmann::json;
    std::ifstream f(input_filename.getValue());
    if (!f)
    {
        OGS_FATAL("Could not open file '{:s}'", input_filename.getValue());
    }
    json const data = json::parse(f);
 
    auto const number_of_anchors = data["anchor_start_points"].size();
    if (number_of_anchors != data["anchor_end_points"].size())
    {
        OGS_FATAL(
            "Number of anchor start points does not match the number of "
            "anchor end points.");
    }
    checkJSONEntries(data, number_of_anchors);
 
    Eigen::MatrixX3d realcoords(2 * number_of_anchors, 3);
 
    auto get_coordinates = [&data](const char* key, std::size_t const i)
    {
        const auto& v = data[key][i].get_ref<json::array_t const&>();
        if (v.size() != 3)
        {
            OGS_FATAL(
                "Expected a vector of length three for {:s} {}. Got vector of "
                "size {}.",
                key, i, v.size());
        }
        return Eigen::RowVector3d{v[0].get<double>(), v[1].get<double>(),
                                  v[2].get<double>()};
    };
 
    for (std::size_t i = 0; i < number_of_anchors; i++)
    {
        realcoords.row(2 * i).noalias() =
            get_coordinates("anchor_start_points", i);
        realcoords.row(2 * i + 1).noalias() =
            get_coordinates("anchor_end_points", i);
    }
    Eigen::VectorXd initial_anchor_stress(number_of_anchors);
    Eigen::VectorXd maximum_anchor_stress(number_of_anchors);
    Eigen::VectorXd residual_anchor_stress(number_of_anchors);
    Eigen::VectorXd anchor_cross_sectional_area(number_of_anchors);
    Eigen::VectorXd anchor_stiffness(number_of_anchors);
    Eigen::VectorXd free_fraction(number_of_anchors);
    if (!data.contains("initial_anchor_stress"))
    {
        initial_anchor_stress.setZero();
    }
    else
    {
        for (size_t i = 0; i < number_of_anchors; ++i)
        {
            initial_anchor_stress(i) =
                data["initial_anchor_stress"][i].get<double>();
        }
    }
    if (!data.contains("maximum_anchor_stress"))
    {
        maximum_anchor_stress = Eigen::VectorXd::Constant(
            number_of_anchors, std::numeric_limits<double>::max());
    }
    else
    {
        for (size_t i = 0; i < number_of_anchors; ++i)
        {
            maximum_anchor_stress(i) =
                data["maximum_anchor_stress"][i].get<double>();
        }
    }
    if (!data.contains("residual_anchor_stress"))
    {
        residual_anchor_stress = Eigen::VectorXd::Constant(
            number_of_anchors, std::numeric_limits<double>::max());
    }
    else
    {
        for (size_t i = 0; i < number_of_anchors; ++i)
        {
            residual_anchor_stress(i) =
                data["residual_anchor_stress"][i].get<double>();
        }
    }
    if (!data.contains("free_fraction"))
    {
        free_fraction = Eigen::VectorXd::Constant(number_of_anchors, 1.0);
    }
    else
    {
        for (size_t i = 0; i < number_of_anchors; ++i)
        {
            free_fraction(i) = data["free_fraction"][i].get<double>();
        }
    }
 
    for (size_t i = 0; i < number_of_anchors; ++i)
    {
        anchor_cross_sectional_area(i) =
            data["anchor_cross_sectional_area"][i].get<double>();
        anchor_stiffness(i) = data["anchor_stiffness"][i].get<double>();
    }
    AU::ComputeNaturalCoordsResult json_data;
    json_data.real_coords = realcoords;
    json_data.initial_anchor_stress = initial_anchor_stress;
    json_data.maximum_anchor_stress = maximum_anchor_stress;
    json_data.residual_anchor_stress = residual_anchor_stress;
    json_data.anchor_cross_sectional_area = anchor_cross_sectional_area;
    json_data.anchor_stiffness = anchor_stiffness;
    json_data.success = true;
    return {json_data, free_fraction};
}

References ApplicationUtils::ComputeNaturalCoordsResult::anchor_cross_sectional_area, ApplicationUtils::ComputeNaturalCoordsResult::anchor_stiffness, checkJSONEntries(), ApplicationUtils::ComputeNaturalCoordsResult::initial_anchor_stress, ApplicationUtils::ComputeNaturalCoordsResult::maximum_anchor_stress, OGS_FATAL, ApplicationUtils::ComputeNaturalCoordsResult::real_coords, ApplicationUtils::ComputeNaturalCoordsResult::residual_anchor_stress, and ApplicationUtils::ComputeNaturalCoordsResult::success.

Referenced by main().

writeGrid()

void writeGrid	(	vtkUnstructuredGrid *	grid,
		std::string const &	output_filename )

Definition at line 37 of file CreateAnchors.cpp.

{
    vtkNew<vtkXMLUnstructuredGridWriter> writer;
    writer->SetFileName(output_filename.c_str());
    writer->SetInputData(grid);
    writer->Write();
}

Referenced by main().