7_extended_write_serial.cpp

#include <openPMD/openPMD.hpp>

#include <algorithm>
#include <iostream>

int main()
{
    namespace io = openPMD;

    {
        auto f =
            io::Series("working/directory/2D_simData.h5", io::Access::CREATE);

        // all required openPMD attributes will be set to reasonable default
        // values (all ones, all zeros, empty strings,...) manually setting them
        // enforces the openPMD standard
        f.setMeshesPath("custom_meshes_path");
        f.setParticlesPath("long_and_very_custom_particles_path");

        // it is possible to add and remove attributes
        f.setComment("This is fine and actually encouraged by the standard");
        f.setAttribute(
            "custom_attribute_name",
            std::string("This attribute is manually added and can contain "
                        "about any datatype you would want"));
        // note that removing attributes required by the standard typically
        // makes the file unusable for post-processing
        f.deleteAttribute("custom_attribute_name");

        // everything that is accessed with [] should be interpreted as
        // permanent storage the objects sunk into these locations are deep
        // copies
        {
            // setting attributes can be chained in JS-like syntax for compact
            // code
            f.iterations[1].setTime(42.0).setDt(1.0).setTimeUnitSI(1.39e-16);
            f.iterations[2].setComment(
                "This iteration will not appear in any output");
            f.iterations.erase(2);
        }

        {
            // everything is a reference
            io::Iteration reference = f.iterations[1];
            reference.setComment(
                "Modifications to a copied iteration refer to the same "
                "iteration");
        }
        f.iterations[1].deleteAttribute("comment");

        io::Iteration cur_it = f.iterations[1];

        // the underlying concept for numeric data is the openPMD Record
        // https://github.com/openPMD/openPMD-standard/blob/1.0.1/STANDARD.md#scalar-vector-and-tensor-records
        // Meshes are specialized records
        cur_it.meshes["generic_2D_field"].setUnitDimension(
            {{io::UnitDimension::L, -3}, {io::UnitDimension::M, 1}});

        {
            // copies of objects are handles/references to the same underlying
            // object
            io::Mesh lowRez = cur_it.meshes["generic_2D_field"];
            lowRez.setGridSpacing(std::vector<double>{6, 1})
                .setGridGlobalOffset({0, 600});

            io::Mesh highRez = cur_it.meshes["generic_2D_field"];
            highRez.setGridSpacing(std::vector<double>{6, 0.5})
                .setGridGlobalOffset({0, 1200});

            cur_it.meshes.erase("generic_2D_field");
            cur_it.meshes["lowRez_2D_field"] = lowRez;
            cur_it.meshes["highRez_2D_field"] = highRez;
        }
        cur_it.meshes.erase("highRez_2D_field");

        {
            // particles are handled very similar
            io::ParticleSpecies electrons = cur_it.particles["electrons"];
            electrons.setAttribute(
                "NoteWorthyParticleSpeciesProperty",
                std::string("Observing this species was a blast."));
            electrons["displacement"].setUnitDimension(
                {{io::UnitDimension::M, 1}});
            electrons["displacement"]["x"].setUnitSI(1e-6);
            electrons.erase("displacement");
            electrons["weighting"]
                .resetDataset({io::Datatype::FLOAT, {1}})
                .makeConstant(1.e-5);
        }

        io::Mesh mesh = cur_it.meshes["lowRez_2D_field"];
        mesh.setAxisLabels({"x", "y"});

        // data is assumed to reside behind a pointer as a contiguous
        // column-major array shared data ownership during IO is indicated with
        // a smart pointer
        std::shared_ptr<double> partial_mesh(
            new double[5], [](double const *p) {
                delete[] p;
                p = nullptr;
            });

        // before storing record data, you must specify the dataset once per
        // component this describes the datatype and shape of data as it should
        // be written to disk
        io::Datatype dtype = io::determineDatatype(partial_mesh);
        auto d = io::Dataset(dtype, io::Extent{2, 5});
        std::string datasetConfig = R"END(
{
  "adios2": {
    "dataset": {
      "operators": [
        {
          "type": "zlib",
          "parameters": {
            "clevel": 9
          }
        }
      ]
    }
  }
})END";
        d.options = datasetConfig;
        mesh["x"].resetDataset(d);

        io::ParticleSpecies electrons = cur_it.particles["electrons"];

        io::Extent mpiDims{4};
        std::shared_ptr<float> partial_particlePos(
            new float[2], [](float const *p) {
                delete[] p;
                p = nullptr;
            });
        dtype = io::determineDatatype(partial_particlePos);
        d = io::Dataset(dtype, mpiDims);
        electrons["position"]["x"].resetDataset(d);

        std::shared_ptr<uint64_t> partial_particleOff(
            new uint64_t[2], [](uint64_t const *p) {
                delete[] p;
                p = nullptr;
            });
        dtype = io::determineDatatype(partial_particleOff);
        d = io::Dataset(dtype, mpiDims);
        electrons["positionOffset"]["x"].resetDataset(d);

        auto dset = io::Dataset(io::determineDatatype<uint64_t>(), {2});
        electrons.particlePatches["numParticles"].resetDataset(dset);
        electrons.particlePatches["numParticlesOffset"].resetDataset(dset);

        dset = io::Dataset(io::Datatype::FLOAT, {2});
        electrons.particlePatches["offset"].setUnitDimension(
            {{io::UnitDimension::L, 1}});
        electrons.particlePatches["offset"]["x"].resetDataset(dset);
        electrons.particlePatches["extent"].setUnitDimension(
            {{io::UnitDimension::L, 1}});
        electrons.particlePatches["extent"]["x"].resetDataset(dset);

        // at any point in time you may decide to dump already created output to
        // disk note that this will make some operations impossible (e.g.
        // renaming files)
        f.flush();

        // chunked writing of the final dataset at a time is supported
        // this loop writes one row at a time
        double mesh_x[2][5] = {{1, 3, 5, 7, 9}, {11, 13, 15, 17, 19}};
        float particle_position[4] = {0.1f, 0.2f, 0.3f, 0.4f};
        uint64_t particle_positionOffset[4] = {0u, 1u, 2u, 3u};
        for (uint64_t i = 0u; i < 2u; ++i)
        {
            for (int col = 0; col < 5; ++col)
                partial_mesh.get()[col] = mesh_x[i][col];

            io::Offset o = io::Offset{i, 0};
            io::Extent e = io::Extent{1, 5};
            mesh["x"].storeChunk(partial_mesh, o, e);
            // operations between store and flush MUST NOT modify the pointed-to
            // data
            f.flush();
            // after the flush completes successfully, access to the shared
            // resource is returned to the caller

            for (int idx = 0; idx < 2; ++idx)
            {
                partial_particlePos.get()[idx] = particle_position[idx + 2 * i];
                partial_particleOff.get()[idx] =
                    particle_positionOffset[idx + 2 * i];
            }

            uint64_t numParticlesOffset = 2 * i;
            uint64_t numParticles = 2;

            o = io::Offset{numParticlesOffset};
            e = io::Extent{numParticles};
            electrons["position"]["x"].storeChunk(partial_particlePos, o, e);
            electrons["positionOffset"]["x"].storeChunk(
                partial_particleOff, o, e);

            electrons.particlePatches["numParticles"].store(i, numParticles);
            electrons
                .particlePatches["numParticlesOffset"]

                .store(i, numParticlesOffset);

            electrons.particlePatches["offset"]["x"].store(
                i, particle_position[numParticlesOffset]);
            electrons.particlePatches["extent"]["x"].store(
                i,
                particle_position[numParticlesOffset + numParticles - 1] -
                    particle_position[numParticlesOffset]);
        }

        mesh["y"].resetDataset(d);
        mesh["y"].setUnitSI(4);
        double constant_value = 0.3183098861837907;
        // for datasets that contain a single unique value, openPMD offers
        // constant records
        mesh["y"].makeConstant(constant_value);

        // The iteration can be closed in order to help free up resources.
        // The iteration's content will be flushed automatically.
        // An iteration once closed cannot (yet) be reopened.
        cur_it.close();

        /* The files in 'f' are still open until the object is destroyed, on
         * which it cleanly flushes and closes all open file handles.
         * When running out of scope on return, the 'Series' destructor is
         * called. Alternatively, one can call `series.close()` to the same
         * effect as calling the destructor, including the release of file
         * handles.
         */
        f.close();
    } // namespace ;

    return 0;
}