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‎src/amr/data/electromag/electromag_initializer.hpp

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#ifndef _PHARE_AMR_DATA_ELECTROMAG_ELECTROMAG_INITIALIZER_HPP_
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#define _PHARE_AMR_DATA_ELECTROMAG_ELECTROMAG_INITIALIZER_HPP_
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// #include "core/data/electromag/electromag.hpp"
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#include "core/data/vecfield/vecfield_initializer.hpp"
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#include "amr/data/field/initializers/samrai_hdf5_field_initializer.hpp"
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#include "initializer/data_provider.hpp"
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#include <array>
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namespace PHARE::amr
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{
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template<typename Electromag_t, typename GridLayout>
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class ElectromagInitializer
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{
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public:
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virtual void init(Electromag_t& /*em*/, GridLayout const& /*layout*/) const { /*noop*/ }
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virtual ~ElectromagInitializer() {}
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};
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template<typename Electromag_t, typename GridLayout>
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class ElectromagUserFuncInitializer : public ElectromagInitializer<Electromag_t, GridLayout>
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{
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using VecFieldInit = core::VecFieldInitializer<Electromag_t::dimension>;
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public:
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ElectromagUserFuncInitializer(initializer::PHAREDict const& dict)
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: Binit_{dict["magnetic"]["initializer"]}
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{
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}
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virtual ~ElectromagUserFuncInitializer() {}
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void init(Electromag_t& em, GridLayout const& layout) const override
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{
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Binit_.initialize(em.B, layout);
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}
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VecFieldInit Binit_;
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};
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/*
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/EM_B_y##default/d_box
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/EM_B_x##default/field_EM_B_x
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/EM_B_y##default/field_EM_B_y
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/EM_B_z##default/field_EM_B_z
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*/
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template<typename Electromag_t, typename GridLayout>
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class ElectromagSamraiH5Initializer : public ElectromagInitializer<Electromag_t, GridLayout>
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{
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using vecfield_type = typename Electromag_t::vecfield_type;
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using field_type = typename vecfield_type::field_type;
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public:
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ElectromagSamraiH5Initializer(initializer::PHAREDict const& dict)
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: dict_{dict}
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{
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}
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virtual ~ElectromagSamraiH5Initializer() {}
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void init(Electromag_t& em, GridLayout const& layout) const override
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{
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for (auto& field : em.B)
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SamraiHDF5FieldInitializer<field_type, GridLayout>{}.load(field, layout);
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}
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initializer::PHAREDict const dict_;
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};
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class ElectromagInitializerFactory
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{
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public:
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template<typename Electromag_t, typename GridLayout>
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NO_DISCARD static std::unique_ptr<ElectromagInitializer<Electromag_t, GridLayout>>
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create(initializer::PHAREDict const& dict)
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{
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if (dict["magnetic"]["initializer"].contains("x_component"))
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return std::make_unique<ElectromagUserFuncInitializer<Electromag_t, GridLayout>>(dict);
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else
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return std::make_unique<ElectromagSamraiH5Initializer<Electromag_t, GridLayout>>(dict);
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}
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};
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} // namespace PHARE::amr
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#endif // _PHARE_AMR_DATA_ELECTROMAG_ELECTROMAG_INITIALIZER_HPP_

‎src/amr/data/field/initializers/samrai_hdf5_field_initializer.hpp

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#ifndef _PHARE_AMR_DATA_FIELD_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
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#define _PHARE_AMR_DATA_FIELD_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
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#include <memory>
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#include <random>
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#include <cassert>
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#include <functional>
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#include "core/data/grid/gridlayoutdefs.hpp"
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#include "core/hybrid/hybrid_quantities.hpp"
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#include "core/utilities/types.hpp"
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#include "core/data/ions/particle_initializers/particle_initializer.hpp"
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#include "core/data/particles/particle.hpp"
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#include "initializer/data_provider.hpp"
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#include "core/utilities/point/point.hpp"
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#include "core/def.hpp"
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#include "core/logger.hpp"
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#include "hdf5/detail/h5/h5_file.hpp"
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#include "SAMRAI/hier/PatchDataRestartManager.h"
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#include "amr/data/initializers/samrai_hdf5_initializer.hpp"
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namespace PHARE::amr
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{
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template<typename Field_t, typename GridLayout>
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class SamraiHDF5FieldInitializer // no virtual classes needed (yet)
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{
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public:
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static constexpr auto dimension = GridLayout::dimension;
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SamraiHDF5FieldInitializer() {}
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void load(Field_t& Field, GridLayout const& layout) const;
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};
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template<typename Field_t, typename GridLayout>
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void SamraiHDF5FieldInitializer<Field_t, GridLayout>::load(Field_t& field,
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GridLayout const& layout) const
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{
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PHARE_LOG_LINE_STR("SamraiHDF5FieldInitializer::loadParticles");
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}
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} // namespace PHARE::amr
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#endif

‎src/amr/data/initializers/samrai_hdf5_initializer.hpp

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#ifndef _PHARE_AMR_DATA_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
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#define _PHARE_AMR_DATA_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
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#include <memory>
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#include <random>
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#include <cassert>
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#include <functional>
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#include "core/data/grid/gridlayoutdefs.hpp"
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#include "core/hybrid/hybrid_quantities.hpp"
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#include "core/utilities/types.hpp"
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#include "core/data/ions/particle_initializers/particle_initializer.hpp"
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#include "core/data/particles/particle.hpp"
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#include "initializer/data_provider.hpp"
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#include "core/utilities/point/point.hpp"
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#include "core/def.hpp"
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#include "core/logger.hpp"
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#include "hdf5/detail/h5/h5_file.hpp"
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#include "amr/utilities/box/amr_box.hpp"
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#include "SAMRAI/hier/PatchDataRestartManager.h"
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namespace PHARE::amr
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{
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/*
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example paths
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/d_box
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/d_ghost_box
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/d_ghosts
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/d_timestamp
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/domainParticles_charge
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/domainParticles_delta
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/domainParticles_iCell
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/domainParticles_v
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/protons##default/domainParticles_weight
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/EM_B_y##default/d_box
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/EM_B_x##default/field_EM_B_x
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/EM_B_y##default/field_EM_B_y
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/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/EM_B_z##default/field_EM_B_z
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*/
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template<typename ParticleArray, typename GridLayout>
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class SamraiH5Interface
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{
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struct SamraiHDF5File; // : PHARE::hdf5::h5::HighFiveFile;
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public:
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static SamraiH5Interface& INSTANCE()
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{
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static SamraiH5Interface i;
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return i;
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}
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void populate_from(std::string const& dir, int const& idx, int const& mpi_size);
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NO_DISCARD auto static getRestartFileFullPath(std::string path, int const& idx,
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int const& mpi_size, int const& rank)
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{
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return path //
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+ "/restore." + SAMRAI::tbox::Utilities::intToString(idx, 6) //
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+ "/nodes." + SAMRAI::tbox::Utilities::nodeToString(mpi_size) //
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+ "/proc." + SAMRAI::tbox::Utilities::processorToString(rank);
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}
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private:
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std::vector<std::unique_ptr<SamraiHDF5File>> restart_files;
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std::unordered_map<std::string, std::string> box2dataset;
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};
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template<typename ParticleArray, typename GridLayout>
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struct SamraiH5Interface<ParticleArray, GridLayout>::SamraiHDF5File : public hdf5::h5::HighFiveFile
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{
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using Super = hdf5::h5::HighFiveFile;
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using Box_t = core::Box<int, ParticleArray::dimension>;
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SamraiHDF5File(std::string const& filepath)
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: Super{filepath, HighFive::File::ReadOnly, /*para=*/false}
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{
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// auto box_type = box_compound_type();
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// box_type.commit(file(), "d_box");
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// getBoxFromPath("/PHARE_hierarchy/level_0000/level_0000-patch_0000000-block_0000000/"
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// "EM_B_y##default/d_box");
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}
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/*
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DATASET "d_box" {
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DATATYPE H5T_COMPOUND {
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H5T_STD_I32BE "dim";
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H5T_ARRAY { [3] H5T_STD_I32BE } "lo";
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H5T_ARRAY { [3] H5T_STD_I32BE } "hi";
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}
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DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
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DATA {
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(0): {
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1,
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[ 0, 0, 0 ],
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[ 199, 0, 0 ]
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}
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}
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ATTRIBUTE "Type" {
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DATATYPE H5T_STD_I8BE
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DATASPACE SCALAR
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DATA {
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(0): 2
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}
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}
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}
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*/
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struct BoxData
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{
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std::int32_t dim;
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std::array<std::int32_t, 3> lo;
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std::array<std::int32_t, 3> hi;
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};
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// struct BoxData
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// {
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// int dim;
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// int lo0, lo1, lo2;
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// int hi0, hi1, hi2;
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// };
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HighFive::CompoundType static box_compound_type()
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{
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return {{"dim", HighFive::create_datatype<std::int32_t>()},
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{"lo", HighFive::create_datatype<std::array<std::int32_t, 3>>()},
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{"hi", HighFive::create_datatype<std::array<std::int32_t, 3>>()}};
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}
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auto getBoxFromPath(std::string const& path) const
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{
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// auto const& data = Super::read_data_set<int>(path);
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// PHARE_LOG_LINE_STR(data.size());
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std::vector<BoxData> boxes;
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Super::file().getDataSet(path).read(boxes);
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assert(boxes.size() == 1);
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// auto const& bx = boxes[0];
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// return Box_t{core::as_sized_array<ParticleArray::dimension>(bx.lo0, bx.lo1, bx.lo2),
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// core::as_sized_array<ParticleArray::dimension>(bx.hi0, bx.hi1, bx.hi2)};
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return Box_t{core::sized_array<ParticleArray::dimension>(boxes[0].lo),
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core::sized_array<ParticleArray::dimension>(boxes[0].hi)};
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}
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};
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template<typename ParticleArray, typename GridLayout>
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void SamraiH5Interface<ParticleArray, GridLayout>::populate_from(std::string const& dir,
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int const& idx,
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int const& mpi_size)
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{
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for (int rank = 0; rank < mpi_size; ++rank)
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{
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auto const hdf5_filepath = getRestartFileFullPath(dir, idx, mpi_size, rank);
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hdf5::h5::HighFiveFile h5File{hdf5_filepath, HighFive::File::ReadOnly, /*para=*/false};
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PHARE_LOG_LINE_STR("SamraiH5Interface::populate_from");
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auto groups = h5File.scan_for_groups({"level_0000", "domainParticles_charge"});
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for (auto const& g : groups)
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{
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PHARE_LOG_LINE_STR(g);
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}
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restart_files.emplace_back(std::make_unique<SamraiHDF5File>(hdf5_filepath));
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}
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}
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} // namespace PHARE::amr
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#endif

‎src/amr/data/particles/initializers/particle_initializer_factory.hpp

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#include "core/data/ions/particle_initializers/maxwellian_particle_initializer.hpp"
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#include "samrai_hdf5_particle_initializer.hpp"
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#include "amr/data/initializers/samrai_hdf5_initializer.hpp"
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#include <memory>
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