arbitrary mpirun N restarts

[PhilipDeegan]

Summary by CodeRabbit

• New Features

  • Introduced a new framework for initializing electromagnetic data structures, enhancing flexibility in initialization strategies.
  • Enhanced functionality for scanning groups in HDF5 files, providing better navigation and filtering options.
  • Added a utility function for converting vectors to fixed-size arrays, improving type safety and performance.
  • Introduced a new class for initializing particles from HDF5 data, streamlining particle management.
  • Improved the AMRToLocal function with new overloads for enhanced performance and flexibility.
  • Added new methods for calculating domain and ghost boxes, enhancing grid layout functionality.
  • Updated particle initialization logic to include population names, improving specificity.

• Bug Fixes

  • Improved method signatures for const-correctness, enhancing clarity and usability.
  • Enhanced the robustness of data handling in particle initialization logic.

• Chores

  • Updated namespace structures for better organization and clarity.
  • Modified CMake configurations to reflect updated library dependencies.

[coderabbitai[bot]]

📝 Walkthrough

## Walkthrough The changes involve significant updates across multiple files, focusing on the restructuring of the simulation initialization process, particularly for electromagnetic fields and particle handling. Several functions and classes have been removed or redefined to enhance modularity and flexibility. New modules have been introduced for managing simulation parameters, including HDF5 file interactions and initialization strategies. The updates reflect a shift towards a more organized approach to simulation configuration and data management. ## Changes | Files | Change Summary | |---------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | `pyphare/pyphare/pharein/__init__.py` | Removed several functions and classes related to simulation handling; modified `populateDict` to delegate to `initialize.general.populateDict(sim)`. | | `pyphare/pyphare/pharein/initialize/__init__.py` | Added imports for `general`, `user_fns`, and `samrai_hdf5`; defined `__all__` for public interface. | | `pyphare/pyphare/pharein/initialize/general.py` | Introduced functions and classes for managing simulation data, including `_patch_data_ids`, `_serialized_simulation_string`, and various utility functions for adding data types. | | `pyphare/pyphare/pharein/initialize/samrai_hdf5.py` | Added `populateDict` function for populating simulation parameters from a model. | | `pyphare/pyphare/pharein/initialize/user_fns.py` | Introduced functions for populating electromagnetic and particle properties in simulation dictionaries. | | `pyphare/pyphare/pharein/simulation.py` | Added `check_init_options` function for validating initialization options; updated `Simulation` constructor to handle new `init_options` parameter. | | `pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py` | Enhanced `EqualityReport` class; modified `__repr__` method for better error message representation. | | `pyphare/pyphare/pharesee/hierarchy/patchdata.py` | Updated constructors for `FieldData` and `ParticleData` classes to improve initialization and data handling capabilities. | | `res/cmake/test.cmake` | Removed and added subdirectories for test directories, shifting focus in test structure. | | `src/amr/data/electromag/electromag_initializer.hpp` | Introduced classes for initializing electromagnetic fields, including a factory for creating initializers based on configuration. | | `src/amr/data/field/initializers/samrai_hdf5_field_initializer.hpp` | Added `SamraiHDF5FieldInitializer` class for loading field data from HDF5 files. | | `src/amr/data/initializers/samrai_hdf5_initializer.hpp` | Established `SamraiH5Interface` for handling HDF5 file interactions and data population. | | `src/amr/data/particles/initializers/particle_initializer_factory.hpp` | Updated `ParticleInitializerFactory` to reflect new namespace and added handling for new initializers. | | `src/amr/data/particles/initializers/samrai_hdf5_particle_initializer.hpp` | Defined `SamraiHDF5ParticleInitializer` class for loading particle data from HDF5 files. | | `src/core/CMakeLists.txt` | Removed reference to `particle_initializer_factory.hpp` from compilation sources. | | `src/core/data/electromag/electromag.hpp` | Updated type aliases and removed initialization logic from constructors. | | `src/core/data/grid/gridlayout.hpp` | Modified method signatures for AMR coordinate conversions to enhance flexibility and maintain backward compatibility. | | `src/core/data/ions/ions.hpp` | Removed include directive for `particle_initializer_factory.hpp`. | | `tests/amr/data/particles/initializer/CMakeLists.txt` | Updated linked library from `phare_core` to `phare_amr`. | | `tests/amr/data/particles/initializer/test_main.cpp` | Adjusted imports and updated dictionary keys for consistency in test cases. | | `tests/amr/models/test_models.cpp` | Renamed keys in initialization dictionary for consistency. | | `tests/amr/tagging/test_tagging.cpp` | Introduced structured initialization logic using `PHAREDict` in the `SinglePatchHybridModel`. | | `tests/core/numerics/ion_updater/test_updater.cpp` | Enhanced initialization logic for electromagnetic fields and particles in tests. | | `tests/simulator/test_init_from_restart.py` | Introduced tests for restarting simulations, focusing on data comparison between outputs. | | `tools/test_data_gen.py` | Added functionality for generating test data for simulations, including functions for running simulations with specified parameters. | ## Possibly related PRs - **#879**: The changes in this PR involve modifications to the `pyphare/pyphare/pharein/__init__.py` and `pyphare/pyphare/pharein/simulation.py` files, which relate to the handling of simulation parameters and tagging thresholds. This is relevant to the main PR's restructuring of simulation initialization and handling of options, indicating a shared focus on improving the configurability and modularity of simulation processes.

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