├── .clang-format ├── .devcontainer └── devcontainer.json ├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── apply-formatting.yml │ ├── check-compilers.yml │ ├── check-docs-toc.yml │ ├── check-formatting.yml │ ├── ci-extended.yml │ ├── ci-macos.yml │ ├── ci-short.yml │ ├── docs.yml │ └── pr-dependencies.yml ├── .gitignore ├── .gitlab-ci-darwin.yml ├── .gitmodules ├── CHANGELOG.md ├── CMakeLists.txt ├── CONTRIBUTING.md ├── CPPLINT.cfg ├── LICENSE ├── README.md ├── benchmarks ├── CMakeLists.txt └── burgers │ ├── CMakeLists.txt │ ├── README.md │ ├── burgers.pin │ ├── burgers_diff.py │ ├── burgers_driver.cpp │ ├── burgers_driver.hpp │ ├── burgers_package.cpp │ ├── burgers_package.hpp │ ├── data │ ├── amr_hist.png │ ├── pvibe_cpu_scaling.png │ └── pvibe_gpu_throughput.png │ ├── main.cpp │ ├── parthenon_app_inputs.cpp │ └── recon.hpp ├── cmake ├── CTestCustom.cmake.in ├── CheckCopyright.cmake ├── CheckCopyrightScript.cmake ├── CodeCov.cmake ├── CodeCovBashDownloadScript.cmake ├── FindFilesystem.cmake ├── Format.cmake ├── Lint.cmake ├── MachineCfg.cmake ├── Provenance.cmake ├── PythonModuleCheck.cmake ├── TestSetup.cmake ├── machinecfg │ ├── CI.cmake │ ├── Darwin.cmake │ ├── FrontierAndCrusher.cmake │ ├── GitHubActions.cmake │ ├── Ookami.cmake │ ├── RZAnsel.cmake │ ├── Snow.cmake │ ├── Spock.cmake │ └── Summit.cmake └── parthenonConfig.cmake.in ├── codecov.yml ├── doc ├── index.html ├── latex │ ├── MG_grid_hierarchy.pdf │ ├── convergence.pdf │ ├── coordinate_transform.tex │ ├── indexed_cube.tex │ ├── main.pdf │ ├── main.tex │ ├── mesh_overview.tex │ ├── node_valence.tex │ ├── offset_cube.tex │ ├── parthenon.bib │ ├── r.png │ └── x.png └── sphinx │ ├── .gitignore │ ├── Makefile │ ├── README │ ├── _static │ ├── custom.css │ └── placeholder │ ├── _templates │ └── versions.html │ ├── conf.py │ ├── index.rst │ ├── make.bat │ └── src │ ├── 0_input_parameters_ref.rst │ ├── README.rst │ ├── amr.rst │ ├── boundary_communication.rst │ ├── boundary_conditions.rst │ ├── building.rst │ ├── chapters │ ├── advanced_features.rst │ ├── api_reference.rst │ ├── core_concepts.rst │ ├── developer_guide.rst │ ├── getting_started.rst │ ├── parallelism_performance.rst │ └── reference.rst │ ├── constants.rst │ ├── coordinates.rst │ ├── development.rst │ ├── driver.rst │ ├── figs │ ├── Curtis_et_al-ApJL-2023-1dhist.png │ ├── TaskDiagram.png │ ├── diffusion_contour.png │ ├── sagert_icf_spacetime.png │ └── yt_doc-2dhist.png │ ├── generated │ ├── burgers-table.csv │ ├── diffusion-parth-table.csv │ └── diffusion-table.csv │ ├── inputs.rst │ ├── instrumentation.rst │ ├── integrators.rst │ ├── interface │ ├── boundary.rst │ ├── containers.rst │ ├── metadata.rst │ ├── refinement_operations.rst │ ├── sparse.rst │ └── state.rst │ ├── load_balancing.rst │ ├── mesh │ ├── IndexShape.jpg │ ├── domain.rst │ └── mesh.rst │ ├── nested_par_for.rst │ ├── outputs.rst │ ├── par_for.rst │ ├── parthenon_arrays.rst │ ├── parthenon_manager.rst │ ├── particles.rst │ ├── reductions.rst │ ├── solvers.rst │ ├── sparse_packs.rst │ ├── sphinx-doc.rst │ ├── tasks.rst │ ├── tests.rst │ ├── utilities.rst │ └── weak_scaling.rst ├── example ├── CMakeLists.txt ├── advection │ ├── CMakeLists.txt │ ├── advection_driver.cpp │ ├── advection_driver.hpp │ ├── advection_package.cpp │ ├── advection_package.hpp │ ├── custom_ascent_actions.yaml │ ├── main.cpp │ ├── parthenon_app_inputs.cpp │ └── parthinput.advection ├── boundary_exchange │ ├── CMakeLists.txt │ ├── boundary_exchange.cpp │ ├── boundary_exchange.hpp │ ├── boundary_exchange_driver.cpp │ ├── boundary_exchange_driver.hpp │ └── parthinput.example ├── calculate_pi │ ├── CMakeLists.txt │ ├── calculate_pi.cpp │ ├── calculate_pi.hpp │ ├── parthinput.example │ ├── pi_driver.cpp │ └── pi_driver.hpp ├── diffusion │ ├── CMakeLists.txt │ ├── diffusion_driver.cpp │ ├── diffusion_driver.hpp │ ├── diffusion_equation.hpp │ ├── diffusion_package.cpp │ ├── diffusion_package.hpp │ ├── main.cpp │ ├── parthenon_app_inputs.cpp │ └── parthinput.diffusion ├── fine_advection │ ├── CMakeLists.txt │ ├── README.md │ ├── advection_driver.cpp │ ├── advection_driver.hpp │ ├── advection_package.cpp │ ├── advection_package.hpp │ ├── main.cpp │ ├── parthenon_app_inputs.cpp │ ├── parthinput.advection │ └── stokes.hpp ├── kokkos_pi │ ├── CMakeLists.txt │ └── kokkos_pi.cpp ├── particle_leapfrog │ ├── CMakeLists.txt │ ├── main.cpp │ ├── parthinput.particle_leapfrog │ ├── particle_leapfrog.cpp │ └── particle_leapfrog.hpp ├── particle_tracers │ ├── CMakeLists.txt │ ├── main.cpp │ ├── parthinput.particle_tracers │ ├── particle_tracers.cpp │ └── particle_tracers.hpp ├── particles │ ├── CMakeLists.txt │ ├── main.cpp │ ├── parthinput.particles │ ├── particles.cpp │ └── particles.hpp ├── poisson │ ├── CMakeLists.txt │ ├── main.cpp │ ├── parthenon_app_inputs.cpp │ ├── parthinput.poisson │ ├── poisson_driver.cpp │ ├── poisson_driver.hpp │ ├── poisson_package.cpp │ └── poisson_package.hpp ├── poisson_gmg │ ├── CMakeLists.txt │ ├── main.cpp │ ├── parthenon_app_inputs.cpp │ ├── parthinput.poisson │ ├── plot_convergence.py │ ├── poisson_driver.cpp │ ├── poisson_driver.hpp │ ├── poisson_equation.hpp │ ├── poisson_package.cpp │ └── poisson_package.hpp ├── sparse_advection │ ├── CMakeLists.txt │ ├── main.cpp │ ├── parthenon_app_inputs.cpp │ ├── parthinput.sparse_advection │ ├── sparse_advection_driver.cpp │ ├── sparse_advection_driver.hpp │ ├── sparse_advection_package.cpp │ └── sparse_advection_package.hpp └── stochastic_subgrid │ ├── CMakeLists.txt │ ├── main.cpp │ ├── parthenon_app_inputs.cpp │ ├── parthinput.stochastic_subgrid │ ├── stochastic_subgrid_driver.cpp │ ├── stochastic_subgrid_driver.hpp │ ├── stochastic_subgrid_package.cpp │ └── stochastic_subgrid_package.hpp ├── requirements.txt ├── scripts ├── check_docs_toc.py ├── combine_coverage.sh ├── darwin │ ├── base_setup.sh │ ├── build_fast.sh │ ├── install_python_scripts.sh │ ├── metrics.sh │ └── setup.sh ├── device_check.sh ├── docker │ ├── Dockerfile.hip-rocm │ ├── Dockerfile.nvcc │ └── ascent_build.patch ├── mathematica │ └── sparse_integrators.nb ├── python │ ├── .gitignore │ └── packages │ │ ├── parthenon_performance_app │ │ ├── LICENSE.txt │ │ ├── README.md │ │ ├── bin │ │ │ └── parthenon_metrics_app.py │ │ ├── parthenon_performance_app │ │ │ ├── __init__.py │ │ │ ├── githubapp.py │ │ │ ├── parthenon_performance_advection_analyzer.py │ │ │ ├── parthenon_performance_json_parser.py │ │ │ └── parthenon_performance_plotter.py │ │ ├── setup.cfg │ │ └── setup.py │ │ ├── parthenon_process_kernel_timer │ │ └── process_timer.py │ │ └── parthenon_tools │ │ ├── LICENSE.txt │ │ ├── README.md │ │ ├── parthenon_tools │ │ ├── __init__.py │ │ ├── compare_analytic.py │ │ ├── compute_asymmetry.py │ │ ├── contour1d.py │ │ ├── mergecsv.py │ │ ├── movie2d.py │ │ ├── phdf.py │ │ ├── phdf_diff.py │ │ ├── prettyparams.py │ │ └── report_asymmetry.py │ │ ├── pyproject.toml │ │ ├── setup.cfg │ │ └── setup.py └── retrigger-ci.sh ├── src ├── CMakeLists.txt ├── amr_criteria │ ├── amr_criteria.cpp │ ├── amr_criteria.hpp │ ├── refinement_package.cpp │ └── refinement_package.hpp ├── application_input.cpp ├── application_input.hpp ├── argument_parser.hpp ├── basic_types.hpp ├── bvals │ ├── boundary_conditions.cpp │ ├── boundary_conditions.hpp │ ├── boundary_conditions_generic.hpp │ ├── boundary_flag.cpp │ ├── bvals.cpp │ ├── bvals.hpp │ ├── comms │ │ ├── bnd_id.cpp │ │ ├── bnd_id.hpp │ │ ├── bnd_info.cpp │ │ ├── bnd_info.hpp │ │ ├── boundary_communication.cpp │ │ ├── build_boundary_buffers.cpp │ │ ├── bvals_in_one.hpp │ │ ├── bvals_utils.hpp │ │ ├── coalesced_buffers.cpp │ │ ├── coalesced_buffers.hpp │ │ ├── tag_map.cpp │ │ └── tag_map.hpp │ ├── neighbor_block.cpp │ └── neighbor_block.hpp ├── config.hpp.in ├── coordinates │ ├── coordinates.hpp │ ├── uniform_cartesian.hpp │ ├── uniform_coordinates.hpp │ ├── uniform_cylindrical.hpp │ └── uniform_spherical.hpp ├── defs.hpp ├── driver │ ├── driver.cpp │ ├── driver.hpp │ ├── multistage.cpp │ └── multistage.hpp ├── globals.cpp ├── globals.hpp ├── interface │ ├── Doxyfile │ ├── data_collection.cpp │ ├── data_collection.hpp │ ├── mesh_data.cpp │ ├── mesh_data.hpp │ ├── meshblock_data.cpp │ ├── meshblock_data.hpp │ ├── metadata.cpp │ ├── metadata.hpp │ ├── packages.hpp │ ├── params.cpp │ ├── params.hpp │ ├── sparse_pool.cpp │ ├── sparse_pool.hpp │ ├── state_descriptor.cpp │ ├── state_descriptor.hpp │ ├── swarm.cpp │ ├── swarm.hpp │ ├── swarm_comms.cpp │ ├── swarm_container.cpp │ ├── swarm_container.hpp │ ├── swarm_device_context.hpp │ ├── update.cpp │ ├── update.hpp │ ├── var_id.hpp │ ├── variable.cpp │ ├── variable.hpp │ ├── variable_pack.hpp │ ├── variable_state.cpp │ └── variable_state.hpp ├── kokkos_abstraction.hpp ├── kokkos_types.hpp ├── loop_bounds.hpp ├── mesh │ ├── domain.hpp │ ├── forest │ │ ├── block_ownership.cpp │ │ ├── block_ownership.hpp │ │ ├── forest.cpp │ │ ├── forest.hpp │ │ ├── forest_node.hpp │ │ ├── forest_topology.cpp │ │ ├── forest_topology.hpp │ │ ├── logical_coordinate_transformation.cpp │ │ ├── logical_coordinate_transformation.hpp │ │ ├── logical_location.cpp │ │ ├── logical_location.hpp │ │ ├── tree.cpp │ │ └── tree.hpp │ ├── mesh-amr_loadbalance.cpp │ ├── mesh-gmg.cpp │ ├── mesh.cpp │ ├── mesh.hpp │ ├── mesh_refinement.cpp │ ├── mesh_refinement.hpp │ ├── meshblock.cpp │ ├── meshblock.hpp │ └── meshblock_pack.hpp ├── outputs │ ├── ascent.cpp │ ├── histogram.cpp │ ├── history.cpp │ ├── io_wrapper.cpp │ ├── io_wrapper.hpp │ ├── output_parameters.hpp │ ├── output_utils.cpp │ ├── output_utils.hpp │ ├── outputs.cpp │ ├── outputs.hpp │ ├── outputs_package.cpp │ ├── outputs_package.hpp │ ├── parthenon_hdf5.cpp │ ├── parthenon_hdf5.hpp │ ├── parthenon_hdf5_attributes.cpp │ ├── parthenon_hdf5_attributes_read.cpp │ ├── parthenon_hdf5_attributes_write.cpp │ ├── parthenon_hdf5_base.hpp │ ├── parthenon_hdf5_types.hpp │ ├── parthenon_xdmf.cpp │ ├── parthenon_xdmf.hpp │ ├── restart.hpp │ ├── restart_hdf5.cpp │ └── restart_hdf5.hpp ├── pack │ ├── block_selector.hpp │ ├── make_pack_descriptor.cpp │ ├── make_pack_descriptor.hpp │ ├── make_swarm_pack_descriptor.hpp │ ├── pack_descriptor.cpp │ ├── pack_descriptor.hpp │ ├── pack_utils.hpp │ ├── scratch_variables.hpp │ ├── sparse_pack.cpp │ ├── sparse_pack.hpp │ ├── sparse_pack_base.cpp │ ├── sparse_pack_base.hpp │ ├── sparse_pack_cache.cpp │ ├── sparse_pack_cache.hpp │ ├── swarm_default_names.hpp │ ├── swarm_pack.hpp │ └── swarm_pack_base.hpp ├── parameter_input.cpp ├── parameter_input.hpp ├── parthenon │ ├── driver.hpp │ ├── package.hpp │ ├── parthenon.hpp │ └── prelude.hpp ├── parthenon_array_generic.hpp ├── parthenon_arrays.cpp ├── parthenon_arrays.hpp ├── parthenon_manager.cpp ├── parthenon_manager.hpp ├── parthenon_mpi.hpp ├── pgen │ └── default_pgen.cpp ├── prolong_restrict │ ├── pr_loops.hpp │ ├── pr_ops.hpp │ ├── prolong_restrict.cpp │ └── prolong_restrict.hpp ├── provenance.cpp.in ├── provenance.hpp ├── reconstruct │ ├── dc_inline.hpp │ └── plm_inline.hpp ├── solvers │ ├── bicgstab_solver.hpp │ ├── cg_solver.hpp │ ├── internal_prolongation.hpp │ ├── mg_solver.hpp │ ├── solver_base.hpp │ ├── solver_utils.hpp │ └── tridiag_solver.hpp ├── sparse │ ├── sparse_management.cpp │ └── sparse_management.hpp ├── tasks │ ├── tasks.cpp │ ├── tasks.hpp │ └── thread_pool.hpp ├── time_integration │ ├── butcher_integrator.cpp │ ├── low_storage_integrator.cpp │ ├── staged_integrator.cpp │ └── staged_integrator.hpp └── utils │ ├── alias_method.cpp │ ├── alias_method.hpp │ ├── array_to_tuple.hpp │ ├── bit_hacks.hpp │ ├── cell_center_offsets.cpp │ ├── cell_center_offsets.hpp │ ├── change_rundir.cpp │ ├── cleantypes.hpp │ ├── communication_buffer.hpp │ ├── concepts_lite.hpp │ ├── constants.hpp │ ├── error_checking.cpp │ ├── error_checking.hpp │ ├── hash.hpp │ ├── index_split.cpp │ ├── index_split.hpp │ ├── indexer.hpp │ ├── instrument.hpp │ ├── interpolation.hpp │ ├── loop_utils.hpp │ ├── morton_number.hpp │ ├── mpi_types.hpp │ ├── multi_pointer.hpp │ ├── object_pool.hpp │ ├── partition_stl_containers.hpp │ ├── reductions.hpp │ ├── robust.hpp │ ├── show_config.cpp │ ├── signal_handler.cpp │ ├── sort.hpp │ ├── string_utils.cpp │ ├── string_utils.hpp │ ├── type_list.hpp │ ├── unique_id.cpp │ ├── unique_id.hpp │ └── utils.hpp └── tst ├── CMakeLists.txt ├── catch2_define.cpp ├── integration └── CMakeLists.txt ├── performance ├── CMakeLists.txt ├── CPPLINT.cfg └── test_meshblock_data_iterator.cpp ├── regression ├── CMakeLists.txt ├── __init__.py ├── gold_standard │ ├── .gitignore │ └── make_tarball.sh ├── run_test.py ├── test_suites │ ├── __init__.py │ ├── advection_convergence │ │ ├── __init__.py │ │ ├── advection_convergence.py │ │ └── parthinput.advection │ ├── advection_outflow │ │ ├── __init__.py │ │ ├── advection_outflow.py │ │ └── parthinput.advection_outflow │ ├── advection_performance │ │ ├── __init__.py │ │ ├── advection_performance.py │ │ └── parthinput.advection_performance │ ├── advection_undersubscribed │ │ ├── __init__.py │ │ ├── advection_undersubscribed.py │ │ └── parthinput.advection_undersubscribed │ ├── boundary_exchange │ │ ├── __init__.py │ │ ├── boundary_exchange.py │ │ └── parthinput.boundary_exchange │ ├── bvals │ │ ├── __init__.py │ │ ├── bvals.py │ │ └── parthinput.advection_bvals │ ├── calculate_pi │ │ ├── __init__.py │ │ ├── calculate_pi.py │ │ └── parthinput.regression │ ├── diffusion │ │ ├── __init__.py │ │ ├── diffusion.py │ │ └── parthinput.diffusion │ ├── output_hdf5 │ │ ├── __init__.py │ │ ├── output_hdf5.py │ │ └── parthinput.advection │ ├── particle_leapfrog │ │ ├── __init__.py │ │ ├── parthinput.particle_leapfrog │ │ └── particle_leapfrog.py │ ├── particle_leapfrog_outflow │ │ ├── __init__.py │ │ ├── parthinput.particle_leapfrog_outflow │ │ └── particle_leapfrog_outflow.py │ ├── particle_tracers │ │ ├── __init__.py │ │ ├── parthinput.particle_tracers │ │ └── particle_tracers.py │ ├── poisson │ │ ├── __init__.py │ │ ├── parthinput.poisson │ │ └── poisson.py │ ├── poisson_gmg │ │ ├── __init__.py │ │ ├── parthinput.poisson │ │ └── poisson_gmg.py │ ├── restart │ │ ├── __init__.py │ │ ├── parthinput.restart │ │ ├── parthinput_override.restart │ │ └── restart.py │ ├── restart_fine │ │ ├── __init__.py │ │ ├── parthinput.restart_fine │ │ └── restart_fine.py │ └── sparse_advection │ │ ├── __init__.py │ │ ├── parthinput.sparse_advection │ │ └── sparse_advection.py └── utils │ ├── __init__.py │ └── test_case.py ├── style └── cpplint.py └── unit ├── CMakeLists.txt ├── test_concepts_lite.cpp ├── test_coordinates.cpp ├── test_data_collection.cpp ├── test_error_checking.cpp ├── test_forest.cpp ├── test_index_split.cpp ├── test_kokkos_abstraction.cpp ├── test_logical_location.cpp ├── test_mesh_data.cpp ├── test_meshblock_data_iterator.cpp ├── test_metadata.cpp ├── test_output_utils.cpp ├── test_parameter_input.cpp ├── test_pararrays.cpp ├── test_partitioning.cpp ├── test_scratch_variables.cpp ├── test_sparse_pack.cpp ├── test_state_descriptor.cpp ├── test_swarm.cpp ├── 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