├── .clang-format ├── .clang-tidy ├── .git-blame-ignore-revs ├── .github └── workflows │ ├── build_and_lint.yml │ ├── build_image.yml │ └── code_formatting.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── Jenkinsfile ├── LICENSE.txt ├── Makefile ├── README.md ├── docker ├── cuda │ └── Dockerfile └── rocm │ └── Dockerfile ├── docs ├── doxygen │ └── Doxyfile └── sphinx │ ├── Makefile │ ├── make.bat │ └── source │ ├── api.rst │ ├── conf.py │ ├── gettingstarted.rst │ ├── index.rst │ └── input.rst ├── examples ├── 1D │ ├── 123.txt │ ├── Creasey_shock.txt │ ├── Shu_Osher.txt │ ├── blast_1D.txt │ ├── constant.txt │ ├── noh_1D.txt │ ├── sod.txt │ ├── sound_wave.txt │ ├── square_wave.txt │ ├── stationary.txt │ ├── strong_shock.txt │ ├── test_3.txt │ ├── trac_pen.txt │ └── two_shocks.txt ├── 2D │ ├── Gresho.txt │ ├── Implosion_2D.txt │ ├── KH_discontinuous_2D.txt │ ├── KH_res_ind_2D.txt │ ├── Noh_2D.txt │ ├── Rayleigh_Taylor.txt │ ├── constant.txt │ ├── disk.txt │ ├── sod.txt │ └── sound_wave.txt ├── 3D │ ├── Brio_and_Wu.txt │ ├── Cosmological_Scaling_128.txt │ ├── Cosmological_Scaling_256.txt │ ├── Cosmological_Scaling_384.txt │ ├── Cosmological_cool_UV_50Mpc.txt │ ├── Cosmological_dm_50Mpc.txt │ ├── Cosmological_hydro_256_50Mpc.txt │ ├── Dai_and_Woodward.txt │ ├── Einfeldt_Strong_Rarefaction.txt │ ├── KH_res_ind_3D.txt │ ├── Noh_3D.txt │ ├── Ryu_and_Jones_1a.txt │ ├── Ryu_and_Jones_4d.txt │ ├── Scaling_128.txt │ ├── Scaling_256.txt │ ├── Spherical_Collapse.txt │ ├── Spherical_Overpressure.txt │ ├── Uniform.txt │ ├── Zeldovich_Pancake.txt │ ├── advecting_field_loop.txt │ ├── alfven_wave.txt │ ├── circularly_polarized_alfven_wave.txt │ ├── constant.txt │ ├── disk.txt │ ├── fast_magnetosonic.txt │ ├── float32_sound_wave.txt │ ├── mhd_blast.txt │ ├── mhd_contact_wave.txt │ ├── orszag_tang_vortex.txt │ ├── slow_magnetosonic.txt │ ├── sod.txt │ ├── sod256.txt │ └── sound_wave.txt ├── sample.txt └── scripts │ ├── acrun-hydro.sh │ ├── acrun-paris-hipfft.sh │ ├── acrun-paris-pfft.sh │ ├── acrun-paris-sor.sh │ ├── acrun-paris.sh │ ├── acrun-sor.sh │ ├── arun-hydro.sh │ ├── arun-paris-hipfft.sh │ ├── arun-paris-pfft.sh │ ├── arun-paris-sor.sh │ ├── arun-paris-sphere.sh │ ├── arun-paris.sh │ ├── arun-sor.sh │ ├── nrun-paris-cufft.sh │ ├── nrun-paris-pfft.sh │ ├── nrun-paris-sor.sh │ ├── nrun-paris.sh │ ├── nrun-sor.sh │ ├── parameter_file.txt │ ├── sphere.txt │ ├── srun-paris-cufft.sh │ ├── srun-paris-pfft.sh │ ├── srun-paris-sor.sh │ └── srun-paris.sh ├── python_scripts ├── Projection_Slice_Tutorial.ipynb ├── README.md ├── combine_hydro_particles.py ├── compress_snapshots.py ├── concat_2d_data.py ├── concat_3d_data.py ├── concat_internals.py ├── concat_particles.py ├── dask_distributed_template.py ├── dask_single_machine_template.py ├── data_compress_grid.py ├── data_compress_particles.py ├── load_cholla_snapshot.py ├── move_files.py ├── numdiff.py ├── plot_sod.py └── tools.py ├── scale_output_files ├── cosmo_outputs_high_redshift.txt ├── cosmo_outputs_z_6_0_100.txt ├── outputs_cosmo_15.txt ├── outputs_cosmo_2048.txt ├── outputs_cosmo_2048_z0.txt ├── outputs_cosmo_60.txt ├── outputs_cosmo_aLin_200.txt ├── outputs_cosmo_aLin_400.txt ├── outputs_cosmo_analysis_150.txt ├── outputs_cosmo_analysis_56.txt ├── outputs_cosmo_crocs.txt ├── outputs_cosmo_crocs_dmo.txt ├── outputs_cosmo_pk_boera.txt ├── outputs_cosmo_testing.txt ├── outputs_cosmo_z_100_0_200.txt ├── outputs_ps_comparison_n6.txt ├── outputs_single_output_z0.txt ├── outputs_single_output_z15.txt ├── outputs_single_output_z16.txt ├── outputs_single_output_z2.2.txt ├── outputs_single_output_z2.txt ├── outputs_single_output_z20.txt ├── outputs_single_output_z5.txt ├── outputs_single_output_z6.txt └── outputs_z_5_4.txt ├── src ├── analysis │ ├── analysis.cpp │ ├── analysis.h │ ├── feedback_analysis.cpp │ ├── feedback_analysis.h │ ├── feedback_analysis_gpu.cu │ ├── io_analysis.cpp │ ├── lya_statistics.cpp │ └── phase_diagram.cpp ├── chemistry_gpu │ ├── chemistry_functions.cpp │ ├── chemistry_functions_gpu.cu │ ├── chemistry_gpu.h │ ├── chemistry_io.cpp │ ├── rates.cuh │ ├── rates_Katz95.cuh │ ├── uvb_rates_P19.txt │ └── uvb_rates_V21.txt ├── cooling │ ├── cloudy_coolingcurve.txt │ ├── cooling_cuda.cu │ ├── cooling_cuda.h │ ├── load_cloudy_texture.cu │ ├── load_cloudy_texture.h │ └── texture_utilities.h ├── cooling_grackle │ ├── cool_grackle.cpp │ ├── cool_grackle.h │ └── grackle_functions.cpp ├── cosmology │ ├── cosmology.cpp │ ├── cosmology.h │ ├── cosmology_functions.cpp │ ├── cosmology_functions_gpu.cu │ ├── cosmology_functions_gpu.h │ └── io_cosmology.cpp ├── dust │ ├── dust_cuda.cu │ ├── dust_cuda.h │ └── dust_cuda_tests.cpp ├── global │ ├── global.cpp │ ├── global.h │ ├── global_cuda.cu │ └── global_cuda.h ├── gravity │ ├── grav3D.cpp │ ├── grav3D.h │ ├── gravity_boundaries.cpp │ ├── gravity_boundaries_gpu.cu │ ├── gravity_functions.cpp │ ├── gravity_functions_gpu.cu │ ├── gravity_restart.cpp │ ├── paris │ │ ├── HenryPeriodic.cu │ │ ├── HenryPeriodic.hpp │ │ ├── ParisPeriodic.cu │ │ ├── ParisPeriodic.hpp │ │ ├── PoissonZero3DBlockedGPU.cu │ │ ├── PoissonZero3DBlockedGPU.hpp │ │ └── README.md │ ├── potential_SOR_3D.cpp │ ├── potential_SOR_3D.h │ ├── potential_SOR_3D_gpu.cu │ ├── potential_paris_3D.cu │ ├── potential_paris_3D.h │ ├── potential_paris_galactic.cu │ ├── potential_paris_galactic.h │ └── static_grav.h ├── grid │ ├── boundary_conditions.cpp │ ├── cuda_boundaries.cu │ ├── cuda_boundaries.h │ ├── grid3D.cpp │ ├── grid3D.h │ ├── grid_enum.h │ ├── initial_conditions.cpp │ └── mpi_boundaries.cpp ├── h_correction │ ├── flux_correction.h │ ├── h_correction_2D_cuda.cu │ ├── h_correction_2D_cuda.h │ ├── h_correction_3D_cuda.cu │ └── h_correction_3D_cuda.h ├── hydro │ ├── hydro_cuda.cu │ ├── hydro_cuda.h │ └── hydro_cuda_tests.cu ├── integrators │ ├── VL_1D_cuda.cu │ ├── VL_1D_cuda.h │ ├── VL_2D_cuda.cu │ ├── VL_2D_cuda.h │ ├── VL_3D_cuda.cu │ ├── VL_3D_cuda.h │ ├── simple_1D_cuda.cu │ ├── simple_1D_cuda.h │ ├── simple_2D_cuda.cu │ ├── simple_2D_cuda.h │ ├── simple_3D_cuda.cu │ └── simple_3D_cuda.h ├── io │ ├── io.cpp │ ├── io.h │ ├── io_gpu.cu │ ├── io_parallel.cpp │ └── io_tests.cpp ├── main.cpp ├── main_tests.cpp ├── mhd │ ├── ct_electric_fields.cu │ ├── ct_electric_fields.h │ ├── ct_electric_fields_tests.cu │ ├── magnetic_divergence.cu │ ├── magnetic_divergence.h │ ├── magnetic_divergence_tests.cu │ ├── magnetic_update.cu │ ├── magnetic_update.h │ └── magnetic_update_tests.cu ├── model │ ├── disk_ICs.cpp │ └── disk_galaxy.h ├── mpi │ ├── cuda_mpi_routines.cu │ ├── cuda_mpi_routines.h │ ├── mpi_routines.cpp │ └── mpi_routines.h ├── particles │ ├── density_CIC.cpp │ ├── density_CIC.h │ ├── density_CIC_gpu.cu │ ├── density_boundaries.cpp │ ├── density_boundaries_gpu.cu │ ├── feedback_CIC_gpu.cu │ ├── gravity_CIC.cpp │ ├── gravity_CIC_gpu.cu │ ├── io_particles.cpp │ ├── particles_3D.cpp │ ├── particles_3D.h │ ├── particles_3D_gpu.cu │ ├── particles_boundaries.cpp │ ├── particles_boundaries_cpu.cpp │ ├── particles_boundaries_gpu.cu │ ├── particles_boundaries_gpu.h │ ├── particles_dynamics.cpp │ ├── particles_dynamics_gpu.cu │ ├── starburst99_snr.txt │ └── supernova.h ├── reconstruction │ ├── pcm_cuda.cu │ ├── pcm_cuda.h │ ├── plmc_cuda.cu │ ├── plmc_cuda.h │ ├── plmc_cuda_tests.cu │ ├── plmp_cuda.cu │ ├── plmp_cuda.h │ ├── ppmc_cuda.cu │ ├── ppmc_cuda.h │ ├── ppmc_cuda_tests.cu │ ├── ppmp_cuda.cu │ ├── ppmp_cuda.h │ ├── reconstruction.h │ └── reconstruction_tests.cu ├── riemann_solvers │ ├── exact_cuda.cu │ ├── exact_cuda.h │ ├── hll_cuda.cu │ ├── hll_cuda.h │ ├── hllc_cuda.cu │ ├── hllc_cuda.h │ ├── hllc_cuda_tests.cu │ ├── hlld_cuda.cu │ ├── hlld_cuda.h │ ├── hlld_cuda_tests.cu │ ├── roe_cuda.cu │ └── roe_cuda.h ├── system_tests │ ├── cooling_system_tests.cpp │ ├── gravity_system_tests.cpp │ ├── hydro_system_tests.cpp │ ├── input_files │ │ ├── blank_settings_file.txt │ │ ├── tCOOLINGSYSTEMConstant5_CorrectInputExpectCorrectOutput.txt │ │ ├── tCOOLINGSYSTEMConstant7_CorrectInputExpectCorrectOutput.txt │ │ ├── tCOOLINGSYSTEMConstant8_CorrectInputExpectCorrectOutput.txt │ │ ├── tGRAVITYSYSTEMSphericalCollapse_CorrectInputExpectCorrectOutput.txt │ │ ├── tHYDROSYSTEMSodShockTube_OneDimensionalCorrectInputExpectCorrectOutput.txt │ │ ├── tHYDROSYSTEMSodShockTube_TwoDimensionalCorrectInputExpectCorrectOutput.txt │ │ ├── tHYDROtMHDReadGridHdf5_RestartSlowWaveExpectCorrectOutput.txt │ │ ├── tHYDROtMHDSYSTEMConstant_CorrectInputExpectCorrectOutput.txt │ │ ├── tHYDROtMHDSYSTEMSodShockTubeParameterizedMpi_CorrectInputExpectCorrectOutput.txt │ │ ├── tHYDROtMHDSYSTEMSoundWave3D_CorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_AdvectingFieldLoopCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_BrioAndWuShockTubeCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_ConstantWithMagneticFieldCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_ConstantWithZeroMagneticFieldCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_DaiAndWoodwardShockTubeCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_EinfeldtStrongRarefactionCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_MhdBlastWaveCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_OrszagTangVortexCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_RyuAndJones1aShockTubeCorrectInputExpectCorrectOutput.txt │ │ ├── tMHDSYSTEMParameterizedMpi_RyuAndJones4dShockTubeCorrectInputExpectCorrectOutput.txt │ │ └── tPARTICLESSYSTEMSphericalCollapse_CorrectInputExpectCorrectOutput.txt │ ├── mhd_system_tests.cpp │ ├── particles_system_tests.cpp │ ├── system_tester.cpp │ └── system_tester.h └── utils │ ├── DeviceVector.h │ ├── DeviceVector_tests.cu │ ├── cuda_utilities.cpp │ ├── cuda_utilities.h │ ├── cuda_utilities_tests.cpp │ ├── debug_utilities.cu │ ├── 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