├── LICENSE ├── Makefile.in ├── README.md ├── configure.py ├── dat ├── C2H2.chem ├── C2H4.chem ├── C2H6.chem ├── CH4.chem ├── CO.chem ├── CO2.chem ├── H2-H2-eq.orton.txt ├── H2-H2-eq.xiz.txt ├── H2-H2-nm.orton.txt ├── H2-H2-nm.xiz.txt ├── H2-He-eq.orton.txt ├── H2-He-eq.xiz.txt ├── H2-He-nm.orton.txt ├── H2-He-nm.xiz.txt ├── H2.chem ├── H2O.chem ├── H2S.chem ├── He.chem ├── N2.chem ├── N2O.chem ├── NH3.chem ├── NH4SH.chem ├── O2.chem ├── O3.chem ├── OCS.chem ├── PH3.chem ├── SO2.chem └── solar.txt ├── inputs ├── athinput.radjup ├── athinput.thermodynamics ├── hydro │ ├── athinput.blast │ ├── athinput.blast_cyl │ ├── athinput.blast_latlon │ ├── athinput.blast_sph │ ├── athinput.disk_cyl │ ├── athinput.disk_sph │ ├── athinput.dmr │ ├── athinput.dmr_amr │ ├── athinput.einfeldt1125 │ ├── athinput.einfeldt1203 │ ├── athinput.hs94 │ ├── athinput.jcrm2d │ ├── athinput.jcrm3d │ ├── athinput.jet │ ├── athinput.kh │ ├── athinput.linear_wave2d │ ├── athinput.linear_wave3d │ ├── athinput.lw_implode │ ├── athinput.noh2d │ ├── athinput.rt2 │ ├── athinput.rt2d │ ├── athinput.rt3d │ ├── athinput.shk_cloud │ ├── athinput.shu_osher │ ├── athinput.sod │ ├── athinput.twogas │ └── athinput.twoibw ├── hydro_gr │ ├── athinput.bondi │ └── athinput.geodesic ├── hydro_sr │ ├── athinput.linear_wave │ ├── athinput.mb_1 │ ├── athinput.mb_2 │ ├── athinput.mb_3 │ └── athinput.mb_4 ├── mhd │ ├── athinput.blast │ ├── athinput.bw │ ├── athinput.cpaw2d │ ├── athinput.field_loop │ ├── athinput.field_loop_poles │ ├── athinput.linear_wave2d │ ├── athinput.linear_wave2d_amr │ ├── athinput.linear_wave3d │ ├── athinput.orszag-tang │ ├── athinput.rj2a │ ├── athinput.rotor │ └── athinput.test_outputs ├── mhd_gr │ ├── athinput.blast │ ├── athinput.fm_torus │ └── athinput.magnetized_inflow ├── mhd_sr │ ├── athinput.linear_wave │ ├── athinput.mub_1 │ ├── athinput.mub_2 │ ├── athinput.mub_3 │ └── athinput.mub_4 └── shallow_water │ ├── athinput.galewsky04 │ ├── athinput.jupole │ ├── athinput.jupole.mpi │ ├── athinput.jupole2 │ ├── athinput.particle1 │ ├── athinput.sw │ ├── athinput.swbeta │ └── athinput.swgv ├── src ├── NOTES ├── athena.hpp ├── athena_arrays.hpp ├── bvals │ ├── bvals.cpp │ ├── bvals.hpp │ ├── bvals_buffer.cpp │ ├── bvals_cc.cpp │ ├── bvals_fc.cpp │ ├── bvals_pt.cpp │ ├── flux_correction_cc.cpp │ ├── flux_correction_fc.cpp │ ├── get_boundary_flag.cpp │ ├── outflow.cpp │ ├── polarwedge.cpp │ └── reflect.cpp ├── chemistry │ ├── chem_solver.hpp │ ├── condensation.hpp │ ├── molecule.cpp │ ├── molecule.hpp │ ├── reaction.cpp │ ├── reaction.hpp │ └── sat_vapor_pres.hpp ├── coordinates │ ├── cartesian.cpp │ ├── coordinates.cpp │ ├── coordinates.hpp │ ├── cylindrical.cpp │ ├── geometry.cpp │ ├── geometry.hpp │ ├── kerr-schild.cpp │ ├── minkowski.cpp │ ├── schwarzschild.cpp │ ├── spherical_latlon.cpp │ └── spherical_polar.cpp ├── defs.hpp ├── defs.hpp.in ├── eos │ ├── adiabatic_hydro.cpp │ ├── adiabatic_hydro_gr.cpp │ ├── adiabatic_hydro_sr.cpp │ ├── adiabatic_mhd.cpp │ ├── adiabatic_mhd_gr.cpp │ ├── adiabatic_mhd_sr.cpp │ ├── eos.hpp │ ├── heterogeneous_hydro.cpp │ ├── isothermal_hydro.cpp │ ├── isothermal_mhd.cpp │ └── shallow_water_hydro.cpp ├── field │ ├── calculate_corner_e.cpp │ ├── ct.cpp │ ├── field.cpp │ └── field.hpp ├── globals.cpp ├── globals.hpp ├── hydro │ ├── add_flux_divergence.cpp │ ├── calculate_fluxes.cpp │ ├── hydro.cpp │ ├── hydro.hpp │ ├── new_blockdt.cpp │ ├── rsolvers │ │ ├── hydro │ │ │ ├── hllc.cpp │ │ │ ├── hllc_rel.cpp │ │ │ ├── hlle.cpp │ │ │ ├── hlle_rel.cpp │ │ │ ├── hlle_rel_no_transform.cpp │ │ │ ├── llf_rel.cpp │ │ │ ├── llf_rel_no_transform.cpp │ │ │ └── roe.cpp │ │ ├── mhd │ │ │ ├── hlld.cpp │ │ │ ├── hlld_iso.cpp │ │ │ ├── hlld_rel.cpp │ │ │ ├── hlle_mhd.cpp │ │ │ ├── hlle_mhd_rel.cpp │ │ │ ├── hlle_mhd_rel_no_transform.cpp │ │ │ ├── llf_mhd_rel.cpp │ │ │ ├── llf_mhd_rel_no_transform.cpp │ │ │ └── roe_mhd.cpp │ │ ├── roe_heterogeneous.cpp │ │ └── roe_shallow_water.cpp │ └── srcterms │ │ ├── constant_acc.cpp │ │ ├── coriolis_acc.cpp │ │ ├── hydro_srcterms.cpp │ │ ├── hydro_srcterms.hpp │ │ └── pointmass.cpp ├── main.template ├── main_dynamics.cpp ├── main_radiation.cpp ├── math_funcs.hpp ├── mesh │ ├── mesh.cpp │ ├── mesh.hpp │ ├── mesh_refinement.cpp │ ├── mesh_refinement.hpp │ ├── meshblock.cpp │ ├── meshblock_tree.cpp │ └── meshblock_tree.hpp ├── misc.cpp ├── misc.hpp ├── outputs │ ├── athena_hdf5.cpp │ ├── formatted_table.cpp │ ├── history.cpp │ ├── io_wrapper.cpp │ ├── io_wrapper.hpp │ ├── netcdf.cpp │ ├── outputs.cpp │ ├── outputs.hpp │ ├── particle_table.cpp │ ├── restart.cpp │ └── vtk.cpp ├── parameter_input.cpp ├── parameter_input.hpp ├── particle │ ├── particle.cpp │ ├── particle.hpp │ └── property_update.cpp ├── pgen │ ├── blast.cpp │ ├── cpaw.cpp │ ├── default_pgen.cpp │ ├── disk.cpp │ ├── dmr.cpp │ ├── field_loop.cpp │ ├── field_loop_poles.cpp │ ├── galewsky04.cpp │ ├── gr_blast.cpp │ ├── gr_bondi.cpp │ ├── gr_geodesic_infall.cpp │ ├── gr_linear_wave.cpp │ ├── gr_mhd_inflow.cpp │ ├── gr_shock_tube.cpp │ ├── gr_torus.cpp │ ├── hs94.cpp │ ├── jcrm.cpp │ ├── jet.cpp │ ├── jupiter_pole.cpp │ ├── jupiter_pole2.cpp │ ├── kh.cpp │ ├── linear_wave.cpp │ ├── lw_implode.cpp │ ├── noh.cpp │ ├── orszag_tang.cpp │ ├── radconv.cpp │ ├── rotor.cpp │ ├── rt.cpp │ ├── rt2.cpp │ ├── saturn1d.cpp │ ├── shk_cloud.cpp │ ├── shock_tube.cpp │ ├── showman06.cpp │ ├── shu_osher.cpp │ ├── sw.cpp │ ├── sw_dambreak.cpp │ ├── swbeta.cpp │ ├── swgv.cpp │ ├── test_particle.cpp │ ├── twogas.cpp │ └── twoibw.cpp ├── physics │ ├── held_suarez_94.cpp │ └── held_suarez_94.hpp ├── radiation │ ├── absorber.cpp │ ├── absorber.hpp │ ├── cia_xiz_orton.cpp │ ├── disort_wrapper.cpp │ ├── disort_wrapper.hpp │ ├── hitran_absorber.cpp │ ├── radiation.cpp │ └── radiation.hpp ├── reconstruct │ ├── dc.cpp │ ├── plm.cpp │ ├── ppm.cpp │ ├── reconstruction.cpp │ ├── reconstruction.hpp │ └── weno3.cpp ├── task_list │ ├── task_list.cpp │ ├── task_list.hpp │ └── time_integrator.cpp └── utils │ 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