Merge branch 'development' into new_shock_flag_call

.github/workflows/flame_wave-compare.yml

@@ -36,7 +36,7 @@ jobs:
       - name: Run flame_wave
         run: |
           cd Exec/science/flame_wave
-          ./Castro2d.gnu.DEBUG.ex inputs_2d.testsuite max_step=2 castro.sum_interval=1 amr.plot_files_output=0 amr.checkpoint_files_output=0
+          ./Castro2d.gnu.DEBUG.ex inputs_2d.testsuite max_step=2 castro.sum_interval=1 amr.plot_files_output=1 amr.checkpoint_files_output=0
 
       - name: Check grid_diag.out
         run: |
@@ -47,3 +47,10 @@ jobs:
         run: |
           cd Exec/science/flame_wave
           diff species_diag.out ci-benchmarks/species_diag.out
+
+      - name: Check job_info parameters
+        run: |
+          cd Exec/science/flame_wave
+          line_no=`grep -n "Inputs File Parameters" plt00000/job_info | cut -d ":" -f 1`
+          tail -n +$(($line_no -1)) plt00000/job_info > tmp.txt
+          diff tmp.txt ci-benchmarks/job_info_params.txt

.github/workflows/gh-pages.yml

@@ -44,7 +44,7 @@ jobs:
         run: ./deploy_docs_action.sh
 
       - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./out

.github/workflows/style/check_trailing_whitespaces.sh

@@ -6,6 +6,7 @@ find . -type d \( -name .git \
                   -o -path ./paper \
                   -o -name build -o -name install \
                   -o -name tmp_build_dir -o -name tmp_install_dir \
+                  -o -name ci-benchmarks \
                   -o -path ./util/gcem \
                \) -prune -o \
        -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \

Exec/science/flame_wave/ci-benchmarks/job_info_params.txt

@@ -0,0 +1,258 @@
+==============================================================================
+ Inputs File Parameters
+==============================================================================
+[*] castro.diffuse_temp = 1
+[*] castro.diffuse_cutoff_density = 20000
+[*] castro.diffuse_cutoff_density_hi = 50000
+[*] castro.diffuse_cond_scale_fac = 10
+    castro.use_point_mass = 0
+    castro.point_mass = 0
+    castro.point_mass_fix_solution = 0
+    castro.gw_dist = 0
+    castro.point_mass_offset_is_true = 0
+    castro.point_mass_location_offset = 0
+[*] castro.rotational_period = 0.001
+[*] castro.rotation_include_centrifugal = 0
+    castro.rotation_include_coriolis = 1
+    castro.rot_source_type = 4
+    castro.implicit_rotation_update = 1
+[*] castro.rot_axis = 2
+    castro.sponge_lower_radius = -1
+    castro.sponge_upper_radius = -1
+[*] castro.sponge_lower_density = 1
+[*] castro.sponge_upper_density = 100
+    castro.sponge_lower_pressure = -1
+    castro.sponge_upper_pressure = -1
+    castro.sponge_lower_factor = 0
+    castro.sponge_upper_factor = 1
+    castro.sponge_target_x_velocity = 0
+    castro.sponge_target_y_velocity = 0
+    castro.sponge_target_z_velocity = 0
+[*] castro.sponge_timescale = 1e-07
+    castro.state_interp_order = 1
+    castro.lin_limit_state_interp = 0
+    castro.do_reflux = 1
+    castro.update_sources_after_reflux = 1
+    castro.allow_non_unit_aspect_zones = 0
+    castro.difmag = 0.1
+[*] castro.small_dens = 1e-05
+[*] castro.small_temp = 1e+06
+[*] castro.small_pres = 2.98096e+09
+[*] castro.small_ener = 8.25345e+14
+[*] castro.do_hydro = 1
+    castro.time_integration_method = 0
+    castro.limit_fourth_order = 1
+    castro.initialization_is_cell_average = 0
+    castro.use_reconstructed_gamma1 = 0
+    castro.add_ext_src = 0
+    castro.hybrid_hydro = 0
+    castro.ppm_type = 1
+    castro.ppm_do_limiting = 1
+    castro.mhd_limit_characteristic = 1
+    castro.ppm_temp_fix = 0
+    castro.plm_iorder = 2
+    castro.plm_limiter = 2
+    castro.hybrid_riemann = 0
+    castro.riemann_solver = 0
+    castro.cg_maxiter = 12
+    castro.cg_tol = 1e-05
+    castro.cg_blend = 2
+    castro.use_flattening = 1
+    castro.transverse_use_eos = 0
+    castro.transverse_reset_density = 1
+    castro.transverse_reset_rhoe = 0
+    castro.dual_energy_eta1 = 1
+    castro.dual_energy_eta2 = 0.0001
+    castro.use_pslope = 0
+    castro.pslope_cutoff_density = -1e+20
+    castro.limit_fluxes_on_small_dens = 0
+    castro.speed_limit = 0
+[*] castro.do_sponge = 1
+    castro.sponge_implicit = 1
+    castro.ext_src_implicit = 0
+    castro.source_term_predictor = 0
+    castro.first_order_hydro = 0
+    castro.xl_ext_bc_type = -1
+    castro.xr_ext_bc_type = -1
+[*] castro.yl_ext_bc_type = 1
+    castro.yr_ext_bc_type = -1
+    castro.zl_ext_bc_type = -1
+    castro.zr_ext_bc_type = -1
+    castro.hse_zero_vels = 0
+[*] castro.hse_interp_temp = 1
+    castro.hse_fixed_temp = -1e+200
+[*] castro.hse_reflect_vels = 1
+[*] castro.fill_ambient_bc = 1
+[*] castro.ambient_fill_dir = 1
+[*] castro.ambient_outflow_vel = 1
+    castro.clamp_ambient_temp = 0
+    castro.ambient_safety_factor = 1.1
+    castro.ambient_density = -1e+200
+    castro.ambient_temp = -1e+200
+    castro.ambient_energy = -1e+200
+    castro.sdc_order = 2
+    castro.sdc_quadrature = 0
+    castro.sdc_extra = 0
+    castro.sdc_solver = 1
+    castro.use_axisymmetric_geom_source = 1
+    castro.add_sdc_react_source_to_advection = 1
+    castro.hydro_memory_footprint_ratio = -1
+    castro.fixed_dt = -1
+    castro.initial_dt = -1
+    castro.dt_cutoff = 1e-12
+    castro.max_dt = 1e+200
+    castro.cfl = 0.8
+[*] castro.init_shrink = 0.1
+    castro.change_max = 1.1
+    castro.check_dt_before_advance = 1
+    castro.check_dt_after_advance = 1
+    castro.plot_per_is_exact = 0
+    castro.small_plot_per_is_exact = 0
+    castro.use_retry = 1
+    castro.retry_subcycle_factor = 0.5
+    castro.retry_small_density_cutoff = -1e+200
+    castro.abundance_failure_tolerance = 0.01
+    castro.abundance_failure_rho_cutoff = -1e+200
+    castro.use_post_step_regrid = 0
+    castro.max_subcycles = 10
+    castro.sdc_iters = 2
+    castro.stopping_criterion_field = 
+    castro.stopping_criterion_value = 1e+200
+    castro.dtnuc_e = 1e+200
+    castro.dtnuc_X = 1e+200
+    castro.dtnuc_X_threshold = 0.001
+[*] castro.do_react = 1
+[*] castro.react_T_min = 6e+07
+    castro.react_T_max = 1e+200
+[*] castro.react_rho_min = 100
+[*] castro.react_rho_max = 5e+07
+    castro.disable_shock_burning = 0
+    castro.shock_detection_threshold = 0.666667
+    castro.shock_detection_include_sources = 1
+    castro.T_guess = 1e+08
+    castro.drive_initial_convection = 0
+    castro.drive_initial_convection_tmax = 1e+200
+    castro.drive_initial_convection_reinit_period = 1e+200
+[*] castro.do_grav = 1
+    castro.moving_center = 0
+[*] castro.grav_source_type = 2
+[*] castro.do_rotation = 1
+    castro.bndry_func_thread_safe = 1
+    castro.grown_factor = 1
+    castro.star_at_center = -1
+    castro.do_scf_initial_model = 0
+    castro.scf_maximum_density = -1e+06
+    castro.scf_equatorial_radius = -1e+09
+    castro.scf_polar_radius = -1e+09
+    castro.scf_relax_tol = 0.001
+    castro.scf_max_iterations = 30
+    castro.do_special_tagging = 0
+    castro.max_tagging_radius = 10
+[*] castro.verbose = 1
+    castro.dump_old = 0
+    castro.domain_is_plane_parallel = 0
+[*] castro.print_update_diagnostics = 1
+[*] castro.sum_interval = 1
+    castro.sum_per = -1
+    castro.job_name = Castro
+    castro.output_at_completion = 1
+    castro.reset_checkpoint_time = -1e+200
+    castro.reset_checkpoint_step = -1
+    castro.store_omegadot = 0
+    castro.store_burn_weights = 0
+    castro.abort_on_invalid_params = 0
+    castro.do_radiation = -1
+[*] gravity.gravity_type = ConstantGrav
+[*] gravity.const_grav = -1.5e+14
+    gravity.direct_sum_bcs = 0
+    gravity.drdxfac = 1
+    gravity.lnum = 0
+    gravity.verbose = 0
+    gravity.no_sync = 0
+    gravity.do_composite_phi_correction = 1
+    gravity.max_solve_level = 14
+    gravity.get_g_from_phi = 0
+    gravity.mlmg_max_fmg_iter = 0
+    gravity.mlmg_agglomeration = 1
+    gravity.mlmg_consolidation = 1
+    gravity.mlmg_nsolve = 0
+    diffusion.verbose = 0
+    diffusion.mlmg_maxorder = 4
+[*] problem.dtemp = 1.2e+09
+[*] problem.x_half_max = 20480
+[*] problem.x_half_width = 2048
+[*] problem.X_min = 0.01
+    problem.tag_by_density = 1
+[*] problem.cutoff_density = 25000
+    problem.refine_height = 3600
+[*] problem.T_hi = 2e+08
+    problem.T_star = 1e+08
+[*] problem.T_lo = 8e+06
+[*] problem.dens_base = 3.43e+06
+[*] problem.H_star = 2000
+[*] problem.atm_delta = 100
+    problem.fuel1_name = helium-4
+    problem.fuel2_name = 
+    problem.fuel3_name = 
+    problem.fuel4_name = 
+[*] problem.ash1_name = nickel-56
+    problem.ash2_name = 
+    problem.ash3_name = 
+    problem.fuel1_frac = 1
+    problem.fuel2_frac = 0
+    problem.fuel3_frac = 0
+    problem.fuel4_frac = 0
+    problem.ash1_frac = 1
+    problem.ash2_frac = 0
+    problem.ash3_frac = 0
+    problem.low_density_cutoff = 0.0001
+    problem.smallx = 1e-10
+[*] problem.x_refine_distance = 61440
+[*] problem.max_hse_tagging_level = 3
+[*] problem.max_base_tagging_level = 2
+    integrator.X_reject_buffer = 1
+    integrator.call_eos_in_rhs = 1
+    integrator.integrate_energy = 1
+    integrator.jacobian = 1
+    integrator.burner_verbose = 0
+[*] integrator.rtol_spec = 1e-06
+    integrator.rtol_enuc = 1e-06
+[*] integrator.atol_spec = 1e-06
+    integrator.atol_enuc = 1e-06
+    integrator.renormalize_abundances = 0
+    integrator.SMALL_X_SAFE = 1e-30
+    integrator.MAX_TEMP = 1e+11
+[*] integrator.react_boost = 10
+    integrator.ode_max_steps = 150000
+    integrator.ode_max_dt = 1e+30
+    integrator.use_jacobian_caching = 1
+    integrator.nonaka_i = 0
+    integrator.nonaka_j = 0
+    integrator.nonaka_k = 0
+    integrator.nonaka_level = 0
+    integrator.nonaka_file = nonaka_plot.dat
+    integrator.use_burn_retry = 0
+    integrator.retry_swap_jacobian = 1
+    integrator.retry_rtol_spec = 1e-12
+    integrator.retry_rtol_enuc = 1e-06
+    integrator.retry_atol_spec = 1e-08
+    integrator.retry_atol_enuc = 1e-06
+    integrator.do_species_clip = 1
+    integrator.use_number_densities = 0
+    integrator.sdc_burn_tol_factor = 1
+    integrator.scale_system = 0
+    integrator.nse_iters = 3
+    integrator.nse_deriv_dt_factor = 0.05
+    integrator.nse_include_enu_weak = 1
+    integrator.linalg_do_pivoting = 1
+    screening.enable_chabrier1998_quantum_corr = 0
+    integrator.subtract_internal_energy = 0
+    eos.use_eos_coulomb = 1
+    eos.eos_input_is_constant = 1
+    eos.eos_ttol = 1e-08
+    eos.eos_dtol = 1e-08
+    eos.prad_limiter_rho_c = -1
+    eos.prad_limiter_delta_rho = -1
+    network.small_x = 1e-30
+[*] network.use_tables = 1
+    network.use_c12ag_deboer17 = 0