add a 3d inputs for the massive star problem

Exec/science/massive_star/inputs_3d.nse

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+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+
+amr.plot_files_output = 1
+amr.checkpoint_files_output = 1
+
+max_step = 50
+stop_time = 360000
+
+geometry.is_periodic = 0 0
+geometry.coord_sys = 0         # r-z coordinates
+
+geometry.prob_lo   =  0.    0.    0.
+geometry.prob_hi   =  1.6384e10 1.6384e10 1.6384e10
+
+amr.n_cell         = 512 512 512
+
+amr.max_level      = 3      # maximum level number allowed
+
+castro.lo_bc       =  2 2 2
+castro.hi_bc       =  2 2 2
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# 0 = Interior           3 = Symmetry
+# 1 = Inflow             4 = SlipWall
+# 2 = Outflow            5 = NoSlipWall
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+
+# GPU options
+castro.hydro_memory_footprint_ratio = 3
+
+
+castro.do_hydro = 1
+castro.do_grav  = 1
+castro.do_react = 1
+castro.do_sponge = 1
+
+castro.ppm_type = 1
+castro.ppm_temp_fix = 0
+castro.use_pslope = 1
+
+castro.use_flattening = 1
+
+castro.riemann_solver = 1
+
+gravity.gravity_type = MonopoleGrav
+gravity.drdxfac = 2
+castro.grav_source_type = 4
+
+castro.sponge_upper_density = 1.e3
+castro.sponge_lower_density = 1.e2
+castro.sponge_timescale     = 1.e-3
+
+castro.cfl            = 0.4     # cfl number for hyperbolic system
+castro.init_shrink    = 0.01     # scale back initial timestep by this factor
+castro.change_max     = 1.2    # factor by which dt is allowed to change each timestep
+castro.sum_interval   = 10       # timesteps between computing and printing volume averages
+
+#castro.dtnuc_e = 0.25
+#castro.dtnuc_X = 0.25
+
+amr.ref_ratio       = 2 2 2 2 # refinement ratio
+amr.regrid_int      = 10000   # how often to regrid
+amr.n_error_buf     = 4 2 2 2 # number of buffer cells in error est
+amr.grid_eff        = 0.7     # what constitutes an efficient grid
+
+amr.check_file      = massive_star_chk     # root name of checkpoint file
+amr.check_int       = 200     # number of timesteps between checkpoints
+
+amr.plot_file       = massive_star_plt     # root name of plot file
+amr.plot_per = 5.0
+amr.derive_plot_vars = ALL
+castro.store_burn_weights = 0
+
+amr.small_plot_file       = massive_star_smallplt     # root name of plot file
+amr.small_plot_per = 0.5
+amr.small_plot_vars = density Temp in_nse\
+amr.derive_small_plot_vars = abar Ye enuc MachNumber magvel magvort
+
+fab.format = NATIVE_32
+
+castro.plot_per_is_exact = 0
+
+
+amr.max_grid_size   = 64       # maximum grid size allowed -- used to control parallelism
+amr.blocking_factor = 32       # block factor in grid generation
+
+amr.v               = 1       # control verbosity in Amr.cpp
+castro.v            = 1       # control verbosity in Castro.cpp
+
+
+castro.small_dens   = 1.0
+castro.small_temp   = 1.e6
+
+castro.time_integration_method = 3
+castro.use_retry = 1
+castro.max_subcycles = 16
+
+# problem initialization
+
+problem.model_name =  "15m_500_sec.aprox19.hse.5.00km"
+
+problem.perturb_model = 1
+problem.velpert_amplitude = 5.e6
+
+problem.interpolate_pres = 1
+
+# convection
+
+castro.drive_initial_convection = 1
+castro.drive_initial_convection_reinit_period = 2
+castro.drive_initial_convection_tmax = 50
+
+# refinement
+
+amr.refinement_indicators = denerr denerr2 denerr3
+
+amr.refine.denerr.max_level = 1
+amr.refine.denerr.value_greater = 1.e3
+amr.refine.denerr.field_name = density
+
+amr.refine.denerr2.max_level = 2
+amr.refine.denerr2.value_greater = 1.e4
+amr.refine.denerr2.field_name = density
+
+amr.refine.denerr3.max_level = 3
+amr.refine.denerr3.value_greater = 1.e5
+amr.refine.denerr3.field_name = density
+
+
+# Microphysics
+
+integrator.rtol_spec = 1.e-5
+integrator.atol_spec = 1.e-5
+integrator.rtol_enuc = 1.e-5
+integrator.atol_enuc = 1.e-5
+
+integrator.jacobian = 1
+
+network.rho_nse = 1.e7
+network.T_nse = 3.e9
+network.Si_nse = 0.02
+network.C_nse = 1.0
+network.O_nse = 1.0
+
+integrator.ode_max_steps = 500000
+
+network.small_x = 1.e-10
+
+network.nse_relax_factor = 0.9
+
+# use cubic interpolation from the NSE table
+network.nse_table_interp_linear = 0
+
+# disable jacobian caching in VODE
+integrator.use_jacobian_caching = 0
+
+# do we include weak rate neutrino losses in the energy?
+integrator.nse_include_enu_weak = 0