initial xrb spherical problem setup

Exec/science/xrb_spherical/GNUmakefile

@@ -0,0 +1,40 @@
+PRECISION  = DOUBLE
+PROFILE    = FALSE
+
+DEBUG      = FALSE
+
+DIM        = 2
+
+COMP       = gnu
+
+USE_MPI    = TRUE
+
+USE_GRAV   = TRUE
+USE_REACT  = TRUE
+
+USE_ROTATION  = TRUE
+USE_DIFFUSION = TRUE
+
+# define the location of the CASTRO top directory
+CASTRO_HOME  ?= ../../..
+
+USE_JACOBIAN_CACHING = TRUE
+USE_MODEL_PARSER = TRUE
+NUM_MODELS := 2
+
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+EOS_DIR     := helmholtz
+
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
+NETWORK_DIR := aprox13
+
+INTEGRATOR_DIR := VODE
+
+CONDUCTIVITY_DIR := stellar
+
+PROBLEM_DIR ?= ./
+
+Bpack   := $(PROBLEM_DIR)/Make.package
+Blocs   := $(PROBLEM_DIR)
+
+include $(CASTRO_HOME)/Exec/Make.Castro

Exec/science/xrb_spherical/Make.package

@@ -0,0 +1,2 @@
+CEXE_headers += initial_model.H
+

Exec/science/xrb_spherical/_prob_params

@@ -0,0 +1,68 @@
+
+dtemp                   real              3.81e8_rt                 y
+
+theta_half_max          real              1.745e-2_rt               y
+
+theta_half_width        real              4.9e-3_rt                 y
+
+# cutoff mass fraction of the first species for refinement
+X_min                   real              1.e-4_rt                  y
+
+# do we dynamically refine based on density? or based on height?
+tag_by_density          integer           1                         y
+
+# used for tagging if tag_by_density = 1
+cutoff_density          real              500.e0_rt                 y
+
+# used if we are refining based on height rather than density
+refine_height           real              3600                      y
+
+T_hi                    real              5.e8_rt                   y
+
+T_star                  real              1.e8_rt                   y
+
+T_lo                    real              5.e7_rt                   y
+
+dens_base               real              2.e6_rt                   y
+
+H_star                  real              500.e0_rt                 y
+
+atm_delta               real              25.e0_rt                  y
+
+fuel1_name              string         "helium-4"                y
+
+fuel2_name              string         ""                        y
+
+fuel3_name              string         ""                        y
+
+fuel4_name              string         ""                        y
+
+ash1_name               string         "iron-56"                 y
+
+ash2_name               string         ""                        y
+
+ash3_name               string         ""                        y
+
+fuel1_frac              real              1.0_rt                    y
+
+fuel2_frac              real              0.0_rt                    y
+
+fuel3_frac              real              0.0_rt                    y
+
+fuel4_frac              real              0.0_rt                    y
+
+ash1_frac               real              1.0_rt                    y
+
+ash2_frac               real              0.0_rt                    y
+
+ash3_frac               real              0.0_rt                    y
+
+low_density_cutoff      real              1.e-4_rt                  y
+
+smallx                  real              1.e-10_rt                 y
+
+r_refine_distance       real              1.e30_rt                  y
+
+max_hse_tagging_level   integer           2                         y
+
+max_base_tagging_level  integer           1                         y

Exec/science/xrb_spherical/initial_model.H

@@ -0,0 +1 @@
+../flame_wave/initial_model.H

Exec/science/xrb_spherical/inputs.He.1000Hz

@@ -0,0 +1,147 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 9900000
+stop_time =  3.0
+
+# PROBLEM SIZE & GEOMETRY
+geometry.is_periodic = 0       0
+geometry.coord_sys   = 2                  # 0 => cart, 1 => RZ  2=>spherical
+geometry.prob_lo     = 0             0
+geometry.prob_hi     = 3.072e4       3.14159
+amr.n_cell           = 192           1152
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# 0 = Interior           3 = Symmetry
+# 1 = Inflow             4 = SlipWall
+# 2 = Outflow            5 = NoSlipWall
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+castro.lo_bc       =  1   3   # Inflow in lower R and Symmetry across Theta
+castro.hi_bc       =  2   2   # Outflow in upper boundaries
+
+# Hydrostatic condition along R-direction
+castro.yl_ext_bc_type = 0
+castro.hse_interp_temp = 0
+castro.hse_fixed_temp = 1.e8   # this should match problem.T_star
+castro.hse_reflect_vels = 0
+
+# Fill ambient states with outflow velocity in R-direction
+castro.fill_ambient_bc = 1
+castro.ambient_fill_dir = 0
+castro.ambient_outflow_vel = 1
+
+# WHICH PHYSICS
+castro.do_hydro = 1
+castro.do_react = 1
+castro.do_rotation = 1
+castro.do_grav = 1
+castro.do_sponge = 1
+
+castro.small_temp = 1.e6
+castro.small_dens = 1.e-5
+
+castro.ppm_type = 1
+castro.grav_source_type = 2
+
+gravity.gravity_type = ConstantGrav
+
+# 1.4 Solar Mass NS with radius ~11 km
+gravity.const_grav   = -1.5e14
+
+# 1000Hz Spinning Frequency
+# Might want to use a more realistic spinning frequency like 500Hz
+castro.rotational_period = 0.001
+# Centrifugal is not important since NS would simply deform to accomondate for it
+castro.rotation_include_centrifugal = 0
+
+castro.diffuse_temp = 1
+castro.diffuse_cutoff_density_hi = 5.e4
+castro.diffuse_cutoff_density = 2.e4
+
+castro.diffuse_cond_scale_fac = 1.0
+
+castro.react_rho_min = 1.e2
+castro.react_rho_max = 1.5e7
+
+castro.react_T_min = 6.e7
+
+castro.sponge_upper_density = 1.e2
+castro.sponge_lower_density = 1.e0
+castro.sponge_timescale     = 1.e-7
+
+castro.abundance_failure_tolerance = 0.1
+castro.abundance_failure_rho_cutoff = 1.0
+
+# TIME STEP CONTROL
+castro.cfl            = 0.8     # cfl number for hyperbolic system
+castro.init_shrink    = 0.1     # scale back initial timestep
+castro.change_max     = 1.1     # max time step growth
+
+castro.use_retry      = 1
+castro.max_subcycles = 16
+
+castro.retry_small_density_cutoff = 1.0
+
+# DIAGNOSTICS & VERBOSITY
+castro.sum_interval   = 0       # timesteps between computing mass
+castro.v              = 1       # verbosity in Castro.cpp
+amr.v                 = 1       # verbosity in Amr.cpp
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 2       # maximum level number allowed
+amr.ref_ratio       = 4 2 2 2 # refinement ratio
+amr.regrid_int      = 2 2 2 2 # how often to regrid
+amr.blocking_factor = 16       # block factor in grid generation
+amr.max_grid_size   = 128
+amr.n_error_buf     = 2 2 2 2 # number of buffer cells in error est
+
+# CHECKPOINT FILES
+amr.check_file      = flame_wave_1000Hz_chk        # root name of checkpoint file
+amr.check_int       = 250        # number of timesteps between checkpoints
+
+# PLOTFILES
+amr.plot_file        = flame_wave_1000Hz_plt        # root name of plotfile
+amr.plot_per         = 5.e-3      # number of seconds between plotfiles
+amr.derive_plot_vars = ALL
+
+amr.small_plot_file        = flame_wave_1000Hz_smallplt        # root name of plotfile
+amr.small_plot_per         = 1.e-4      # number of seconds between plotfiles
+amr.small_plot_vars = density Temp
+amr.derive_small_plot_vars = abar x_velocity y_velocity z_velocity enuc
+
+# problem initialization
+
+problem.dtemp = 1.2e9
+problem.theta_half_max = 1.745e-2
+problem.theta_half_width = 4.9e-3
+
+problem.dens_base = 3.43e6
+
+problem.T_star = 1.e8
+problem.T_hi = 2.e8
+problem.T_lo   = 8.e6
+
+problem.H_star = 2000.e0
+problem.atm_delta  = 50.0
+
+problem.fuel1_name = "helium-4"
+problem.fuel1_frac = 1.0e0
+
+problem.ash1_name  = "nickel-56"
+problem.ash1_frac = 1.0e0
+
+problem.low_density_cutoff = 1.e-4
+
+problem.cutoff_density = 2.5e4
+problem.max_hse_tagging_level = 3
+problem.max_base_tagging_level = 2
+
+problem.X_min = 1.e-2
+
+problem.x_refine_distance = 9.216e4
+
+
+# Microphysics
+
+integrator.rtol_spec = 1.e-6
+integrator.atol_spec = 1.e-6
+
+network.use_tables = 1