[mesa-users] pgstar SIGSEGV using 7184 and latest SDK
Marcin Mackiewicz
astrophysics at o2.pl
Fri Nov 28 08:49:04 EST 2014
Hello MESA Users,
Recently I was testing 1M_pre_ms_to_wd case from the test suite.
The files I modified were history_colums.list, profile_colums.list and
inlist _1.0. The rest I left intact.
The mases tested were between 0.15 and 1.30 Msun with 0.05 step.
All test cases ran fine with one exeption for 1.05 Msun.
When I commented out pgstar_flag option situation did not occur.
When I left pgstar_flag option set to .true. but commented out
*_win_flag options problem occured again.
Test environment was Ubuntu 14.10 x64 with 8 GB of RAM.
MESA v. 7184 with latest SDK.
All modified MESA files and a terminal output with error message are
attached.
Terminal output suggests that SIGSEGV happened when pgplot was trying to
save .png file.
Can you try to reproduce this error on Ubuntu x64 or any other platforms?
Regards
Marcin Mackiewicz
-------------- next part --------------
! history_columns.list -- determines the contents of star history logs
! you can use a non-standard version by setting history_columns_file in your inlist
! units are cgs unless otherwise noted.
! reorder the following names as desired to reorder columns.
! comment out the name to omit a column (fewer columns => less IO => faster running).
! remove '!' to restore a column.
! if you have a situation where you want a non-standard set of columns,
! make a copy of this file, edit as desired, and give the new filename in your inlist
! as history_columns_file. if you are just adding columns, you can 'include' this file,
! and just list the additions in your file. note: to include the standard default
! version, use include '' -- the 0 length string means include the default file.
! blank lines and comments can be used freely.
! if a column name appears more than once in the list, only the first occurrence is used.
! if you need to have something added to the list of options, let me know....
! the first few lines of the log file contain parameter values as of the start of the run
! for completeness, those items are described here:
! initial_mass -- star mass at start of run (Msun units)
! initial_z -- starting metallicity
! h1_boundary_limit -- defines abundance limit for h1_boundary_mass
! he4_boundary_limit -- defines abundance limit for he4_boundary_mass
! burn_min1 -- 1st limit for reported burning, in erg/g/s
! burn_min2 -- 2nd limit for reported burning, in erg/g/s
! note: you can include another list by doing
! include 'filename'
! include '' means include the default standard list file
! the following lines of the log file contain info about 1 model per row
! some general info about the model
model_number ! counting from the start of the run
star_age ! elapsed simulated time in years since the start of the run
star_mass ! in Msun units
log_abs_mdot ! log10(abs(star_mdot)) (in msolar per year)
!star_mdot ! d(star_mass)/dt (in msolar per year)
time_step ! timestep in years since previous model
log_dt ! log10 time_step
!num_zones ! number of zones in the model
log_total_angular_momentum
!log_rotational_mdot_boost
! mixing regions
! mx1 refers to the largest (by mass) convective region.
! mx2 is the 2nd largest.
! conv_mx1_top and conv_mx1_bot are the region where mixing_type == convective_mixing.
! mx1_top and mx1_bot are the extent of all kinds of mixing, convective and other.
!conv_mx1_top
!conv_mx1_bot
!conv_mx2_top
!conv_mx2_bot
!mx1_top
!mx1_bot
!mx2_top
!mx2_bot
! regions of strong nuclear burning
! 2 zones where eps_nuc > burn_min1 erg/g/s
! for each zone have 4 numbers: start1, start2, end2, end1
! start1 is mass of inner edge where first goes > burn_min1 (or -20 if none such)
! start2 is mass of inner edge where first zone reaches burn_min2 erg/g/sec (or -20 if none such)
! end2 is mass of outer edge where first zone drops back below burn_min2 erg/g/s
! end1 is mass of outer edge where first zone ends (i.e. eps_nuc < burn_min1)
! similar for the second zone
!epsnuc_M_1 ! start1 for 1st zone
!epsnuc_M_2 ! start2
!epsnuc_M_3 ! end2
!epsnuc_M_4 ! end1
!epsnuc_M_5 ! start1 for 2nd zone
!epsnuc_M_6 ! start2
!epsnuc_M_7 ! end2
!epsnuc_M_8 ! end1
! information about abundance transitions
he_core_mass
c_core_mass
o_core_mass
si_core_mass
fe_core_mass
! info about locations where optical depth is 10 or 100
!tau10_mass ! mass in solar units where optical depth = 10
!tau10_radius ! radius in solar units where optical depth = 10
!tau10_lgP ! estimate for log10(P) at tau = 10
!tau10_lgT ! estimate for log10(T) at tau = 10
!tau10_lgRho ! estimate for log10(density) at tau = 10
!tau10_L ! estimate for L/Lsun at tau = 10
!tau100_mass ! location in solar units where optical depth = 100
!tau100_radius ! location in solar units where optical depth = 100
!tau100_lgP ! estimates for values at tau = 100
!tau100_lgT
!tau100_lgRho
!tau100_L
! timescales
!dynamic_timescale ! dynamic timescale (seconds) -- estimated by 2*pi*sqrt(r^3/(G*m))
!kh_timescale ! kelvin-helmholtz timescale (years)
!nuc_timescale ! nuclear timescale (years) -- proportional to mass divided by luminosity
! integrated power from hydrogen and helium burning
!power_h_burn ! total thermal power from PP and CNO, excluding neutrinos (in Lsun units)
!power_he_burn ! total thermal power from triple-alpha, excluding neutrinos (in Lsun units)
log_LH ! log10 power_h_burn
log_LHe ! log10 power_he_burn
log_LZ !
! conditions near surface
log_L ! log10 luminosity in Lsun units
log_Teff ! log10 effective temperature
log_R ! log10 radius in Rsun units
log_g ! log10 gravity
!surf_avg_j_rot
surf_avg_omega
!surf_avg_omega_crit
surf_avg_omega_div_omega_crit
surf_avg_v_rot ! km/sec rotational velocity at equator
!surf_avg_v_crit ! critical rotational velocity at equator
!surf_avg_v_div_v_crit
surf_avg_L_div_Ledd
! conditions near center
log_center_T ! temperature
log_center_Rho ! density
log_center_P ! pressure
center_degeneracy ! the electron chemical potential in units of k*T
center_gamma ! plasma interaction parameter at the centermost meshpoint.
!center_omega
!center_omega_div_omega_crit
center_ye
center_entropy ! in kerg per baryon
surface h1
surface he4
surface c12
surface n14
surface o16
! mass fractions near center
center h1
center he4
center c12
center n14
center o16
center ne20
center si28
center s32
center ar36
center ca40
center fe54
center fe56
center ni56
center cr56
! etc. -- do as many of these 'center' commands as desired
! log10 mass fractions for entire star
log_average h1
log_average h2
log_average he3
log_average he4
log_average li7
! log10 total ergs/sec for reaction categories (Lsun units)
!pp
!cno
!tri_alfa
!c12_alfa
!n14_alfa
!o16_alfa
! log10 total ergs/sec for specific reactions (names from rates_def; Lsun units)
!rpp
! info about the max burning locations for hydrogen, helium, and metals
! info about location where have max rate of hydrogen burning (PP and CNO)
!eps_h_max ! erg/g/s
!eps_h_max_lgT ! log10 temperature at location of max burn
!eps_h_max_lgRho ! log10 density at location of max burn
!eps_h_max_m ! mass coordinate at location of max burn (Msun units)
!eps_h_max_lgP ! log10 pressure at location of max burn
!eps_h_max_lgR ! log10 radius at location of max burn
!eps_h_max_opacity ! opacity at location of max burn
! info about location where have max rate of helium burning
! triple-alpha plus alpha capture on C12, N14, O16, and Ne20.
!eps_he_max ! erg/g/s
!eps_he_max_lgT ! log10 temperature at location of max burn
!eps_he_max_lgRho ! log10 density at location of max burn
!eps_he_max_m ! mass coordinate at location of max burn (Msun units)
!eps_he_max_lgP ! log10 pressure at location of max burn
!eps_he_max_lgR ! log10 radius at location of max burn
!eps_he_max_opacity ! opacity at location of max burn
! info about location where have max rate of burning of metals
! alpha capture on heavy elements plus C+C, C+O, O+O, etc.
!eps_z_max ! erg/g/s
!eps_z_max_lgT ! log10 temperature at location of max burn
!eps_z_max_lgRho ! log10 density at location of max burn
!eps_z_max_m ! mass coordinate at location of max burn (Msun units)
!eps_z_max_lgP ! log10 pressure at location of max burn
!eps_z_max_lgR ! log10 radius at location of max burn
!eps_z_max_opacity ! opacity at location of max burn
! you might want to get a more complete list of mixing regions by using the following
!mixing_regions 40
!mixing_regions <integer> ! note: this includes regions where the mixing type is no_mixing.
! the <integer> is the number of regions to report
! there will be 2*<integer> columns for this in the log file, 2 for each region.
! the first column for a region gives the mixing type using the values defined in const_def
! the types are no_mixing, convective_mixing, overshoot_mixing, semiconvective_mixing,
! and salt_finger_mixing, numbered from 0 to 4.
! entries for extra columns after the last region in the star will have an invalid mixing_type value of -1.
! the second column for a region gives the m/mstar location of the top of the region
! mstar is the total mass of the star, so these locations range from 0 to 1
! all regions are include starting from the center, so the bottom of one region
! is the top of the previous one. since we start at the center, the bottom of the 1st region is 0.
! the columns in the log file will have names like 'mix_type_1' and 'mix_qtop_1'
!burning_regions 80
! misc
v_div_csound_surf ! velocity divided by sound speed at outermost grid point
!surface_accel_div_grav ! (v - v_old)/dt divided by GM/R^2 at outermost grid point
!num_retries ! total during the run
!num_backups ! total during the run
-------------- next part --------------
&star_job
show_log_description_at_start = .false.
!show_net_species_info = .true.
!show_net_reactions_info = .true.
create_pre_main_sequence_model = .true.
save_model_when_terminate = .true.
save_model_filename = 'final.mod'
write_profile_when_terminate = .true.
filename_for_profile_when_terminate = 'final_profile.data'
kappa_file_prefix = 'gs98'
change_lnPgas_flag = .true.
new_lnPgas_flag = .true.
change_initial_net = .true.
new_net_name = 'o18_and_ne22.net'
pre_ms_relax_num_steps = 50
new_surface_rotation_v = 2 ! solar (km sec^1)
set_near_zams_surface_rotation_v_steps = 10 ! to turn on rotation when near zams
! if rotation_flag is false and L_nuc_burn_total >= L_phot and this control > 0
! then turn on rotation and set set_surf_rotation_v_step_limit to
! the current model_number plus this control
pgstar_flag = .true.
/ ! end of star_job namelist
&controls
! check for retries and backups as part of test_suite
! you can/should delete this for use outside of test_suite
max_number_backups = 200
max_number_retries = 500
max_model_number = 20000
initial_mass = 1.05
initial_z = 0.02d0
use_Type2_opacities = .true.
Zbase = 0.02d0
am_nu_visc_factor = 0
am_D_mix_factor = 0.0333333333333333d0
D_DSI_factor = 0
D_SH_factor = 1
D_SSI_factor = 1
D_ES_factor = 1
D_GSF_factor = 1
D_ST_factor = 1
varcontrol_target = 1d-3
mesh_delta_coeff = 1.5
photostep = 50
profile_interval = 50
history_interval = 1
terminal_cnt = 5
write_header_frequency = 50
!log_L_lower_limit = -1
smooth_convective_bdy = .true.
convective_bdy_weight = 1
RGB_wind_scheme = 'Reimers'
AGB_wind_scheme = 'Blocker'
RGB_to_AGB_wind_switch = 1d-4
Reimers_wind_eta = 0.7d0
Blocker_wind_eta = 0.7d0
! FOR DEBUGGING
!report_hydro_solver_progress = .true. ! set true to see info about newton iterations
!report_ierr = .true. ! if true, produce terminal output when have some internal error
!hydro_show_correction_info = .true.
!max_years_for_timestep = 1.0d7
!report_why_dt_limits = .true.
!report_all_dt_limits = .true.
!show_mesh_changes = .true.
!mesh_dump_call_number = 5189
!okay_to_remesh = .false.
!trace_evolve = .true.
! hydro debugging
!hydro_check_everything = .true.
!hydro_inspectB_flag = .true.
!hydro_numerical_jacobian = .true.
!hydro_save_numjac_plot_data = .true.
!small_mtx_decsol = 'lapack'
!large_mtx_decsol = 'lapack'
!hydro_dump_call_number = 195
!trace_newton_bcyclic_solve_input = .true. ! input is "B" j k iter B(j,k)
!trace_newton_bcyclic_solve_output = .true. ! output is "X" j k iter X(j,k)
!trace_newton_bcyclic_steplo = 1 ! 1st model number to trace
!trace_newton_bcyclic_stephi = 1 ! last model number to trace
!trace_newton_bcyclic_iterlo = 2 ! 1st newton iter to trace
!trace_newton_bcyclic_iterhi = 2 ! last newton iter to trace
!trace_newton_bcyclic_nzlo = 1 ! 1st cell to trace
!trace_newton_bcyclic_nzhi = 10000 ! last cell to trace; if < 0, then use nz as nzhi
!trace_newton_bcyclic_jlo = 1 ! 1st var to trace
!trace_newton_bcyclic_jhi = 100 ! last var to trace; if < 0, then use nvar as jhi
!trace_k = 0
/ ! end of controls namelist
&pgstar
Grid6_win_flag = .true.
Grid6_win_width = 11
Grid6_file_flag = .true.
Grid6_file_dir = 'png'
Grid6_file_prefix = 'grid6_'
Grid6_file_cnt = 10 ! output when mod(model_number,Grid6_file_cnt)==0
Grid6_file_width = -1 ! (inches) negative means use same value as for window
Grid6_file_aspect_ratio = -1 ! negative means use same value as for window
Summary_Burn_xaxis_name = 'mass'
Summary_Burn_xaxis_reversed = .false.
Summary_Burn_xmin = 0.00 ! -101d0 ! only used if /= -101d0
Summary_Burn_xmax = 2.1 ! only used if /= -101d0
Abundance_xaxis_name = 'mass'
Abundance_xaxis_reversed = .false.
! power xaxis limits -- to override system default selections
Abundance_xmin = 0.00 ! -101d0 ! only used if /= -101d0
Abundance_xmax = 2.1 ! only used if /= -101d0
Abundance_log_mass_frac_min = -6 ! only used if < 0
!Profile_Panels4_win_flag = .true.
!Profile_Panels4_win_width = 6
! Abundance window -- current model abundance profiles
!Abundance_win_flag = .true.
Abundance_win_width = 9
Abundance_win_aspect_ratio = 0.75 ! aspect_ratio = height/width
/ ! end of pgstar namelist
-------------- next part --------------
DATE: 2014-11-26
TIME: 14:37:10
version_number 7184
read inlist_1.0
create pre-main-sequence model
species 10
abundances
h1 6.9999999999999996D-01
he3 2.9797635251138618D-05
he4 2.7997020236474884D-01
c12 3.4416106108120406D-03
n14 1.0081585468366041D-03
o16 9.3393731281944965D-03
o18 2.1073480945478206D-05
ne20 1.9423584493049016D-03
ne22 1.5710150039274719D-04
mg24 4.0903242835137500D-03
relax_num_steps
5 5.476884 5216.296 -20.933225 -20.933225 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148759 442 0
-5.000000 -3.335753 1.492946 -99.000000 -22.331093 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065312 4 0
5.0000E-05 10.264862 2.808822 -99.000000 3.149906 -8.372538 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.653E+01 max_dt
10 5.476840 5039.860 -20.933232 -20.933232 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148449 429 0
-5.000000 -3.335682 1.492041 -99.000000 -22.331100 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065322 4 0
1.0000E-04 10.264889 2.747238 -99.000000 3.206698 -8.300627 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.289E+01 max_dt
15 5.476830 4925.514 -20.933233 -20.933233 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148384 429 0
-5.000000 -3.335670 1.491572 -99.000000 -22.331101 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065324 4 0
1.5000E-04 10.264890 2.706432 -99.000000 3.225139 -8.272141 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.165E+01 max_dt
20 5.476826 4839.757 -20.933235 -20.933235 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148366 426 0
-5.000000 -3.335667 1.491267 -99.000000 -22.331102 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065325 4 0
2.0000E-04 10.264890 2.675311 -99.000000 3.230762 -8.258847 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.118E+01 max_dt
25 5.476825 4770.237 -20.933237 -20.933237 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148361 423 0
-5.000000 -3.335666 1.491037 -99.000000 -22.331105 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065325 4 0
2.5000E-04 10.264890 2.649716 -99.000000 3.232047 -8.251255 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.933E+00 max_dt
30 5.476824 4711.137 -20.933237 -20.933237 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148358 420 0
-5.000000 -3.335666 1.490847 -99.000000 -22.331105 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065325 4 0
3.0000E-04 10.264889 2.627679 -99.000000 3.231851 -8.246024 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.791E+00 max_dt
35 5.476825 4661.661 -20.933238 -20.933238 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148357 422 0
-5.000000 -3.335665 1.490682 -99.000000 -22.331106 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065325 4 0
3.5000E-04 10.264890 2.609009 -99.000000 3.231266 -8.242021 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.700E+00 max_dt
40 5.476824 4618.847 -20.933240 -20.933240 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148356 421 0
-5.000000 -3.335665 1.490536 -99.000000 -22.331107 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065325 4 0
4.0000E-04 10.264889 2.592689 -99.000000 3.230630 -8.238644 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.626E+00 max_dt
45 5.476824 4580.333 -20.933240 -20.933240 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148355 420 0
-5.000000 -3.335664 1.490403 -99.000000 -22.331108 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065325 4 0
4.5000E-04 10.264890 2.577877 -99.000000 3.230088 -8.235545 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.577E+00 max_dt
50 5.476824 4546.877 -20.933238 -20.933238 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148354 420 0
-5.000000 -3.335665 1.490282 -99.000000 -22.331106 -99.000000 0.000000 0.280000 0.009339 0.020000 0.280000 0.065325 4 0
5.0000E-04 10.264890 2.564898 -99.000000 3.229746 -8.232697 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.535E+00 max_dt
finished relax_num_steps
change to o18_and_ne22.net
number of species = 10
new_lnPgas_flag = T
net name o18_and_ne22.net
lnPgas_flag = T
kappa_file_prefix gs98
kappa_lowT_prefix lowT_fa05_gs98
eos_file_prefix mesa
OMP_NUM_THREADS 2
save LOGS/profile1.data for model 1
5 5.476838 4502.295 -20.933905 -20.933905 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148728 414 0
-4.683275 -3.335652 1.490150 -99.000000 -22.331772 -8.531694 0.000000 0.280000 0.009339 0.020000 0.280000 0.065324 4 0
7.4416E-05 10.264926 2.547518 -99.000000 3.229594 -8.228554 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.492E+00 max increase
10 5.476837 4415.505 -20.933906 -20.933906 1.050000 1.050000 0.700000 0.001008 0.280000 0.700000 -8.148728 413 0
-4.287369 -3.335652 1.489794 -99.000000 -22.331774 -8.562270 0.000000 0.280000 0.009339 0.020000 0.280000 0.065324 4 0
2.5959E-04 10.264926 2.512992 -99.000000 3.231368 -8.218288 0.000000 0.003442 0.001942 2.000E-02 2.000E-02 -0.412E+00 max increase
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7F57FB9CD557
#1 0x7F57FB9CDB6E
#2 0x7F57FAA95D9F
#3 0x7F57FCBFC96F
#4 0x7F57FCBDACF0
#5 0x7F57FCBDDEA6
#6 0x7F57FCBDDB64
#7 0x7F57FCBE3FF2
#8 0x7F57FCBF32A1
#9 0x5BBE2A in do1.9632.constprop.0 at pgstar_abundance.f:?
#10 0x5BC272 in do_all.9638 at pgstar_abundance.f:?
#11 0x5BCA36 in __mod_pgstar_abundance_MOD_do_abundance_panel
#12 0x5BCD57 in __mod_pgstar_abundance_MOD_do_abundance_plot
#13 0x5D234D in __mod_pgstar_grid_MOD_grid_plot
#14 0x5D3829 in __mod_pgstar_grid_MOD_grid6_plot
#15 0x4F285E in __mod_pgstar_MOD_onscreen_plots
#16 0x4F2A27 in __mod_pgstar_MOD_do_pgstar_plots
#17 0x4072C1 in __star_lib_MOD_update_pgstar_plots
#18 0x41B577 in __run_star_support_MOD_after_step_loop
#19 0x41CBF9 in __run_star_support_MOD_run1_star
#20 0x405C9F in __run_star_MOD_do_run_star at run_star.f:34
#21 0x405CEF in run at run.f:38
./rn: line 8: 1633 Segmentation fault (core dumped) ./star
DATE: 2014-11-26
TIME: 14:37:19
-------------- next part --------------
! profile_columns.list -- determines the contents of star model profiles
! you can use a non-standard version by setting profile_columns_file in your inlist
! units are cgs unless otherwise noted.
! reorder the following names as desired to reorder columns.
! comment out the name to omit a column (fewer columns => less IO => faster running).
! remove '!' to restore a column.
! if you have a situation where you want a non-standard set of columns,
! make a copy of this file, edit as desired, and give the new filename in your inlist
! as profile_columns_file. if you are just adding columns, you can 'include' this file,
! and just list the additions in your file. note: to include the standard default
! version, use include '' -- the 0 length string means include the default file.
! if you need to have something added to the list of options, let me know....
! the first few lines of the profile contain general info about the model.
! for completeness, those items are described at the end of this file.
! note: you can include another list by doing
! include 'filename'
! include '' means include the default standard list file
! the following lines of the profile contain info for 1 zone per row, surface to center.
zone ! numbers start with 1 at the surface
logT ! log10(temperature) at center of zone
logRho ! log10(density) at center of zone
logP ! log10(pressure) at center of zone
logR ! log10(radius/Rsun) at outer boundary of zone
luminosity ! luminosity at outer boundary of zone (in Lsun units)
logL ! log(max(1d-6,L/Lsun))
velocity ! velocity at outer boundary of zone -- 0 if no velocity variable
entropy ! specific entropy divided by (avo*kerg)
conv_mixing_type ! mixing types are defined in mesa/const
csound ! sound speed
v_div_csound ! velocity divided by sound speed
total_energy ! v^2/2 - G m / r + E (ergs/g). negative if bound
v_div_r ! velocity divided by radius
!scale_height ! pressure scale height; P / (g rho) (in Rsun units)
eta ! electron degeneracy parameter (eta >> 1 for significant degeneracy)
mu ! mean molecular weight per gas particle (ions + free electrons)
logdq ! log10(dq)
dq_ratio ! dq(k-1)/dq(k)
q ! fraction of star mass interior to outer boundary of this zone
radius ! radius at outer boundary of zone (in Rsun units)
temperature ! temperature at center of zone
tau ! optical depth
logtau ! log10(optical depth) at center of zone
pressure ! total pressure at center of zone (pgas + prad)
!pgas ! gas pressure at center of zone (electrons and ions)
!pgas_div_ptotal ! pgas/pressure
!logPgas ! log10(pgas)
!prad ! radiation pressure at center of zone
!energy ! internal energy (ergs/g)
!logE ! log10(specific internal energy) at center of zone
!grada ! dlnT_dlnP at constant S
!dE_dRho ! at constant T
!cv ! specific heat at constant volume
!cp ! specific heat at constant total pressure
!logS ! log10(specific entropy)
!gamma1 ! dlnP_dlnRho at constant S
!gamma3 ! gamma3 - 1 = dlnT_dlnRho at constant S
!theta_e ! electron degeneracy factor for graboske screening
!gam ! plasma interaction parameter (> 160 or so means starting crystallization)
free_e ! free_e is mean number of free electrons per nucleon
!logfree_e ! log10(free_e), free_e is mean number of free electrons per nucleon
!chiRho ! dlnP_dlnRho at constant T
!chiT ! dlnP_dlnT at constant Rho
!abar ! average atomic weight (g/mole)
!zbar ! average charge
!z2bar ! average charge^2
ye ! average charge per baryon = proton fraction
opacity ! opacity measured at center of zone
log_opacity ! log10(opacity)
eps_nuc ! ergs/g/sec from nuclear reactions (neutrinos subtracted)
non_nuc_neu ! non-nuclear-reaction neutrino losses
!nonnucneu_plas ! plasmon neutrinos (for collective reactions like gamma_plasmon => nu_e + nubar_e)
!nonnucneu_brem ! bremsstrahlung (for reactions like e- + (z,a) => e- + (z,a) + nu + nubar)
!nonnucneu_phot ! photon neutrinos (for reactions like e- + gamma => e- + nu_e + nubar_e)
!nonnucneu_pair ! pair production (for reactions like e+ + e- => nu_e + nubar_e)
eps_grav ! heat from gravitational contraction (negative for expansion)
!mlt_mixing_length ! mixing length for mlt (cm)
!log_D_mix ! log10 diffusion coefficient in units of cm^2/second (Eulerian)
!log_conv_vel ! log10 convection velocity (cm/sec)
!conv_vel_div_csound ! convection velocity divided by sound speed
!log_mlt_D_mix ! log10 cdc from mlt (cm^2/sec)
!use_gradr_for_gradT ! if = 1, then zone has been forced radiative in spite of mlt results.
pressure_scale_height ! in Rsun units
!gradT ! mlt value for required temperature gradient dlnT/dlnP
!gradr ! dlnT/dlnP required for purely radiative transport
!dlnd_dt ! time derivative of log(density) at fixed mass coordinate (Langranian)
!dlnT_dt ! time derivative of log(temperature) at fixed mass coordinate (Langranian)
!dv_dt ! time derivative of velocity at fixed mass coordinate (Langranian)
!accel_div_grav ! dv_dt/grav -- only if v_flag is true. 0 otherwise.
mass ! m/Msun. mass coordinate of outer boundary of cell.
!mmid ! mass at midpoint of cell (average of mass coords of the cell boundaries) Msun units.
!logM ! log10(m/Msun)
!xm ! mass exterior to point (Msun units)
!dq ! mass of zone as a fraction of total star mass
!logxq ! log10(1-q)
log_D_conv
log_D_semi
log_D_thrm
log_D_ovr
log_D_anon
! rotation
omega ! angular velocity = j_rot/i_rot
log_omega
log_j_rot
log_J_div_M53 ! J is j*1e-15 integrated from center; M53 is m^(5/3)
log_J_inside ! J_inside is j_rot integrated from center
!shear ! abs(dlnomega/dlnR)
log_abs_shear ! log10(abs(dlnomega/dlnR))
v_rot ! rotation velocity at cell boundary (km/sec)
i_rot ! specific moment of interia at cell boundary
j_rot ! specific angular momentum at cell boundary
fp_rot ! rotation factor for pressure
ft_rot ! rotation factor for temperature
log_am_nu ! angular momentum diffusion coef at cell boundary
! this is the rotational viscosity, nu, from Heger 2000 eqn for ang. mom. transport.
r_polar ! (Rsun)
log_r_polar ! log10 (Rsun)
r_equatorial ! (Rsun)
log_r_equatorial ! log10 (Rsun)
r_e_div_r_p ! r_equatorial/r_polar
omega_crit ! breakup angular velocity = sqrt(G M / r_equatorial^3)
omega_div_omega_crit
!am_log_sig
!am_log_D_DSI ! diffusion coeff for dynamical shear instability
!am_log_D_SH ! diffusion coeff for Solberg-Hoiland instability
!am_log_D_SSI ! diffusion coeff for secular shear instability
!am_log_D_ES ! diffusion coeff for Eddington-Sweet circulation
!am_log_D_GSF ! diffusion coeff for Goldreich-Schubert-Fricke instability
!am_log_D_ST ! Spruit dynamo mixing diffusivity
!am_log_nu_ST ! Spruit dynamo effective viscosity
dynamo_log_B_r ! (Gauss)
dynamo_log_B_phi ! (Gauss)
add_abundances ! this adds all of the isos that are in the current net
! NOTE: you can list specific isotopes by giving their names (from chem_def)
!h1
!he3
!he4
!c12
!n14
!o16
! electric field from element diffusion calculation
!e_field
!log_e_field
! element diffusion velocity for species
!edv h1
!edv he4
!edv c12
!edv n14
!edv o16
!edv ne20
!edv mg24
!log_concentration h1
!log_concentration he4
!log_concentration c12
!log_concentration n14
!log_concentration o16
!log_concentration ne20
!log_concentration mg24
!diffusion_D h1
!diffusion_D he4
!diffusion_D c12
!diffusion_D n14
!diffusion_D o16
!diffusion_D ne20
!diffusion_D mg24
! typical charge for given species
!typical_charge h1
!typical_charge he3
!typical_charge he4
!typical_charge c12
!typical_charge n14
!typical_charge o16
!typical_charge ne20
!typical_charge mg24
! change in particular abundances during hydro solve
!xadot h1
!xadot he3
! particular abundances before hydro solve
!xaprev h1
!xaprev he3
! ergs/g/sec for reaction categories
add_reaction_categories ! this adds all the reaction categories
! NOTE: you can list specific categories by giving their names (from net_def)
!pp
!cno
!tri_alfa
! ergs/g/sec for specific reactions (names from rates_def)
!rpp
! misc
!gradr_sub_grada ! gradr - grada; > 0 => Schwarzschild unstable for convection
!dlnR_dm ! for structure equation
!dlnP_dm ! for structure equation
!dlnT_dm ! for structure equation
!dL_dm ! for structure equation
!delta_r ! r(outer edge) - r(inner edge); radial extent of cell in cm.
!delta_v ! v(inner edge) - v(outer edge); rate at which delta_r is shrinking (cm/sec).
!dt_dv_div_dr ! dt*delta_v/delta_r; need to have this << 1 for every cell
!cno_div_z ! abundance of c12, n14, and o16 as a fraction of total z
!dlog_h1_dlogP ! (log(h1(k)) - log(h1(k-1)))/(log(P(k)) - log(P(k-1)))
!dlog_he3_dlogP
!dlog_he4_dlogP
!dlog_c12_dlogP
!dlog_c13_dlogP
!dlog_n14_dlogP
!dlog_o16_dlogP
!dlog_ne20_dlogP
!dlog_mg24_dlogP
!dlog_si28_dlogP
!dlog_pp_dlogP
!dlog_cno_dlogP
!dlog_3alf_dlogP
!dlog_burn_c_dlogP
!dlog_burn_n_dlogP
!dlog_burn_o_dlogP
!dlog_burn_ne_dlogP
!dlog_burn_na_dlogP
!dlog_burn_mg_dlogP
!dlog_cc_dlogP
!dlog_co_dlogP
!dlog_oo_dlogP
!dlog_burn_si_dlogP
!dlog_burn_s_dlogP
!dlog_burn_ar_dlogP
!dlog_burn_ca_dlogP
!dlog_burn_ti_dlogP
!dlog_burn_cr_dlogP
!dlog_burn_fe_dlogP
!dlog_pnhe4_dlogP
!dlog_photo_dlogP
!dlog_other_dlogP
!brunt_nu
!log_brunt_nu
!log_lamb_Sl1
!log_lamb_Sl2
!log_lamb_Sl3
!log_lamb_Sl10
!brunt_B
!brunt_N2 ! brunt-vaisala frequency squared
!brunt_N2_structure_term
!brunt_N2_composition_term
!brunt_A ! = N^2*r/g
!brunt_N2_dimensionless ! N2 in units of 3GM/R^3
!brunt_N_dimensionless ! N in units of sqrt(3GM/R^3)
brunt_frequency ! cycles per day
!acoustic_radius ! sound time from center to outer cell boundary (sec)
!acoustic_r_div_R_phot ! sound time from center to outer cell boundary div time to photosphere
!cs_at_cell_bdy ! sound speed at cell boundary (csound is at cell center)
!dlnmu_dr ! for salt-finger mixing
!semiconvection_criterion ! positive means stable
! 1/chiRho - dlnT_dlnP*chiT/chiRho - dlnRho_dlnP
! the first few lines of the profile contain general info about the model.
! for completeness, those items are described here.
! initial mass and Z
! initial_mass
! initial_z
! general properties of the current state
! model_number
! num_zones
! star_age
! time_step
! properties at the photosphere
! Teff
! photosphere_L
! photosphere_r
! properties at the outermost zone of the model
! log_surface_L
! log_surface_radius
! log_surface_temp
! properties near the center of the model
! log_center_temp
! log_center_density
! log_center_P
! center_eta
! abundances near the center
! center_h1
! center_he3
! center_he4
! center_c12
! center_n14
! center_o16
! center_ne20
! information about total mass
! star_mass
! star_mdot
! star_mass_h1
! star_mass_he3
! star_mass_he4
! star_mass_c12
! star_mass_n14
! star_mass_o16
! star_mass_ne20
! locations of abundance transitions
! h1_boundary_mass
! he4_boundary_mass
! c12_boundary_mass
! location of optical depths 10 and 100
! tau10_mass
! tau10_radius
! tau100_mass
! tau100_radius
! time scales
! dynamic_time
! kh_timescale
! nuc_timescale
! various kinds of total power
! power_nuc_burn
! power_h_burn
! power_he_burn
! power_neu
! a few control parameter values
! h1_boundary_limit
! he4_boundary_limit
! c12_boundary_limit
! burn_min1
! burn_min2
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