From 97b333a366c0aba579b63cc00058e398a5ab975a Mon Sep 17 00:00:00 2001 From: Eb Date: Fri, 29 Mar 2024 10:17:50 -0700 Subject: [PATCH 01/66] [ci optional] prevent TDC with predictive mixing --- star/defaults/controls.defaults | 12 ++++++++++++ star/private/predictive_mix.f90 | 9 +++++++-- 2 files changed, 19 insertions(+), 2 deletions(-) diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index 23edc597e..c8c5b9c04 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -2301,6 +2301,15 @@ ! Note that TDC does not respect the ``alt_scale_height`` option, and continues to use ``h = P / rho g`` ! even if that flag is set. + ! We caution that combining different mixing models in a stellar evolution + ! calculation might lead to physically inconsistent solutions, + ! because the different models have been developed separately, + ! and their underlying assumptions might not be compatible with each other. + ! Examples include combining the newly implemented time-dependent local limit + ! convection model ``TDC`` with an overshooting model, or combining ``TDC`` + ! with other models for chemical composition gradients + ! (predictive mixing or convective premixing), rotation, etc. (MESA VI) + ! :: MLT_option = 'TDC' @@ -2773,6 +2782,9 @@ ! Set to .true. to enable this set of parameters + ! ``predictive_mix`` is incompattible with ``convective premixing`` + ! and mlt_option = ``TDC``, due to conflicting assumptions. + ! :: predictive_mix(1) = .false. diff --git a/star/private/predictive_mix.f90 b/star/private/predictive_mix.f90 index fc768195c..5aa634f55 100644 --- a/star/private/predictive_mix.f90 +++ b/star/private/predictive_mix.f90 @@ -96,7 +96,7 @@ subroutine add_predictive_mixing (s, ierr) criteria_loop : do j = 1, NUM_PREDICTIVE_PARAM_SETS - if (.NOT. s%predictive_mix(j)) cycle criteria_loop + if (.NOT. s% predictive_mix(j)) cycle criteria_loop ! Check if the criteria match the current boundary @@ -170,11 +170,16 @@ subroutine add_predictive_mixing (s, ierr) ! Perform the predictive mixing for this boundary - if (s%do_conv_premix) then + if (s% do_conv_premix) then call mesa_error(__FILE__,__LINE__,'Predictive mixing and convective premixing cannot be enabled at the same time') stop end if + if (s% MLT_option == 'TDC') then + call mesa_error(__FILE__,__LINE__,'Predictive mixing and TDC cannot be enabled at the same time') + stop + end if + call do_predictive_mixing(s, i, j, ierr, mix_mask) if (ierr /= 0) return From 2127ac15f61b4317a4ab1076125d23fe6c9c1620 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 23 Jul 2024 16:47:01 -0400 Subject: [PATCH 02/66] adding figure to starspot --- .../conv_core_cpm/inlist_conv_core_cpm | 2 +- star/test_suite/starspots/README.rst | 25 ++- .../starspots/docs/hr_starspots_000794.svg | 1 + star/test_suite/starspots/inlist_starspots | 208 ++++++++++-------- .../starspots/inlist_starspots_header | 22 +- 5 files changed, 148 insertions(+), 110 deletions(-) create mode 100644 star/test_suite/starspots/docs/hr_starspots_000794.svg diff --git a/star/test_suite/conv_core_cpm/inlist_conv_core_cpm b/star/test_suite/conv_core_cpm/inlist_conv_core_cpm index 5ce04d518..daa68d8c7 100644 --- a/star/test_suite/conv_core_cpm/inlist_conv_core_cpm +++ b/star/test_suite/conv_core_cpm/inlist_conv_core_cpm @@ -35,7 +35,7 @@ kap_file_prefix = 'a09' kap_lowT_prefix = 'lowT_fa05_a09p' kap_CO_prefix = 'a09_co' - / ! end of kap namelist +/ ! end of kap namelist &controls diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index 4ec0ed87b..e5bae4e7e 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -4,18 +4,31 @@ starspots ****************** -This test suite case evolves a 1 solar mass, solar metallicity (Z=0.02) model to an age of 0.8 Gyr using MESA's implementation of the YREC (Yale Rotating Evolution Code) SPOTS formalism introduced by Somers et al. (2020; ApJ). +This test suite case evolves a 1.0 |Msun|, solar metallicity (Z=0.02) model +to an age of 0.8 Gyr using MESA's implementation of the +YREC (Yale Rotating Evolution Code) SPOTS formalism introduced by +`Somers et al. (2020; ApJ) `__ -The impedence of the surface flux due to magnetic pressure from starspots is parameterized in the style of an atmospheric boundary modification. -As first described by Somers et al. (2015; ApJ), the degree of "spottiness" on the stellar surface is characterized using two parameters: +The impedence of the surface flux due to magnetic pressure from starspots is parameterized +in the style of an atmospheric boundary modification. As first described by +`Somers et al. (2015; ApJ) `__, +the degree of "spottiness" on the stellar surface is characterized using two parameters: * SPOTF (hereafter fspot): a coverage fraction, or "spot filling factor" (in the notation of the YREC documentation); and * SPOTX (hereafter xspot): the temperature contrast between the spotted and unspotted regions: xspot = T_spot/T_photosphere. -Currently, x_ctrl(1) corresponds to fspot, and x_ctrl(2) corresponds to xspot. The coverage fraction is set to fspot = 0.34 (for consistency with observations of low-mass stars: Cao et al., 2022) and the temperature contrast is set to xspot = 0.85 (also from fits to observations). +The coverage fraction is set to fspot = 0.34 +(for consistency with observations of low-mass stars: +`Cao et al., 2022 `__) +and the temperature contrast is set to xspot = 0.85 (also from fits to observations). -Detailed discussion of this functionality can be found in MESA Instrument Paper VI: Starspots +Detailed discussion of this functionality can be found in +`MESA Instrument Paper VI: Starspots `__. -Last-Updated: 2022-07-28 by Meridith Joyce +A plot of the HR diagram for the problem is included below: +.. image:: ../../../star/test_suite/starspots/docs/hr_starspots_000794.svg + :width: 100% + +Last-Updated: 23Jul2024 (MESA 6d0b0f29) by pmocz on C916PXT6XW in 207 seconds using 8 threads. diff --git a/star/test_suite/starspots/docs/hr_starspots_000794.svg b/star/test_suite/starspots/docs/hr_starspots_000794.svg new file mode 100644 index 000000000..7109c199f --- /dev/null +++ b/star/test_suite/starspots/docs/hr_starspots_000794.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 4ea11c6d7..c14f8d049 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -5,146 +5,170 @@ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &star_job - history_columns_file = 'history_master.list' - profile_columns_file = 'profile_master.list' - - required_termination_code_string = 'max_age' + history_columns_file = 'history_master.list' + profile_columns_file = 'profile_master.list' - save_pulse_data_when_terminate = .false. + required_termination_code_string = 'max_age' - create_pre_main_sequence_model = .true. - pre_ms_relax_to_start_radiative_core = .false. !.true. ! by default, but it should not be!!! + save_pulse_data_when_terminate = .false. + create_pre_main_sequence_model = .true. + pre_ms_relax_to_start_radiative_core = .false. !.true. ! by default, but it should not be!!! - ! save a model at the end of the run - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - new_rotation_flag = .false. + ! save a model at the end of the run + save_model_when_terminate = .true. + save_model_filename = 'final.mod' - pre_ms_T_c = 3d5 ! default -- any lower doesn't work - pre_ms_check_radiative_core_min_mass = 0.3d0 ! default is 0.3d0 - pre_ms_check_radiative_core_Lnuc_div_L_limit = 1d-6 + new_rotation_flag = .false. + pre_ms_T_c = 3d5 ! default -- any lower doesn't work + pre_ms_check_radiative_core_min_mass = 0.3d0 ! default is 0.3d0 + pre_ms_check_radiative_core_Lnuc_div_L_limit = 1d-6 - set_uniform_initial_composition = .true. - initial_h1 = 0.7349 - initial_h2 = 2.75d-5 ! Lodders 2009 - initial_he3 = 8.5d-5 ! Lodders 2009 - initial_he4 = 0.24 + set_uniform_initial_composition = .true. + initial_h1 = 0.7349 + initial_h2 = 2.75d-5 ! Lodders 2009 + initial_he3 = 8.5d-5 ! Lodders 2009 + initial_he4 = 0.24 - initial_zfracs = 6 !! scaling of the rest of the elements according to someone's solar abundance - ! display on-screen plots - pgstar_flag = .false. + initial_zfracs = 6 !! scaling of the rest of the elements according to someone's solar abundance - !network - change_net = .true. - new_net_name= 'pp_extras.net' ! + ! display on-screen plots + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. -/ !end of star_job namelist + ! network + change_net = .true. + new_net_name= 'pp_extras.net' ! + +/ ! end of star_job namelist &eos / &kap - Zbase = 0.0200 !0.014 + Zbase = 0.0200 !0.014 - !opacities with AGSS09 abundances - kap_file_prefix = 'a09' - kap_lowT_prefix = 'lowT_fa05_a09p' - kap_CO_prefix = 'a09_co' + ! opacities with AGSS09 abundances + kap_file_prefix = 'a09' + kap_lowT_prefix = 'lowT_fa05_a09p' + kap_CO_prefix = 'a09_co' / &controls - star_history_name = 'history.data' + star_history_name = 'history.data' + + max_age = 0.8d9 + + use_other_mlt_results = .true. !.true. + use_other_surface_PT = .true. !.True. - max_age = 0.8d9 + x_ctrl(1) = 0.34d0 ! fspot + x_ctrl(2) = 0.85d0 ! xspot - use_other_mlt_results = .true. !.true. - use_other_surface_PT = .true. !.True. + atm_option = 'table' + atm_table = 'photosphere' - x_ctrl(1) = 0.34d0 ! fspot - x_ctrl(2) = 0.85d0 ! xspot - atm_option = 'table' - atm_table = 'photosphere' - + warn_when_large_rel_run_E_err = 99d0 !0.02d0 + log_directory = 'LOGS' + write_profiles_flag = .false. - warn_when_large_rel_run_E_err = 99d0 !0.02d0 - log_directory = 'LOGS' - write_profiles_flag = .false. + max_num_profile_models = -1 + history_interval = 1 + terminal_interval = 100 + write_header_frequency = 10 + photo_digits = 5 + photo_interval = 100 - max_num_profile_models = -1 - history_interval = 1 - terminal_interval = 100 - write_header_frequency = 10 - photo_digits = 5 - photo_interval = 100 + ! starting specifications + initial_mass = 1.0 ! in Msun units + min_timestep_limit=0 + max_model_number = -1 !1500 - ! starting specifications - initial_mass = 1.0 ! in Msun units - min_timestep_limit=0 - max_model_number = -1!1500 - - cool_wind_RGB_scheme = 'Reimers' - cool_wind_AGB_scheme = 'Blocker' - RGB_to_AGB_wind_switch = 1d-4 - Reimers_scaling_factor = 0.1 - Blocker_scaling_factor = 0.2 - max_wind = 1d-3 + cool_wind_RGB_scheme = 'Reimers' + cool_wind_AGB_scheme = 'Blocker' + RGB_to_AGB_wind_switch = 1d-4 + Reimers_scaling_factor = 0.1 + Blocker_scaling_factor = 0.2 + max_wind = 1d-3 - mixing_length_alpha = 1.9500 !1.95 - MLT_option = 'Henyey' + mixing_length_alpha = 1.9500 !1.95 + MLT_option = 'Henyey' - do_element_diffusion = .false. - report_solver_progress = .false. + do_element_diffusion = .false. + report_solver_progress = .false. - ! Solver - use_gold2_tolerances = .true. - - ! Timestep and grid - mesh_delta_coeff = 0.8 - time_delta_coeff = 1.0 !0.8 !0.5 + ! Solver + use_gold2_tolerances = .true. - varcontrol_target = 1e-4 - !max_allowed_nz = 50000 + ! Timestep and grid + mesh_delta_coeff = 0.8 + time_delta_coeff = 1.0 !0.8 !0.5 - !to help with convergence - okay_to_reduce_gradT_excess = .true. - Pextra_factor = 2.0 + varcontrol_target = 1e-4 + !max_allowed_nz = 50000 + + ! to help with convergence + okay_to_reduce_gradT_excess = .true. + Pextra_factor = 2.0 !------------------------------------------- !! convective overshoot, new formalism !------------------------------------------- - overshoot_scheme(:) = 'exponential' ! ``exponential``, ``step``, ``other`` - overshoot_zone_type(:) = 'any' ! ``burn_H``, ``burn_He``, ``burn_Z``, ``nonburn``, ``any`` - overshoot_zone_loc(:) = 'any' ! ``core``, ``shell``, ``any`` - overshoot_bdy_loc(:) = 'any' ! ``bottom``, ``top``, ``any`` - - ! Amount of overshooting from edge of convective zone - ! These are arrays of size ``NUM_OVERSHOOT_PARAM_SETS`` which is defined in - ! ``star_data/public/star_data_def.inc`` (currently 16) + overshoot_scheme(:) = 'exponential' ! ``exponential``, ``step``, ``other`` + overshoot_zone_type(:) = 'any' ! ``burn_H``, ``burn_He``, ``burn_Z``, ``nonburn``, ``any`` + overshoot_zone_loc(:) = 'any' ! ``core``, ``shell``, ``any`` + overshoot_bdy_loc(:) = 'any' ! ``bottom``, ``top``, ``any`` - overshoot_f(:) = 0.014d0 - overshoot_f0(:) = 0.004d0 + ! Amount of overshooting from edge of convective zone + ! These are arrays of size ``NUM_OVERSHOOT_PARAM_SETS`` which is defined in + ! ``star_data/public/star_data_def.inc`` (currently 16) - ! Convergence checking - use_gold_tolerances = .true. - + overshoot_f(:) = 0.014d0 + overshoot_f0(:) = 0.004d0 - max_number_retries = -1 !1000 !100!100 - max_model_number = 10000 !-1 + ! Convergence checking + use_gold_tolerances = .true. - !better resolution of the Henyey hook - delta_lg_XH_cntr_max = -1 + max_number_retries = -1 !1000 !100!100 + max_model_number = 10000 !-1 + ! better resolution of the Henyey hook + delta_lg_XH_cntr_max = -1 / ! end of controls namelist + +&pgstar + + pgstar_interval = 50 + + ! device + file_white_on_black_flag = .true. + file_device = 'vcps' ! postscript + file_extension = 'ps' + + HR_win_flag = .false. ! switch to .true. to visualize in real-time + HR_file_flag = .true. + HR_file_dir = 'pgstar_out' + HR_file_prefix = 'hr_starspots_' + HR_win_width = 9 + HR_win_aspect_ratio = 1.0 + HR_title = 'HR' + + ! set static plot bounds + HR_logT_min = 3.0 + HR_logT_max = 6.5 + HR_logL_min = -2.0 + HR_logL_max = 2.0 + +/ ! end of pgstar namelist diff --git a/star/test_suite/starspots/inlist_starspots_header b/star/test_suite/starspots/inlist_starspots_header index 5af82e6f7..a4c8dc792 100644 --- a/star/test_suite/starspots/inlist_starspots_header +++ b/star/test_suite/starspots/inlist_starspots_header @@ -1,41 +1,41 @@ &star_job - mesa_dir = '../../..' + mesa_dir = '../../..' - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_starspots' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_starspots' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_starspots' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_starspots' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_starspots' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_starspots' / ! end of kap namelist &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_starspots' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_starspots' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_starspots' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_starspots' / ! end of pgstar namelist From 92a4b3b5fd332533ff90a138c14fc4f8c97bad72 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 23 Jul 2024 16:52:42 -0400 Subject: [PATCH 03/66] spaces --- star/test_suite/starspots/inlist_starspots | 7 ------- 1 file changed, 7 deletions(-) diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index c14f8d049..4ac93cd09 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -15,7 +15,6 @@ create_pre_main_sequence_model = .true. pre_ms_relax_to_start_radiative_core = .false. !.true. ! by default, but it should not be!!! - ! save a model at the end of the run save_model_when_terminate = .true. save_model_filename = 'final.mod' @@ -26,7 +25,6 @@ pre_ms_check_radiative_core_min_mass = 0.3d0 ! default is 0.3d0 pre_ms_check_radiative_core_Lnuc_div_L_limit = 1d-6 - set_uniform_initial_composition = .true. initial_h1 = 0.7349 @@ -34,7 +32,6 @@ initial_he3 = 8.5d-5 ! Lodders 2009 initial_he4 = 0.24 - initial_zfracs = 6 !! scaling of the rest of the elements according to someone's solar abundance ! display on-screen plots @@ -74,12 +71,10 @@ atm_option = 'table' atm_table = 'photosphere' - warn_when_large_rel_run_E_err = 99d0 !0.02d0 log_directory = 'LOGS' write_profiles_flag = .false. - max_num_profile_models = -1 history_interval = 1 terminal_interval = 100 @@ -92,7 +87,6 @@ min_timestep_limit=0 max_model_number = -1 !1500 - cool_wind_RGB_scheme = 'Reimers' cool_wind_AGB_scheme = 'Blocker' RGB_to_AGB_wind_switch = 1d-4 @@ -138,7 +132,6 @@ ! Convergence checking use_gold_tolerances = .true. - max_number_retries = -1 !1000 !100!100 max_model_number = 10000 !-1 From 1b7c3ae0d278cb35f43e311426a7f43941b06bf9 Mon Sep 17 00:00:00 2001 From: pmocz Date: Thu, 25 Jul 2024 12:58:13 -0400 Subject: [PATCH 04/66] cleanup --- star/test_suite/starspots/inlist_starspots | 2 +- star/test_suite/starspots/src/run_star_extras.f90 | 12 ++++-------- 2 files changed, 5 insertions(+), 9 deletions(-) diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 4ac93cd09..027bbe669 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -132,7 +132,7 @@ ! Convergence checking use_gold_tolerances = .true. - max_number_retries = -1 !1000 !100!100 + max_number_retries = -1 !1000 !100 max_model_number = 10000 !-1 ! better resolution of the Henyey hook diff --git a/star/test_suite/starspots/src/run_star_extras.f90 b/star/test_suite/starspots/src/run_star_extras.f90 index cd61e1ec1..3aabef591 100644 --- a/star/test_suite/starspots/src/run_star_extras.f90 +++ b/star/test_suite/starspots/src/run_star_extras.f90 @@ -97,7 +97,7 @@ end subroutine extras_startup integer function extras_start_step(id) integer, intent(in) :: id integer :: ierr - real(dp) :: mu_ideal_gas, R2 !! pi can be deleted + real(dp) :: mu_ideal_gas, R2 type (star_info), pointer :: s real(dp) :: power_he_burn, power_c_burn, power_neutrinos, & center_h1, center_he4, ocz_top_mass, ocz_bot_mass, & @@ -186,7 +186,6 @@ subroutine starspot_tweak_PT(id, skip_partials, & use const_def, only: dp - integer, intent(in) :: id logical, intent(in) :: skip_partials @@ -198,7 +197,7 @@ subroutine starspot_tweak_PT(id, skip_partials, & integer, intent(out) :: ierr ! For my tweaks - real(dp) :: alp !, fspot, xspot + real(dp) :: alp ! Call the stock get_surf_PT type (star_info), pointer :: s @@ -222,7 +221,7 @@ subroutine starspot_tweak_PT(id, skip_partials, & s% L(1) = s% L(1) / alp ! Now, set the Teff. Used in atm table lookup to set boundary conditions - s% Teff = pow(s% L(1)/(pi4*s% r(1)*s% r(1)*boltz_sigma), 0.25_dp) + s% Teff = pow(s% L(1)/(pi4*pow2(s% r(1))*boltz_sigma), 0.25_dp) ! Set everything with Lamb. call star_get_surf_PT(id, skip_partials, need_atm_Psurf, need_atm_Tsurf, & @@ -230,7 +229,7 @@ subroutine starspot_tweak_PT(id, skip_partials, & lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap, & ierr) - s% Teff = pow(L_init/(pi4*s% r(1)*s% r(1)*boltz_sigma), 0.25_dp) + s% Teff = pow(L_init/(pi4*pow2(s% r(1))*boltz_sigma), 0.25_dp) s% L(1) = L_init end subroutine starspot_tweak_PT @@ -251,7 +250,6 @@ integer function extras_check_model(id) if (ierr /= 0) return extras_check_model = keep_going - if (.false. .and. s% star_mass_h1 < 0.35d0) then ! stop when star hydrogen mass drops to specified level extras_check_model = terminate @@ -289,7 +287,6 @@ subroutine data_for_extra_history_columns(id, n, names, vals, ierr) ! note: do NOT add the extras names to history_columns.list ! the history_columns.list is only for the built-in history column options. ! it must not include the new column names you are adding here. - end subroutine data_for_extra_history_columns @@ -397,4 +394,3 @@ subroutine extras_after_evolve(id, ierr) end subroutine extras_after_evolve end module run_star_extras - From 8b152605af4172f8e3263a6d3892ebc0e473aab8 Mon Sep 17 00:00:00 2001 From: Joey Mombarg Date: Tue, 6 Aug 2024 16:30:18 +0200 Subject: [PATCH 05/66] updating test_suite 17 --- .../7M_prems_to_AGB/docs/hr000785.png | Bin 0 -> 16960 bytes .../7M_prems_to_AGB/inlist_7M_prems_to_AGB | 15 +++++---- .../inlist_7M_prems_to_AGB_header | 2 +- star/test_suite/7M_prems_to_AGB/inlist_pgstar | 30 ++++++++++++++++++ star/test_suite/7M_prems_to_AGB/inlist_start | 15 +++++---- 5 files changed, 49 insertions(+), 13 deletions(-) create mode 100644 star/test_suite/7M_prems_to_AGB/docs/hr000785.png create mode 100644 star/test_suite/7M_prems_to_AGB/inlist_pgstar diff --git a/star/test_suite/7M_prems_to_AGB/docs/hr000785.png b/star/test_suite/7M_prems_to_AGB/docs/hr000785.png new file mode 100644 index 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zxu``A$FKcL>*=5T2JV#BA&_Kpf?ZLhViMHZE zfhzgE=P*5z<=LL~%z7_C_4p8E8Nuh$dT`yno*r``*Ydl_ Date: Tue, 6 Aug 2024 10:39:28 -0400 Subject: [PATCH 06/66] updating TP 32 --- .../diffusion_smoothness/README.rst | 44 +--- .../docs/brunt_000036.svg | 243 +----------------- .../inlist_diffusion_smoothness | 39 ++- .../inlist_diffusion_smoothness_header | 2 - .../diffusion_smoothness/inlist_zams | 2 - .../diffusion_smoothness/inlist_zams_header | 1 - 6 files changed, 37 insertions(+), 294 deletions(-) diff --git a/star/test_suite/diffusion_smoothness/README.rst b/star/test_suite/diffusion_smoothness/README.rst index 46bf4dbdb..409b5f6f4 100644 --- a/star/test_suite/diffusion_smoothness/README.rst +++ b/star/test_suite/diffusion_smoothness/README.rst @@ -17,44 +17,10 @@ This test case has 2 part2. Click to see a larger view of a plot. pgstar commands used for the plot: -.. code-block:: console +.. literalinclude:: ../../../star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness + :language: console + :start-at: &pgstar + :end-at: ! end of pgstar namelist - &pgstar - - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - - !file_device = 'vcps' ! postscript - !file_extension = 'ps' - - pgstar_interval = 1 - - ! Brunt B profile - Profile_Panels1_win_flag = .true. - Profile_Panels1_win_width = 14 - Profile_Panels1_show_grid = .false - Profile_Panels1_title = 'diffusion_smoothness' - - Profile_Panels1_xaxis_name = 'zone' - Profile_Panels1_xmin = -101d0 - Profile_Panels1_xmax = -101d0 - Profile_Panels1_xaxis_reversed = .true. - Profile_Panels1_show_mix_regions_on_xaxis = .true. - - Profile_Panels1_num_panels = 1 - Profile_Panels1_yaxis_name(1) = 'brunt_B' - Profile_Panels1_ymin(:) = -101d0 - Profile_Panels1_ymax(:) = -101d0 - Profile_Panels1_other_yaxis_name(1) = '' - - Profile_Panels1_file_flag = .true. - Profile_Panels1_file_dir = 'png' - Profile_Panels1_file_prefix = 'brunt_' - Profile_Panels1_file_interval = 10000 - Profile_Panels1_file_width = 14 - - / ! end of pgstar namelist - -Last-Updated: 06Jun2021 (MESA 5be9e57) by fxt +Last-Updated: 06Aug2024 (MESA 8b152605) by pmocz on C916PXT6XW in 82 seconds using 8 threads. diff --git a/star/test_suite/diffusion_smoothness/docs/brunt_000036.svg b/star/test_suite/diffusion_smoothness/docs/brunt_000036.svg index b872075e7..715714029 100644 --- a/star/test_suite/diffusion_smoothness/docs/brunt_000036.svg +++ b/star/test_suite/diffusion_smoothness/docs/brunt_000036.svg @@ -1,242 +1 @@ - - - - - - - - - - - - - - - - - - - - - + \ No newline at end of file diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness index a6b192683..ef39217c5 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness @@ -26,8 +26,8 @@ set_initial_cumulative_energy_error = .true. new_cumulative_energy_error = 0d0 - !pgstar_flag = .true. - + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / ! end of star_job namelist @@ -116,13 +116,36 @@ / ! end of controls namelist - &pgstar - - ! top level controls - !pause = .true. - ! if true, the code waits for user to enter a RETURN on the command line - + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'vcps' ! postscript + file_extension = 'ps' + + pgstar_interval = 1 + + ! Brunt B profile + Profile_Panels1_win_flag = .true. + Profile_Panels1_win_width = 14 + Profile_Panels1_show_grid = .false + Profile_Panels1_title = 'diffusion_smoothness' + + Profile_Panels1_xaxis_name = 'zone' + Profile_Panels1_xmin = -101d0 + Profile_Panels1_xmax = -101d0 + Profile_Panels1_xaxis_reversed = .true. + Profile_Panels1_show_mix_regions_on_xaxis = .true. + + Profile_Panels1_num_panels = 1 + Profile_Panels1_yaxis_name(1) = 'brunt_B' + Profile_Panels1_ymin(:) = -101d0 + Profile_Panels1_ymax(:) = -101d0 + Profile_Panels1_other_yaxis_name(1) = '' + + Profile_Panels1_file_flag = .true. + Profile_Panels1_file_dir = 'pgstar_out' + Profile_Panels1_file_prefix = 'brunt_' + Profile_Panels1_file_interval = 10000 + Profile_Panels1_file_width = 14 / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header index 90d444869..af5d6b624 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header @@ -1,7 +1,6 @@ &star_job - read_extra_star_job_inlist(1) = .true. extra_star_job_inlist_name(1) = 'inlist_diffusion_smoothness' @@ -24,7 +23,6 @@ / ! end of kap namelist - &controls read_extra_controls_inlist(1) = .true. diff --git a/star/test_suite/diffusion_smoothness/inlist_zams b/star/test_suite/diffusion_smoothness/inlist_zams index 8bfa87a5f..cccd02ef5 100644 --- a/star/test_suite/diffusion_smoothness/inlist_zams +++ b/star/test_suite/diffusion_smoothness/inlist_zams @@ -65,7 +65,6 @@ / ! end of controls namelist - &pgstar ! top level controls @@ -73,5 +72,4 @@ !pause = .true. ! if true, the code waits for user to enter a RETURN on the command line - / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_zams_header b/star/test_suite/diffusion_smoothness/inlist_zams_header index 9b647ddf7..a387c02e0 100644 --- a/star/test_suite/diffusion_smoothness/inlist_zams_header +++ b/star/test_suite/diffusion_smoothness/inlist_zams_header @@ -1,7 +1,6 @@ &star_job - read_extra_star_job_inlist(1) = .true. extra_star_job_inlist_name(1) = 'inlist_zams' From 8b7b2e03072c5553d5bb17ed4a483b8d848e3606 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 10:52:11 -0400 Subject: [PATCH 07/66] TP 17. change png to svg --- star/test_suite/7M_prems_to_AGB/README.rst | 43 +++--------------- .../7M_prems_to_AGB/docs/hr000785.png | Bin 16960 -> 0 bytes .../7M_prems_to_AGB/docs/hr000785.svg | 1 + .../inlist_7M_prems_to_AGB_header | 1 - star/test_suite/7M_prems_to_AGB/inlist_pgstar | 6 +-- .../7M_prems_to_AGB/inlist_start_header | 1 - 6 files changed, 11 insertions(+), 41 deletions(-) delete mode 100644 star/test_suite/7M_prems_to_AGB/docs/hr000785.png create mode 100644 star/test_suite/7M_prems_to_AGB/docs/hr000785.svg diff --git a/star/test_suite/7M_prems_to_AGB/README.rst b/star/test_suite/7M_prems_to_AGB/README.rst index 8a1ffc48f..dd63a4d53 100644 --- a/star/test_suite/7M_prems_to_AGB/README.rst +++ b/star/test_suite/7M_prems_to_AGB/README.rst @@ -4,7 +4,7 @@ 7M_prems_to_AGB *************** -This test case checks that the evolution of a 7 Msun, metal-poor Z = 0.001, model reaches the AGB. +This test case checks that the evolution of a 7 |Msun|, metal-poor Z = 0.001, model reaches the AGB. This test case has two parts. Click to see a larger view of a plot. @@ -12,45 +12,16 @@ This test case has two parts. Click to see a larger view of a plot. * Part 2 (``inlist_7M_prems_to_AGB``) continues the evolution as core hydrogen and helium burning proceed, terminating when log10(L/Lsun)=4.3 is reached. The model executes a blue loop as helium depletes, with the red edge and blue edge of the classical Cepheid instability strip boundaries shown in the HR diagram: -.. image:: ../../../star/test_suite/7M_prems_to_AGB/docs/hr000794.svg +.. image:: ../../../star/test_suite/7M_prems_to_AGB/docs/hr000785.svg :width: 100% pgstar commands used: -.. code-block:: console +.. literalinclude:: ../../../star/test_suite/7M_prems_to_AGB/inlist_pgstar + :language: console + :start-at: &pgstar + :end-at: ! end of pgstar namelist - &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - - !file_device = 'vcps' ! postscript - !file_extension = 'ps' - - pgstar_interval = 10 - - HR_win_flag = .true. - HR_win_width = 12 - HR_win_aspect_ratio = 1.2 ! aspect_ratio = height/width - - HR_logT_min = 3.5 - HR_logT_max = 4.5 - HR_logL_min = 2.7 - HR_logL_max = 4.4 - - ! file output - HR_file_flag = .true. - HR_file_dir = 'pgstar_out' - HR_file_prefix = 'hr' - HR_file_interval = 100 ! output when mod(model_number,HR_file_interval)==0 - HR_file_width = 15 ! negative means use same value as for window - HR_file_aspect_ratio = -1 ! negative means use same value as for window - - / ! end of pgstar namelist - - - - -Last-Updated: 29May2021 (MESA e37f76f) by fxt +Last-Updated: 06Aug2024 (MESA f50b3763) by pmocz on C916PXT6XW in 410 seconds using 8 threads. diff --git a/star/test_suite/7M_prems_to_AGB/docs/hr000785.png b/star/test_suite/7M_prems_to_AGB/docs/hr000785.png deleted file mode 100644 index df1fe2ed008d159d5ec00924f39b33fddecd55c5..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16960 zcmeIZ3piBW+c2(!r-M)=l~5r$PG`wso{|)0DxngioGNLGL@|3h$te^$RZLMyV$w;H z*&T*SPLC)>*%=|nF$S~8Y%|~5TRrdZ`rh~Vz2E!(|KIPrzW?>FtJPljy3gxgYp+@N zy`#4~+9^(-KV42vPI1fTjXUM!CS!7P@{*~O0Oa}==XY{)ljOE<-DL~9GVllgkNAf_ 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b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header index 1cc9ef4c0..d496188f4 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header +++ b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header @@ -1,7 +1,6 @@ &star_job - read_extra_star_job_inlist(2) = .true. extra_star_job_inlist_name(2) = 'inlist_7M_prems_to_AGB' diff --git a/star/test_suite/7M_prems_to_AGB/inlist_pgstar b/star/test_suite/7M_prems_to_AGB/inlist_pgstar index 10359a49f..9e82833e9 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_pgstar +++ b/star/test_suite/7M_prems_to_AGB/inlist_pgstar @@ -2,10 +2,10 @@ file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! postscript - file_extension = 'png' + file_device = 'vcps' ! postscript + file_extension = 'ps' - pgstar_interval = 10 + pgstar_interval = 10 HR_win_flag = .true. HR_win_width = 12 diff --git a/star/test_suite/7M_prems_to_AGB/inlist_start_header b/star/test_suite/7M_prems_to_AGB/inlist_start_header index 8852b908a..687756114 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_start_header +++ b/star/test_suite/7M_prems_to_AGB/inlist_start_header @@ -1,7 +1,6 @@ &star_job - read_extra_star_job_inlist(2) = .true. extra_star_job_inlist_name(2) = 'inlist_start' From 4604cefe81651d80be24890701a72ca1a5c5965a Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 11:07:38 -0400 Subject: [PATCH 08/66] format inlists --- .../7M_prems_to_AGB/inlist_7M_prems_to_AGB | 92 +++---- .../inlist_7M_prems_to_AGB_header | 20 +- star/test_suite/7M_prems_to_AGB/inlist_pgstar | 40 +-- star/test_suite/7M_prems_to_AGB/inlist_start | 40 +-- .../7M_prems_to_AGB/inlist_start_header | 20 +- .../inlist_diffusion_smoothness | 242 +++++++++--------- .../inlist_diffusion_smoothness_header | 20 +- .../diffusion_smoothness/inlist_zams | 100 ++++---- .../diffusion_smoothness/inlist_zams_header | 20 +- 9 files changed, 297 insertions(+), 297 deletions(-) diff --git a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB index 9baf6422d..976cdabaa 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB +++ b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB @@ -2,20 +2,20 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. - load_saved_model = .true. - load_model_filename = 'start.mod' + load_saved_model = .true. + load_model_filename = 'start.mod' - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - required_termination_code_string = 'log_L_upper_limit' + save_model_when_terminate = .true. + save_model_filename = 'final.mod' + required_termination_code_string = 'log_L_upper_limit' - set_initial_cumulative_energy_error = .true. - new_cumulative_energy_error = 0d0 + set_initial_cumulative_energy_error = .true. + new_cumulative_energy_error = 0d0 - pgstar_flag = .true. - save_pgstar_files_when_terminate = .true. + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / ! end of star_job namelist @@ -25,7 +25,7 @@ / ! end of eos namelist &kap - Zbase = 0.001 + Zbase = 0.001 use_Type2_opacities = .true. @@ -33,50 +33,50 @@ &controls - energy_eqn_option = 'dedt' - use_gold2_tolerances = .true. - max_abs_rel_run_E_err = 1d-2 + energy_eqn_option = 'dedt' + use_gold2_tolerances = .true. + max_abs_rel_run_E_err = 1d-2 - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' - ! limit max_model_number as part of test_suite - max_model_number = 3000 + ! limit max_model_number as part of test_suite + max_model_number = 3000 - initial_mass = 7.00 - initial_z = 0.001 + initial_mass = 7.00 + initial_z = 0.001 - mixing_length_alpha = 1.73 + mixing_length_alpha = 1.73 - log_L_upper_limit = 4.3 + log_L_upper_limit = 4.3 - overshoot_scheme(1) = 'exponential' - overshoot_zone_type(1) = 'any' - overshoot_zone_loc(1) = 'any' - overshoot_bdy_loc(1) = 'any' - overshoot_f(1) = 0.014 - overshoot_f0(1) = 0.004 + overshoot_scheme(1) = 'exponential' + overshoot_zone_type(1) = 'any' + overshoot_zone_loc(1) = 'any' + overshoot_bdy_loc(1) = 'any' + overshoot_f(1) = 0.014 + overshoot_f0(1) = 0.004 - atm_option = 'T_tau' - atm_T_tau_relation = 'Eddington' - atm_T_tau_opacity = 'fixed' + atm_option = 'T_tau' + atm_T_tau_relation = 'Eddington' + atm_T_tau_opacity = 'fixed' ! mass loss - cool_wind_full_on_T = 9.99d9 - hot_wind_full_on_T = 1d10 - cool_wind_RGB_scheme = 'Reimers' - cool_wind_AGB_scheme = 'Blocker' - RGB_to_AGB_wind_switch = 1d-4 - Reimers_scaling_factor = 0.5d0 - Blocker_scaling_factor = 0.0003d0 - - - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 - write_header_frequency = 10 + cool_wind_full_on_T = 9.99d9 + hot_wind_full_on_T = 1d10 + cool_wind_RGB_scheme = 'Reimers' + cool_wind_AGB_scheme = 'Blocker' + RGB_to_AGB_wind_switch = 1d-4 + Reimers_scaling_factor = 0.5d0 + Blocker_scaling_factor = 0.0003d0 + + + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 + write_header_frequency = 10 / ! end of controls namelist diff --git a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header index d496188f4..0f6e5d9a4 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header +++ b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header @@ -1,39 +1,39 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_7M_prems_to_AGB' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_7M_prems_to_AGB' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_7M_prems_to_AGB' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_7M_prems_to_AGB' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_7M_prems_to_AGB' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_7M_prems_to_AGB' / ! end of kap namelist &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_7M_prems_to_AGB' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_7M_prems_to_AGB' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_pgstar' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_pgstar' / ! end of pgstar namelist diff --git a/star/test_suite/7M_prems_to_AGB/inlist_pgstar b/star/test_suite/7M_prems_to_AGB/inlist_pgstar index 9e82833e9..c2c0cbe65 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_pgstar +++ b/star/test_suite/7M_prems_to_AGB/inlist_pgstar @@ -1,30 +1,30 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'vcps' ! postscript - file_extension = 'ps' + file_device = 'vcps' ! postscript + file_extension = 'ps' - pgstar_interval = 10 + pgstar_interval = 10 - HR_win_flag = .true. - HR_win_width = 12 - HR_win_aspect_ratio = 1.2 ! aspect_ratio = height/width + HR_win_flag = .true. + HR_win_width = 12 + HR_win_aspect_ratio = 1.2 ! aspect_ratio = height/width - HR_logT_min = 3.5 - HR_logT_max = 4.5 - HR_logL_min = 2.7 - HR_logL_max = 4.4 + HR_logT_min = 3.5 + HR_logT_max = 4.5 + HR_logL_min = 2.7 + HR_logL_max = 4.4 - ! file output - HR_file_flag = .true. - HR_file_dir = 'pgstar_out' - HR_file_prefix = 'hr' - HR_file_interval = 100 ! output when mod(model_number,HR_file_interval)==0 - HR_file_width = 15 ! negative means use same value as for window - HR_file_aspect_ratio = -1 ! negative means use same value as for window + ! file output + HR_file_flag = .true. + HR_file_dir = 'pgstar_out' + HR_file_prefix = 'hr' + HR_file_interval = 100 ! output when mod(model_number,HR_file_interval)==0 + HR_file_width = 15 ! negative means use same value as for window + HR_file_aspect_ratio = -1 ! negative means use same value as for window - show_HR_classical_instability_strip = .true. - show_HR_Mira_instability_region = .false. + show_HR_classical_instability_strip = .true. + show_HR_Mira_instability_region = .false. / ! end of pgstar namelist diff --git a/star/test_suite/7M_prems_to_AGB/inlist_start b/star/test_suite/7M_prems_to_AGB/inlist_start index 4c75cbdf4..d1055e923 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_start +++ b/star/test_suite/7M_prems_to_AGB/inlist_start @@ -1,24 +1,24 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. - create_pre_main_sequence_model = .true. + create_pre_main_sequence_model = .true. - save_model_when_terminate = .true. - save_model_filename = 'start.mod' - required_termination_code_string = 'max_age' + save_model_when_terminate = .true. + save_model_filename = 'start.mod' + required_termination_code_string = 'max_age' - change_initial_net = .true. - new_net_name = 'o18_and_ne22.net' + change_initial_net = .true. + new_net_name = 'o18_and_ne22.net' / ! end of star_job namelist &kap - Zbase = 0.001 - use_Type2_opacities = .true. + Zbase = 0.001 + use_Type2_opacities = .true. / !end of kap namelist &eos @@ -27,20 +27,20 @@ &controls - ! limit max_model_number as part of test_suite - max_model_number = 150 - use_gold2_tolerances = .true. + ! limit max_model_number as part of test_suite + max_model_number = 150 + use_gold2_tolerances = .true. - max_age = 0.5d0 + max_age = 0.5d0 - initial_mass = 7.00 - initial_z = 0.001 + initial_mass = 7.00 + initial_z = 0.001 - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 - write_header_frequency = 10 + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 + write_header_frequency = 10 / ! end of controls namelist diff --git a/star/test_suite/7M_prems_to_AGB/inlist_start_header b/star/test_suite/7M_prems_to_AGB/inlist_start_header index 687756114..3a86b4deb 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_start_header +++ b/star/test_suite/7M_prems_to_AGB/inlist_start_header @@ -1,24 +1,24 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_start' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_start' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_start' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_start' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_start' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_start' / ! end of kap namelist @@ -26,15 +26,15 @@ &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_start' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_start' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_start' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_start' / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness index ef39217c5..262a63ea6 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness @@ -1,33 +1,33 @@ &star_job - show_log_description_at_start = .false. - - !show_net_species_info = .true. - !show_net_reactions_info = .true. + show_log_description_at_start = .false. - load_saved_model = .true. - load_model_filename = 'zams.mod' - - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - required_termination_code_string = 'max_age' + !show_net_species_info = .true. + !show_net_reactions_info = .true. + load_saved_model = .true. + load_model_filename = 'zams.mod' - change_initial_net = .true. - new_net_name = 'o18_and_ne22.net' - - set_initial_age = .true. - initial_age = 0 + save_model_when_terminate = .true. + save_model_filename = 'final.mod' + required_termination_code_string = 'max_age' - set_initial_model_number = .true. - initial_model_number = 0 - set_initial_cumulative_energy_error = .true. - new_cumulative_energy_error = 0d0 + change_initial_net = .true. + new_net_name = 'o18_and_ne22.net' - pgstar_flag = .true. - save_pgstar_files_when_terminate = .true. + set_initial_age = .true. + initial_age = 0 + + set_initial_model_number = .true. + initial_model_number = 0 + + set_initial_cumulative_energy_error = .true. + new_cumulative_energy_error = 0d0 + + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / ! end of star_job namelist @@ -35,117 +35,117 @@ / ! end of eos namelist &kap - Zbase = 0.02d0 - kap_file_prefix = 'gs98' + Zbase = 0.02d0 + kap_file_prefix = 'gs98' / ! end of kap namelist &controls - energy_eqn_option = 'dedt' - calculate_Brunt_N2 = .true. - use_gold2_tolerances = .true. - - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' - - ! limit max_model_number as part of test_suite - max_model_number = 100 - - x_integer_ctrl(1) = 1 ! part number - - max_age = 3d9 - - initial_mass = 1.0 - initial_z = 0.02d0 - - varcontrol_target = 1d-3 - mesh_delta_coeff = 0.7 - - limit_for_rel_error_in_energy_conservation = 1d-6 ! this makes d2N2 too large. takes 63 steps. log_rel_run_E_err -3.5859393528096946 - limit_for_rel_error_in_energy_conservation = 1d-5 ! this is smooth enough. takes 58 steps. log_rel_run_E_err -3.4820705862368895 - hard_limit_for_rel_error_in_energy_conservation = 1d-4 - - convective_bdy_weight = 1 - - cool_wind_RGB_scheme = 'Reimers' - cool_wind_AGB_scheme = 'Blocker' - RGB_to_AGB_wind_switch = 1d-4 - Reimers_scaling_factor = 0.7d0 - Blocker_scaling_factor = 0.7d0 + energy_eqn_option = 'dedt' + calculate_Brunt_N2 = .true. + use_gold2_tolerances = .true. + + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' + + ! limit max_model_number as part of test_suite + max_model_number = 100 + + x_integer_ctrl(1) = 1 ! part number + + max_age = 3d9 + + initial_mass = 1.0 + initial_z = 0.02d0 + + varcontrol_target = 1d-3 + mesh_delta_coeff = 0.7 + + limit_for_rel_error_in_energy_conservation = 1d-6 ! this makes d2N2 too large. takes 63 steps. log_rel_run_E_err -3.5859393528096946 + limit_for_rel_error_in_energy_conservation = 1d-5 ! this is smooth enough. takes 58 steps. log_rel_run_E_err -3.4820705862368895 + hard_limit_for_rel_error_in_energy_conservation = 1d-4 + + convective_bdy_weight = 1 + + cool_wind_RGB_scheme = 'Reimers' + cool_wind_AGB_scheme = 'Blocker' + RGB_to_AGB_wind_switch = 1d-4 + Reimers_scaling_factor = 0.7d0 + Blocker_scaling_factor = 0.7d0 ! set_min_D_mix = .true. - min_D_mix = 1d2 ! D_mix will be at least this large - min_center_Ye_for_min_D_mix = 0.47 ! min_D_mix is only used when center Ye >= this - ! i.e., when center Ye drops below this, min_D_mix is 0 - - - num_cells_for_smooth_brunt_B = 0 - - !show_diffusion_info = .true. ! terminal output for diffusion - !show_diffusion_substep_info = .true. - !show_diffusion_timing = .true. - - do_element_diffusion = .true. ! determines whether or not we do diffusion - - diffusion_calculates_ionization = .true. - - diffusion_num_classes = 4 ! number of classes of species for diffusion calculations - diffusion_class_representative(1) = 'h1' - diffusion_class_representative(2) = 'he4' - diffusion_class_representative(3) = 'o16' - diffusion_class_representative(4) = 'fe56' - - ! in ascending order. species goes into 1st class with A_max >= species A - diffusion_class_A_max(1) = 2 - diffusion_class_A_max(2) = 4 - diffusion_class_A_max(3) = 16 - diffusion_class_A_max(4) = 10000 - - diffusion_use_isolve = .true. - diffusion_rtol_for_isolve = 1d-4 - diffusion_atol_for_isolve = 1d-5 - diffusion_maxsteps_for_isolve = 1000 - diffusion_isolve_solver = 'ros2_solver' - - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 + min_D_mix = 1d2 ! D_mix will be at least this large + min_center_Ye_for_min_D_mix = 0.47 ! min_D_mix is only used when center Ye >= this + ! i.e., when center Ye drops below this, min_D_mix is 0 + + + num_cells_for_smooth_brunt_B = 0 + + !show_diffusion_info = .true. ! terminal output for diffusion + !show_diffusion_substep_info = .true. + !show_diffusion_timing = .true. + + do_element_diffusion = .true. ! determines whether or not we do diffusion + + diffusion_calculates_ionization = .true. + + diffusion_num_classes = 4 ! number of classes of species for diffusion calculations + diffusion_class_representative(1) = 'h1' + diffusion_class_representative(2) = 'he4' + diffusion_class_representative(3) = 'o16' + diffusion_class_representative(4) = 'fe56' + + ! in ascending order. species goes into 1st class with A_max >= species A + diffusion_class_A_max(1) = 2 + diffusion_class_A_max(2) = 4 + diffusion_class_A_max(3) = 16 + diffusion_class_A_max(4) = 10000 + + diffusion_use_isolve = .true. + diffusion_rtol_for_isolve = 1d-4 + diffusion_atol_for_isolve = 1d-5 + diffusion_maxsteps_for_isolve = 1000 + diffusion_isolve_solver = 'ros2_solver' + + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 / ! end of controls namelist &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'vcps' ! postscript - file_extension = 'ps' - - pgstar_interval = 1 - - ! Brunt B profile - Profile_Panels1_win_flag = .true. - Profile_Panels1_win_width = 14 - Profile_Panels1_show_grid = .false - Profile_Panels1_title = 'diffusion_smoothness' - - Profile_Panels1_xaxis_name = 'zone' - Profile_Panels1_xmin = -101d0 - Profile_Panels1_xmax = -101d0 - Profile_Panels1_xaxis_reversed = .true. - Profile_Panels1_show_mix_regions_on_xaxis = .true. - - Profile_Panels1_num_panels = 1 - Profile_Panels1_yaxis_name(1) = 'brunt_B' - Profile_Panels1_ymin(:) = -101d0 - Profile_Panels1_ymax(:) = -101d0 - Profile_Panels1_other_yaxis_name(1) = '' - - Profile_Panels1_file_flag = .true. - Profile_Panels1_file_dir = 'pgstar_out' - Profile_Panels1_file_prefix = 'brunt_' - Profile_Panels1_file_interval = 10000 - Profile_Panels1_file_width = 14 + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'vcps' ! postscript + file_extension = 'ps' + + pgstar_interval = 1 + + ! Brunt B profile + Profile_Panels1_win_flag = .true. + Profile_Panels1_win_width = 14 + Profile_Panels1_show_grid = .false + Profile_Panels1_title = 'diffusion_smoothness' + + Profile_Panels1_xaxis_name = 'zone' + Profile_Panels1_xmin = -101d0 + Profile_Panels1_xmax = -101d0 + Profile_Panels1_xaxis_reversed = .true. + Profile_Panels1_show_mix_regions_on_xaxis = .true. + + Profile_Panels1_num_panels = 1 + Profile_Panels1_yaxis_name(1) = 'brunt_B' + Profile_Panels1_ymin(:) = -101d0 + Profile_Panels1_ymax(:) = -101d0 + Profile_Panels1_other_yaxis_name(1) = '' + + Profile_Panels1_file_flag = .true. + Profile_Panels1_file_dir = 'pgstar_out' + Profile_Panels1_file_prefix = 'brunt_' + Profile_Panels1_file_interval = 10000 + Profile_Panels1_file_width = 14 / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header index af5d6b624..aaf43854c 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header @@ -1,39 +1,39 @@ &star_job - read_extra_star_job_inlist(1) = .true. - extra_star_job_inlist_name(1) = 'inlist_diffusion_smoothness' + read_extra_star_job_inlist(1) = .true. + extra_star_job_inlist_name(1) = 'inlist_diffusion_smoothness' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_diffusion_smoothness' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_diffusion_smoothness' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_diffusion_smoothness' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_diffusion_smoothness' / ! end of kap namelist &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_diffusion_smoothness' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_diffusion_smoothness' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_diffusion_smoothness' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_diffusion_smoothness' / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_zams b/star/test_suite/diffusion_smoothness/inlist_zams index cccd02ef5..fda0c5e76 100644 --- a/star/test_suite/diffusion_smoothness/inlist_zams +++ b/star/test_suite/diffusion_smoothness/inlist_zams @@ -1,75 +1,75 @@ &star_job - show_log_description_at_start = .false. - - !show_net_species_info = .true. - !show_net_reactions_info = .true. + show_log_description_at_start = .false. - create_pre_main_sequence_model = .true. - - save_model_when_terminate = .true. - save_model_filename = 'zams.mod' - required_termination_code_string = 'Lnuc_div_L_zams_limit' + !show_net_species_info = .true. + !show_net_reactions_info = .true. + create_pre_main_sequence_model = .true. - change_initial_net = .true. - new_net_name = 'o18_and_ne22.net' - - !pgstar_flag = .true. + save_model_when_terminate = .true. + save_model_filename = 'zams.mod' + required_termination_code_string = 'Lnuc_div_L_zams_limit' + + + change_initial_net = .true. + new_net_name = 'o18_and_ne22.net' + + !pgstar_flag = .true. / ! end of star_job namelist &kap - Zbase = 0.02d0 + Zbase = 0.02d0 - kap_file_prefix = 'gs98' + kap_file_prefix = 'gs98' / ! end of kap namelist &controls - stop_near_zams = .true. - Lnuc_div_L_zams_limit = 0.98d0 - - ! limit max_model_number as part of test_suite - max_model_number = 10000 - use_gold2_tolerances = .true. - - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' - - x_integer_ctrl(1) = 0 ! part number - - initial_mass = 1.0 - initial_z = 0.02d0 - - varcontrol_target = 1d-3 - mesh_delta_coeff = 0.7 - + stop_near_zams = .true. + Lnuc_div_L_zams_limit = 0.98d0 + + ! limit max_model_number as part of test_suite + max_model_number = 10000 + use_gold2_tolerances = .true. + + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' + + x_integer_ctrl(1) = 0 ! part number + + initial_mass = 1.0 + initial_z = 0.02d0 + + varcontrol_target = 1d-3 + mesh_delta_coeff = 0.7 + ! set_min_D_mix = .true. - min_D_mix = 1d2 ! D_mix will be at least this large - min_center_Ye_for_min_D_mix = 0.47 ! min_D_mix is only used when center Ye >= this - ! i.e., when center Ye drops below this, min_D_mix is 0 - - - num_cells_for_smooth_brunt_B = 0 - - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 + min_D_mix = 1d2 ! D_mix will be at least this large + min_center_Ye_for_min_D_mix = 0.47 ! min_D_mix is only used when center Ye >= this + ! i.e., when center Ye drops below this, min_D_mix is 0 + + + num_cells_for_smooth_brunt_B = 0 + + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 / ! end of controls namelist &pgstar - - ! top level controls - !pause = .true. - ! if true, the code waits for user to enter a RETURN on the command line - + ! top level controls + + !pause = .true. + ! if true, the code waits for user to enter a RETURN on the command line + / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_zams_header b/star/test_suite/diffusion_smoothness/inlist_zams_header index a387c02e0..f855a2d43 100644 --- a/star/test_suite/diffusion_smoothness/inlist_zams_header +++ b/star/test_suite/diffusion_smoothness/inlist_zams_header @@ -1,24 +1,24 @@ &star_job - read_extra_star_job_inlist(1) = .true. - extra_star_job_inlist_name(1) = 'inlist_zams' + read_extra_star_job_inlist(1) = .true. + extra_star_job_inlist_name(1) = 'inlist_zams' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_zams' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_zams' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_zams' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_zams' / ! end of kap namelist @@ -26,15 +26,15 @@ &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_zams' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_zams' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_zams' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_zams' / ! end of pgstar namelist From eac9c0e74c2de3bf9007e3ff2c3b6548e4b4638a Mon Sep 17 00:00:00 2001 From: Joey Mombarg Date: Tue, 6 Aug 2024 17:11:14 +0200 Subject: [PATCH 09/66] updating test_suite 21 --- .../docs/track1_000452.png | Bin 0 -> 8085 bytes .../accreted_material_j/history_columns.list | 1067 +++++++++++++++++ .../inlist_accreted_material_j | 19 +- .../inlist_accreted_material_j_header | 2 +- .../accreted_material_j/inlist_pgstar | 36 + 5 files changed, 1115 insertions(+), 9 deletions(-) create mode 100644 star/test_suite/accreted_material_j/docs/track1_000452.png create mode 100644 star/test_suite/accreted_material_j/history_columns.list create mode 100644 star/test_suite/accreted_material_j/inlist_pgstar diff --git a/star/test_suite/accreted_material_j/docs/track1_000452.png b/star/test_suite/accreted_material_j/docs/track1_000452.png new file mode 100644 index 0000000000000000000000000000000000000000..3ce3eb0b0f9a8d7652a0a6f33e784cde10f7589c GIT binary patch literal 8085 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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 a few items: + + ! version_number -- for the version of mesa being used + ! burn_min1 -- 1st limit for reported burning, in erg/g/s + ! burn_min2 -- 2nd limit for reported burning, in erg/g/s + + +!# other files + +! 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 + +!---------------------------------------------------------------------------------------------- + +!# general info about the model + + model_number ! counting from the start of the run + num_zones ! number of zones in the model + + !## age + + star_age ! elapsed simulated time in years since the start of the run + !star_age_sec ! elapsed simulated time in seconds since the start of the run + !star_age_min ! elapsed simulated time in minutes since the start of the run + !star_age_hr ! elapsed simulated time in hours since the start of the run + !star_age_day ! elapsed simulated time in days since the start of the run + !day ! elapsed simulated time in days since the start of the run + + !log_star_age + !log_star_age_sec + + !## timestep + + !time_step ! timestep in years since previous model + !time_step_sec ! timestep in seconds since previous model + !time_step_days + log_dt ! log10 time_step in years + !log_dt_sec ! log10 time_step in seconds + !log_dt_days ! log10 time_step in days + + !## mass + + star_mass ! in Msun units + !log_star_mass + + !star_gravitational_mass ! star_mass is baryonic mass + !star_mass_grav_div_mass + + !delta_mass ! star_mass - initial_mass in Msun units + log_xmstar ! log10 mass exterior to M_center (grams) + + !## mass change + + !star_mdot ! d(star_mass)/dt (in msolar per year) + log_abs_mdot ! log10(abs(star_mdot)) (in msolar per year) + + !## imposed surface conditions + !Tsurf_factor + !tau_factor + !tau_surface + + !## imposed center conditions + !m_center + !m_center_gm + !r_center + !r_center_cm + !r_center_km + !L_center + !log_L_center + !log_L_center_ergs_s + !v_center + !v_center_kms + + !logt_max + +!---------------------------------------------------------------------------------------------- + +!# mixing and convection + + !max_conv_vel_div_csound + !max_gradT_div_grada + !max_gradT_sub_grada + !min_log_mlt_Gamma + + + !## mixing regions + + mass_conv_core ! (Msun) mass coord of top of convective core. 0 if core is not convective + + ! 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. + + ! values are m/Mstar + conv_mx1_top + conv_mx1_bot + conv_mx2_top + conv_mx2_bot + mx1_top + mx1_bot + mx2_top + mx2_bot + + ! radius -- values are radii in Rsun units + !conv_mx1_top_r + !conv_mx1_bot_r + !conv_mx2_top_r + !conv_mx2_bot_r + !mx1_top_r + !mx1_bot_r + !mx2_top_r + !mx2_bot_r + + ! you might want to get a more complete list of mixing regions by using the following + + !mixing_regions ! note: this includes regions where the mixing type is no_mixing. + + ! the is the number of regions to report + ! there will be 2* columns for this in the log file, 2 for each region. + ! the first column for a region gives the mixing type as defined in const/public/const_def.f90. + + ! the second column for a region gives the m/mstar location of the top of the region + ! entries for extra columns after the last region in the star will have an invalid mixing_type value of -1. + ! 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' + + ! if the star has too many regions to report them all, + ! the smallest regions will be merged with neighbors for reporting purposes only. + + + !mix_relr_regions + ! same as above, but locations given as r/rstar instead of m/mstar. + ! the columns in the log file will have names like 'mix_relr_type_1' and 'mix_relr_top_1' + + + !## conditions at base of largest convection zone (by mass) + !cz_bot_mass ! mass coordinate of base (Msun) + !cz_mass ! mass coordinate of base (Msun) -- same as cz_bot_mass + !cz_log_xmass ! mass exterior to base (g) + !cz_log_xmsun ! mass exterior to base (Msun) + !cz_xm ! mass exterior to base (Msun) + !cz_logT + !cz_logRho + !cz_logP + !cz_bot_radius ! Rsun + !cz_log_column_depth + !cz_log_radial_depth + !cz_luminosity ! Lsun + !cz_opacity + !cz_log_tau + !cz_eta + !cz_log_eps_nuc ! log10(ergs/g/s) + !cz_t_heat ! Cp*T/eps_nuc (seconds) + + !cz_csound + !cz_scale_height + !cz_grav + + !cz_omega + !cz_omega_div_omega_crit + + !cz_zone + + ! mass fractions at base of largest convection zone (by mass) + !cz_log_xa h1 + !cz_log_xa he4 + + !## conditions at top of largest convection zone (by mass) + !cz_top_mass ! mass coordinate of top (Msun) + !cz_top_log_xmass ! mass exterior to top (g) + !cz_top_log_xmsun ! mass exterior to top (Msun) + !cz_top_xm ! mass exterior to top (Msun) + !cz_top_logT + !cz_top_logRho + !cz_top_logP + !cz_top_radius ! Rsun + !cz_top_log_column_depth + !cz_top_log_radial_depth + !cz_top_luminosity ! Lsun + !cz_top_opacity + !cz_top_log_tau + !cz_top_eta + !cz_top_log_eps_nuc ! log10(ergs/g/s) + !cz_top_t_heat ! Cp*T/eps_nuc (seconds) + + !cz_top_csound + !cz_top_scale_height + !cz_top_grav + + !cz_top_omega + !cz_top_omega_div_omega_crit + + !cz_top_zone + !cz_top_zone_logdq + + ! mass fractions at top of largest convection zone (by mass) + !cz_top_log_xa h1 + !cz_top_log_xa he4 + +!---------------------------------------------------------------------------------------------- + +!# nuclear reactions + + !## integrated quantities + + !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) + !power_photo + !power_z_burn + !log_power_nuc_burn ! total thermal power from all burning, excluding photodisintegrations + log_LH ! log10 power_h_burn + log_LHe ! log10 power_he_burn + log_LZ ! log10 total burning power including LC, but excluding LH and LHe and photodisintegrations + log_Lnuc ! log(LH + LHe + LZ) + !log_Lnuc_ergs_s + !log_Lnuc_sub_log_L + !lnuc_photo + + !extra_L ! integral of extra_heat in Lsun units + !log_extra_L ! log10 extra_L + + !## neutrino losses + !log_Lneu ! log10 power emitted in neutrinos, nuclear and thermal (in Lsun units) + !log_Lneu_nuc ! log10 power emitted in neutrinos, nuclear sources only (in Lsun units) + !log_Lneu_nonnuc ! log10 power emitted in neutrinos, thermal sources only (in Lsun units) + + !mass_loc_of_max_eps_nuc ! (in Msun units) + !mass_ext_to_max_eps_nuc ! (in Msun units) + !eps_grav_integral ! (in Lsun units) + !log_abs_Lgrav ! log10 abs(eps_grav_integral) (in Lsun units) + + !## information about reactions (by category) + + ! log10 total luminosity for reaction categories (Lsun units) + + pp + cno + tri_alpha + !c_alpha + !n_alpha + !o_alpha + !ne_alpha + !na_alpha + !mg_alpha + !si_alpha + !s_alpha + !ar_alpha + !ca_alpha + !ti_alpha + !fe_co_ni + !c12_c12 + !c12_o16 + !o16_o16 + !photo + !pnhe4 + !other + + !## information about individual reactions + + ! adds columns for all of the reactions that are in the current net + ! Note that if using op_split_burn=.true. then zones which have been split will report 0 for thier rates + !add_raw_rates ! raw reaction rates, reactions/second + !add_screened_rates ! screened reaction rates reactions/second + !add_eps_nuc_rates ! Nuclear energy (minus neutrino losses) released erg/s + !add_eps_neu_rates ! Neutrino losses erg/s + + ! individual reactions (as many as desired) + ! use list_net_reactions = .true. in star_job to list all reactions in the current net + ! reactions/second + !raw_rate r_h1_h1_ec_h2 + !raw_rate r_h1_h1_wk_h2 + + + + !## nuclear reactions at center + + ! center log10 burn erg/g/s for reaction categories + + !c_log_eps_burn cno + !c_log_eps_burn tri_alfa + + ! center d_eps_nuc_dlnd for reaction categories + + !c_d_eps_dlnd cno + !c_d_eps_dlnd tri_alfa + + ! center d_eps_nuc_dlnT for reaction categories + + !c_d_eps_dlnT cno + !c_d_eps_dlnT tri_alfa + + !## 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 + + + ! you might want to get a more complete list of burning regions by using the following + + !burning_regions + ! the is the number of regions to report + ! there will be 2* columns for this in the log file, 2 for each region. + ! the first column for a region gives int(sign(val)*log10(max(1,abs(val)))) + ! where val = ergs/gm/sec nuclear energy minus all neutrino losses. + ! the second column for a region gives the q location of the top of the region + ! entries for extra columns after the last region in the star will have a value of -9999 + ! all regions are included 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 q=0 and top of last is q=1. + + ! the columns in the log file will have names like 'burn_type_1' and 'burn_qtop_1' + + !burn_relr_regions + ! same as above, but locations given as r/rstar instead of m/mstar. + ! the columns in the log file will have names like 'burn_relr_type_1' and 'burn_relr_top_1' + + + ! if the star has too many regions to report them all, + ! the smallest regions will be merged with neighbors for reporting purposes only. + +!---------------------------------------------------------------------------------------------- + +!# information about core and envelope + + !## helium core + he_core_mass + !he_core_radius + !he_core_lgT + !he_core_lgRho + !he_core_L + !he_core_v + !he_core_omega + !he_core_omega_div_omega_crit + !he_core_k + + !## CO core + co_core_mass + !CO_core + !co_core_radius + !co_core_lgT + !co_core_lgRho + !co_core_L + !co_core_v + !co_core_omega + !co_core_omega_div_omega_crit + !co_core_k + + !## ONe core + one_core_mass + !one_core_radius + !one_core_lgT + !one_core_lgRho + !one_core_L + !one_core_v + !one_core_omega + !one_core_omega_div_omega_crit + !one_core_k + + !## iron core + fe_core_mass + !fe_core_radius + !fe_core_lgT + !fe_core_lgRho + !fe_core_L + !fe_core_v + !fe_core_omega + !fe_core_omega_div_omega_crit + !fe_core_k + + !## neuton rich core + neutron_rich_core_mass + !neutron_rich_core_radius + !neutron_rich_core_lgT + !neutron_rich_core_lgRho + !neutron_rich_core_L + !neutron_rich_core_v + !neutron_rich_core_omega + !neutron_rich_core_omega_div_omega_crit + !neutron_rich_core_k + + !## envelope + + !envelope_mass ! = star_mass - he_core_mass + !envelope_fraction_left ! = envelope_mass / (initial_mass - he_core_mass) + + !h_rich_layer_mass ! = star_mass - he_core_mass + !he_rich_layer_mass ! = he_core_mass - c_core_mass + !co_rich_layer_mass + +!---------------------------------------------------------------------------------------------- + +!# timescales + + !dynamic_timescale ! dynamic timescale (seconds) -- estimated by 2*pi*sqrt(r^3/(G*m)) + !kh_timescale ! kelvin-helmholtz timescale (years) + !mdot_timescale ! star_mass/abs(star_mdot) (years) + !kh_div_mdot_timescales ! kh_timescale/mdot_timescale + !nuc_timescale ! nuclear timescale (years) -- proportional to mass divided by luminosity + + !dt_cell_collapse ! min time for any cell to collapse at current velocities + !dt_div_dt_cell_collapse + + !dt_div_max_tau_conv ! dt/ maximum conv timescale + !dt_div_min_tau_conv ! dt/ minimum conv timescale + + + !min_dr_div_cs ! min over all cells of dr/csound (seconds) + !min_dr_div_cs_k ! location of min + !log_min_dr_div_cs ! log10 min dr_div_csound (seconds) + !min_dr_div_cs_yr ! min over all cells of dr/csound (years) + !log_min_dr_div_cs_yr ! log10 min dr_div_csound (years) + !dt_div_min_dr_div_cs + !log_dt_div_min_dr_div_cs + + !min_t_eddy ! minimum value of scale_height/conv_velocity + +!---------------------------------------------------------------------------------------------- + +!# conditions at or near the surface of the model + + !## conditions at the photosphere + !effective_T + !Teff + log_Teff ! log10 effective temperature + ! Teff is calculated using Stefan-Boltzmann relation L = 4 pi R^2 sigma Teff^4, + ! where L and R are evaluated at the photosphere (tau_factor < 1) + ! or surface of the model (tau_factor >= 1) when photosphere is not inside the model. + + !photosphere_black_body_T + !photosphere_cell_T ! temperature at model location closest to the photosphere, not necessarily Teff + !photosphere_cell_log_T + !photosphere_cell_density + !photosphere_cell_log_density + !photosphere_cell_opacity + !photosphere_cell_log_opacity + !photosphere_L ! Lsun units + !photosphere_log_L ! Lsun units + !photosphere_r ! Rsun units + !photosphere_log_r ! Rsun units + !photosphere_m ! Msun units + !photosphere_v_km_s + !photosphere_cell_k + !photosphere_column_density + !photosphere_csound + !photosphere_log_column_density + !photosphere_opacity + !photosphere_v_div_cs + !photosphere_xm + !photosphere_cell_free_e + !photosphere_cell_log_free_e + !photosphere_logg + !photosphere_T + + !## conditions at or near the surface of the model (outer edge of outer cell) + + !luminosity ! luminosity in Lsun units + !luminosity_ergs_s ! luminosity in cgs units + log_L ! log10 luminosity in Lsun units + !log_L_ergs_s ! log10 luminosity in cgs units + !radius ! Rsun + log_R ! log10 radius in Rsun units + !radius_cm + !log_R_cm + + log_g ! log10 gravity + !gravity + !log_Ledd + !log_L_div_Ledd ! log10(L/Leddington) + !lum_div_Ledd + !log_surf_optical_depth + !surface_optical_depth + + !log_surf_cell_opacity ! old name was log_surf_opacity + !log_surf_cell_P ! old name was log_surf_P + !log_surf_cell_pressure ! old name was log_surf_pressure + !log_surf_cell_density ! old name was log_surf_density + !log_surf_cell_temperature ! old name was log_surf_temperature + !surface_cell_temperature ! old name was surface_temperature + !log_surf_cell_z ! old name was log_surf_z + !surface_cell_entropy ! in units of kerg per baryon + ! old name was surface_entropy + + !v_surf ! (cm/s) + !v_surf_km_s ! (km/s) + v_div_csound_surf ! velocity divided by sound speed at outermost grid point + !v_div_csound_max ! max value of velocity divided by sound speed at face + !v_div_vesc + !v_phot_km_s + !v_surf_div_escape_v + + !v_surf_div_v_kh ! v_surf/(photosphere_r/kh_timescale) + + !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_Lrad_div_Ledd + !surf_avg_logT + !surf_avg_logRho + !surf_avg_opacity + + ! Gravity Darkening, reports the surface averaged L/Lsun and Teff (K) caused by + ! gravity darkening in rotating stars. Based on the model of Espinosa Lara & Rieutord (2011) + ! 'polar' refers to the line of sight being directed along the rotation axis of the star + ! 'equatorial' refers to the line of sight coincident with the stellar equator + !grav_dark_L_polar !Lsun + !grav_dark_Teff_polar !K + !grav_dark_L_equatorial !Lsun + !grav_dark_Teff_equatorial !K + + !surf_escape_v ! cm/s + + !v_wind_Km_per_s ! Km/s + ! = 1d-5*s% opacity(1)*max(0d0,-s% mstar_dot)/ & + ! (4*pi*s% photosphere_r*Rsun*s% tau_base) + ! Lars says: + ! wind_mdot = 4*pi*R^2*rho*v_wind + ! tau = integral(opacity*rho*dr) from R to infinity + ! so tau = opacity*wind_mdot/(4*pi*R*v_wind) at photosphere + ! or v_wind = opacity*wind_mdot/(4*pi*R*tau) at photosphere + + !rotational_mdot_boost ! factor for increase in mass loss mdot due to rotation + !log_rotational_mdot_boost ! log factor for increase in mass loss mdot due to rotation + !surf_r_equatorial_div_r_polar + !surf_r_equatorial_div_r + !surf_r_polar_div_r + +!---------------------------------------------------------------------------------------------- + +!# conditions near center + + !log_center_T ! temperature + !log_center_Rho ! density + !log_center_P ! pressure + + ! shorter names for above + log_cntr_P + log_cntr_Rho + log_cntr_T + + !center_T ! temperature + !center_Rho ! density + !center_P ! pressure + + !center_degeneracy ! the electron chemical potential in units of k*T + !center_gamma ! plasma interaction parameter + center_mu + center_ye + center_abar + !center_zbar + + !center_eps_grav + + !center_non_nuc_neu + !center_eps_nuc + !d_center_eps_nuc_dlnT + !d_center_eps_nuc_dlnd + !log_center_eps_nuc + + !center_entropy ! in units of kerg per baryon + !max_entropy ! in units of kerg per baryon + !fe_core_infall + !non_fe_core_infall + !non_fe_core_rebound + !max_infall_speed + + !compactness_parameter ! (m/Msun)/(R(m)/1000km) for m = 2.5 Msun + !compactness + !m4 ! Mass co-ordinate where entropy=4 + ! mu4 is sensitive to the choice of how much dm/dr you average over, thus we average dm and dr over M(entropy=4) and M(entropy=4)+0.3Msun + !mu4 ! dM(Msun)/dr(1000km) where entropy=4 + + + !center_omega + !center_omega_div_omega_crit + +!---------------------------------------------------------------------------------------------- + +!# abundances + + !species ! size of net + + !## mass fractions near center + + ! the following controls automatically add columns for all of the isos that are in the current net + !add_center_abundances + !add_log_center_abundances + + ! individual central mass fractions (as many as desired) + center h1 + center he4 + center c12 + center o16 + + ! individual log10 central mass fractions (as many as desired) + !log_center h1 + !log_center he4 + ! etc. + + + !## mass fractions near surface + + ! the following controls automatically add columns for all of the isos that are in the current net + !add_surface_abundances + !add_log_surface_abundances + + ! individual surface mass fractions (as many as desired) + !surface h1 + !surface he4 + surface c12 + surface o16 + ! etc. + + ! individual log10 surface mass fractions (as many as desired) + + !log_surface h1 + !log_surface he4 + + + !## mass fractions for entire star + + ! the following controls automatically add columns for all of the isos that are in the current net + !add_average_abundances + !add_log_average_abundances + + ! individual average mass fractions (as many as desired) + !average h1 + !average he4 + ! etc. + + ! individual log10 average mass fractions (as many as desired) + !log_average h1 + !log_average he4 + ! etc. + + + !## mass totals for entire star (in Msun units) + + ! the following controls automatically add columns for all of the isos that are in the current net + !add_total_mass + !add_log_total_mass + + ! individual mass totals for entire star (as many as desired) + total_mass h1 + total_mass he4 + ! etc. + + ! individial log10 mass totals for entire star (in Msun units) + !log_total_mass h1 + !log_total_mass he4 + ! etc. + +!---------------------------------------------------------------------------------------------- + +!# info at specific locations + + !## info at location of max temperature + !max_T + !log_max_T + + +!---------------------------------------------------------------------------------------------- + +!# information about shocks + + !## info about outermost outward moving shock + ! excluding locations with q > max_q_for_outer_mach1_location + ! returns values at location of max velocity + !shock_mass ! baryonic (Msun) + !shock_mass_gm ! baryonic (grams) + !shock_q + !shock_radius ! (Rsun) + !shock_radius_cm ! (cm) + !shock_velocity + !shock_csound + !shock_v_div_cs + !shock_lgT + !shock_lgRho + !shock_lgP + !shock_gamma1 + !shock_entropy + !shock_tau + !shock_k + !shock_pre_lgRho + +!---------------------------------------------------------------------------------------------- + +!# asteroseismology + + !delta_nu ! large frequency separation for p-modes (microHz) + ! 1e6/(seconds for sound to cross diameter of star) + !delta_Pg ! g-mode period spacing for l=1 (seconds) + ! sqrt(2) pi^2/(integral of brunt_N/r dr) + !log_delta_Pg + !nu_max ! estimate from scaling relation (microHz) + ! nu_max = nu_max_sun * M/Msun / ((R/Rsun)^2 (Teff/astero_Teff_sun)^0.5) + !nu_max_3_4th_div_delta_nu ! nu_max^0.75/delta_nu + !acoustic_cutoff ! 0.5*g*sqrt(gamma1*rho/P) at surface + !acoustic_radius ! integral of dr/csound (seconds) + !ng_for_nu_max ! = 1 / (nu_max*delta_Pg) + ! period for g-mode with frequency nu_max = nu_max_ng*delta_Pg + !gs_per_delta_nu ! delta_nu / (nu_max**2*delta_Pg) + ! number of g-modes per delta_nu at nu_max + + !int_k_r_dr_nu_max_Sl1 ! integral of k_r*dr where nu < N < Sl for nu = nu_max, l=1 + !int_k_r_dr_2pt0_nu_max_Sl1 ! integral of k_r*dr where nu < N < Sl for nu = nu_max*2, l=1 + !int_k_r_dr_0pt5_nu_max_Sl1 ! integral of k_r*dr where nu < N < Sl for nu = nu_max/2, l=1 + !int_k_r_dr_nu_max_Sl2 ! integral of k_r*dr where nu < N < Sl for nu = nu_max, l=2 + !int_k_r_dr_2pt0_nu_max_Sl2 ! integral of k_r*dr where nu < N < Sl for nu = nu_max*2, l=2 + !int_k_r_dr_0pt5_nu_max_Sl2 ! integral of k_r*dr where nu < N < Sl for nu = nu_max/2, l=2 + !int_k_r_dr_nu_max_Sl3 ! integral of k_r*dr where nu < N < Sl for nu = nu_max, l=3 + !int_k_r_dr_2pt0_nu_max_Sl3 ! integral of k_r*dr where nu < N < Sl for nu = nu_max*2, l=3 + !int_k_r_dr_0pt5_nu_max_Sl3 ! integral of k_r*dr where nu < N < Sl for nu = nu_max/2, l=3 + +!---------------------------------------------------------------------------------------------- + +!# energy information + + !total_energy ! at end of step + !log_total_energy ! log(abs(total_energy)) + !total_energy_after_adjust_mass ! after mass adjustments + + ! shorter versions of above + !tot_E + !log_tot_E + + + !total_gravitational_energy + !log_total_gravitational_energy ! log(abs(total_gravitational_energy)) + !total_gravitational_energy_after_adjust_mass + + ! shorter versions of above + !tot_PE + !log_tot_PE + + !total_internal_energy + !log_total_internal_energy + !total_internal_energy_after_adjust_mass + + ! shorter versions of above + !tot_IE + !log_tot_IE + + !total_radial_kinetic_energy + !log_total_radial_kinetic_energy + !total_radial_kinetic_energy_after_adjust_mass + + ! shorter versions of above (does not include rot KE) + !tot_KE + !log_tot_KE + + !total_turbulent_energy + !log_total_turbulent_energy + !total_turbulent_energy_after_adjust_mass + !tot_Et + !log_tot_Et + + !total_energy_foe + + !tot_IE_div_IE_plus_KE + !total_IE_div_IE_plus_KE + + !total_entropy + !total_eps_grav + + !total_energy_sources_and_sinks ! for this step + !total_nuclear_heating + !total_non_nuc_neu_cooling + !total_irradiation_heating + !total_extra_heating ! extra heat integrated over the model times dt (erg) + !total_WD_sedimentation_heating + + !rel_run_E_err + + !rel_E_err + !abs_rel_E_err + !log_rel_E_err + + !tot_e_equ_err + !tot_e_err + + + !error_in_energy_conservation ! for this step + ! = total_energy - (total_energy_start + total_energy_sources_and_sinks) + !cumulative_energy_error ! = sum over all steps of abs(error_in_energy_conservation) + !rel_cumulative_energy_error ! = cumulative_energy_error/total_energy + !log_rel_cumulative_energy_error ! = log10 of rel_cumulative_energy_error + !log_rel_run_E_err ! shorter name for rel_cumulative_energy_error + + !rel_error_in_energy_conservation ! = error_in_energy_conservation/total_energy + !log_rel_error_in_energy_conservation + + !virial_thm_P_avg + !virial_thm_rel_err + !work_inward_at_center + !work_outward_at_surface + + +!---------------------------------------------------------------------------------------------- + + !# rotation + + !total_angular_momentum + log_total_angular_momentum + !i_rot_total ! moment of inertia + + !total_rotational_kinetic_energy + !log_total_rotational_kinetic_energy + !total_rotational_kinetic_energy_after_adjust_mass + +!---------------------------------------------------------------------------------------------- + +!# velocities + + !avg_abs_v_div_cs + !log_avg_abs_v_div_cs + !max_abs_v_div_cs + !log_max_abs_v_div_cs + + !avg_abs_v + !log_avg_abs_v + !max_abs_v + !log_max_abs_v + + !u_surf + !u_surf_km_s + !u_div_csound_surf + !u_div_csound_max + + !infall_div_cs + +!---------------------------------------------------------------------------------------------- + +!# misc + + !e_thermal ! sum over all zones of Cp*T*dm + + !## eos + !logQ_max ! logQ = logRho - 2*logT + 12 + !logQ_min + !gamma1_min + + !## core mixing + !mass_semiconv_core + + !## H-He boundary + + !diffusion_time_H_He_bdy + !temperature_H_He_bdy + + + !## optical depth and opacity + + !one_div_yphot + !log_one_div_yphot + + !log_min_opacity + !min_opacity + + !log_tau_center + + !log_max_tau_conv + !max_tau_conv + !log_min_tau_conv + !min_tau_conv + + !tau_qhse_yrs + + !## other + + !Lsurf_m + !dlnR_dlnM + !h1_czb_mass ! location (in Msun units) of base of 1st convection zone above he core + !kh_mdot_limit + !log_cntr_dr_cm + !min_Pgas_div_P + !surf_c12_minus_o16 ! this is useful for seeing effects of dredge up on AGB + !surf_num_c12_div_num_o16 + + !phase_of_evolution ! Integer mapping to the type of evolution see star_data/public/star_data_def.inc for definitions + + !## MLT++ + !gradT_excess_alpha + !gradT_excess_min_beta + !gradT_excess_max_lambda + + !max_L_rad_div_Ledd + !max_L_rad_div_Ledd_div_phi_Joss + + + !## RTI + !rti_regions + + !## Ni & Co + !total_ni_co_56 + + + !## internal structure constants + + ! this is evaluated assuming a spherical star and does not account for rotation + !apsidal_constant_k2 + + +!---------------------------------------------------------------------------------------------- + +!# accretion + + !k_below_const_q + !q_below_const_q + !logxq_below_const_q + + !k_const_mass + !q_const_mass + !logxq_const_mass + + !k_below_just_added + !q_below_just_added + !logxq_below_just_added + + !k_for_test_CpT_absMdot_div_L + !q_for_test_CpT_absMdot_div_L + !logxq_for_test_CpT_absMdot_div_L + +!---------------------------------------------------------------------------------------------- + +!# Color output + + ! Outputs the bolometric correction (bc) for the star in filter band ``filter'' (case sensitive) + !bc filter + + ! Outputs the absolute magnitude for the star in filter band ``filter'' (case sensitive) + !abs_mag filter + + ! Adds all the bc's to the output + !add_bc + + ! Adds all the absolute magnitudes to the output + !add_abs_mag + + ! Outputs luminosity in filter band ``filter'' (erg s^-1) (case sensitive) + ! lum_band filter + + ! Adds all the filter band luminosities to the output (erg s^-1) + ! add_lum_band + + ! Outputs log luminosity in filter band ``filter'' (log erg s^-1) (case sensitive) + ! log_lum_band filter + + ! Adds all the filter band luminosities to the output (log erg s^-1) + ! add_log_lum_band + +!---------------------------------------------------------------------------------------------- + +!# RSP + + !rsp_DeltaMag ! absolute magnitude difference between minimum and maximum light (mag) + !rsp_DeltaR ! R_max - R_min difference in the max and min radius (Rsun) + !rsp_GREKM ! fractional growth of the kinetic energy per pulsation period ("nonlinear growth rate") - see equation 5 in MESA5 + !rsp_num_periods ! Count of the number of pulsation cycles completed + !rsp_period_in_days ! Running period, ie., period between two consecutive values of R_max (days) + !rsp_phase ! Running pulsation phase for a cycle + +!---------------------------------------------------------------------------------------------- +!# debugging + + !## retries + num_retries ! total during the run + + !## solver iterations + + num_iters ! same as num_solver_iterations + !num_solver_iterations ! iterations at this step + !total_num_solver_iterations ! total iterations during the run + !avg_num_solver_iters + + !rotation_solver_steps + + !diffusion_solver_steps + !diffusion_solver_iters + + !avg_setvars_per_step + !avg_skipped_setvars_per_step + !avg_solver_setvars_per_step + + !burn_solver_maxsteps + + !total_num_solver_calls_converged + !total_num_solver_calls_failed + !total_num_solver_calls_made + !total_num_solver_relax_calls_converged + !total_num_solver_relax_calls_failed + !total_num_solver_relax_calls_made + !total_num_solver_relax_iterations + + !total_step_attempts + !total_step_redos + !total_step_retries + !total_steps_finished + !total_steps_taken + + !TDC_num_cells + + !## Relaxation steps + !total_relax_step_attempts + !total_relax_step_redos + !total_relax_step_retries + !total_relax_steps_finished + !total_relax_steps_taken + + !## conservation during mesh adjust + !log_mesh_adjust_IE_conservation + !log_mesh_adjust_KE_conservation + !log_mesh_adjust_PE_conservation + + !## amr + !num_hydro_merges + !num_hydro_splits + + !## timing + !elapsed_time ! time since start of run (seconds) diff --git a/star/test_suite/accreted_material_j/inlist_accreted_material_j b/star/test_suite/accreted_material_j/inlist_accreted_material_j index ab0f3db53..ec18219df 100644 --- a/star/test_suite/accreted_material_j/inlist_accreted_material_j +++ b/star/test_suite/accreted_material_j/inlist_accreted_material_j @@ -1,6 +1,6 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. load_saved_model = .true. load_model_filename = 'zams.mod' @@ -31,6 +31,9 @@ !required_termination_code_string = 'xa_central_lower_limit' required_termination_code_string = 'star_mass_max_limit' + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. + / !end of star_job &eos @@ -55,9 +58,9 @@ ! limit max_model_number as part of test_suite max_model_number = 1000 - + premix_omega = .true. - + am_nu_visc_factor = 0 am_D_mix_factor = 0.0333333333333333d00 D_DSI_factor = 1 @@ -69,7 +72,7 @@ !set_min_D_mix = .true. !min_D_mix = 1d10 - + ! starting specifications initial_mass = 20 ! in Msun units initial_Z = 0.02 @@ -96,23 +99,23 @@ !varcontrol_target = 5d-4 delta_lg_star_mass_limit = 2d-4 delta_lg_star_mass_hard_limit = 4d-4 - + ! output to files and terminal photo_interval = 50 profile_interval = 100 max_num_profile_models = 3000 history_interval = 10 terminal_interval = 10 - + write_header_frequency = 10 - + !report_solver_progress = .true. / &pgstar - + / ! end of pgstar namelist diff --git a/star/test_suite/accreted_material_j/inlist_accreted_material_j_header b/star/test_suite/accreted_material_j/inlist_accreted_material_j_header index 54bd3ff57..2008891f8 100644 --- a/star/test_suite/accreted_material_j/inlist_accreted_material_j_header +++ b/star/test_suite/accreted_material_j/inlist_accreted_material_j_header @@ -36,6 +36,6 @@ &pgstar read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_accreted_material_j' + extra_pgstar_inlist_name(1)= 'inlist_pgstar' / ! end of pgstar namelist diff --git a/star/test_suite/accreted_material_j/inlist_pgstar b/star/test_suite/accreted_material_j/inlist_pgstar new file mode 100644 index 000000000..5c3005611 --- /dev/null +++ b/star/test_suite/accreted_material_j/inlist_pgstar @@ -0,0 +1,36 @@ +&pgstar + + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'png' ! png + file_extension = 'png' + + !file_device = 'vcps' ! postscript + !file_extension = 'ps' + + pgstar_interval = 10 + + + History_Track1_win_flag = .true. + History_Track1_win_width = 12 + History_Track1_title = 'accreted_material_j' + History_Track1_xname = 'star_mass' + History_Track1_yname = 'log_total_angular_momentum' + History_Track1_yaxis_label = 'log J' + History_Track1_xaxis_label = 'M\d\(2281)' + History_Track1_reverse_xaxis = .false. + History_Track1_reverse_yaxis = .false. + + History_Track1_xmin = 20.0 + History_Track1_xmax = 25.0 + History_Track1_ymin = 51.9 + History_Track1_ymax = 52.7 + +! file output + History_Track1_file_flag = .true. + History_Track1_file_dir = 'pgstar_out' + History_Track1_file_prefix = 'track1_' + History_Track1_file_interval = 10 + History_Track1_file_width =12 + History_Track1_file_aspect_ratio = -1 + +/ ! end of pgstar namelist From 7a3e4ee44a5b3369aa2bffe2a5c86540abaa4db0 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 11:36:01 -0400 Subject: [PATCH 10/66] changing file to svg --- .../test_suite/accreted_material_j/README.rst | 44 +---- .../docs/track1_000452.png | Bin 8085 -> 0 bytes .../docs/track1_000452.svg | 187 +----------------- .../inlist_accreted_material_j | 146 +++++++------- .../inlist_accreted_material_j_header | 20 +- .../accreted_material_j/inlist_pgstar | 10 +- .../accreted_material_j/inlist_zams | 54 ++--- .../accreted_material_j/inlist_zams_header | 20 +- 8 files changed, 129 insertions(+), 352 deletions(-) delete mode 100644 star/test_suite/accreted_material_j/docs/track1_000452.png diff --git a/star/test_suite/accreted_material_j/README.rst b/star/test_suite/accreted_material_j/README.rst index f952de46c..5ebf013fa 100644 --- a/star/test_suite/accreted_material_j/README.rst +++ b/star/test_suite/accreted_material_j/README.rst @@ -19,46 +19,12 @@ This test case has two parts. Click to see a larger view of a plot. pgstar commands used for the plots above: -.. code-block:: console +.. literalinclude:: ../../../star/test_suite/accreted_material_j/inlist_pgstar + :language: console + :start-at: &pgstar + :end-at: ! end of pgstar namelist - &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - !file_device = 'vcps' ! postscript - !file_extension = 'ps' - - pgstar_interval = 10 - - - History_Track1_win_flag = .true. - History_Track1_win_width = 12 - History_Track1_title = 'accreted_material_j' - History_Track1_xname = 'star_mass' - History_Track1_yname = 'log_total_angular_momentum' - History_Track1_yaxis_label = 'log J' - History_Track1_xaxis_label = 'M\d\(2281)' - History_Track1_reverse_xaxis = .false. - History_Track1_reverse_yaxis = .false. - - History_Track1_xmin = 20.0 - History_Track1_xmax = 25.0 - History_Track1_ymin = 51.9 - History_Track1_ymax = 52.7 - - ! file output - History_Track1_file_flag = .true. - History_Track1_file_dir = 'png' - History_Track1_file_prefix = 'track1_' - History_Track1_file_interval = 10 - History_Track1_file_width =12 - History_Track1_file_aspect_ratio = -1 - - / ! end of pgstar namelist - - - -Last-Updated: 30May2021 (MESA e37f76f) by fxt +Last-Updated: 06Aug2024 (MESA ba042c9d) by pmocz on C916PXT6XW in 178 seconds using 8 threads. diff --git a/star/test_suite/accreted_material_j/docs/track1_000452.png b/star/test_suite/accreted_material_j/docs/track1_000452.png deleted file mode 100644 index 3ce3eb0b0f9a8d7652a0a6f33e784cde10f7589c..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8085 zcmeHLX;c&0wnn|Jw&POU0a2nYkQNnM5D*pOj1e#@lT4;%o+Gmeq`VH$f{F$O!xU|l zfCwmq$QW%}5eWo|hy((y5F$f}21p2%s(PnF_j-5Tb>E-&^R35P@Kw&9_x|=t$kpS= ztQId=yFf!jV=?*2!IK&qa}W)U+35T^;N;Eh%SXV0#&H|_L*OL_esEC#;?L^ehZ;sL 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z!)+(Jikdu39;O7Ee67>35$12s)*IzqI<(1piG9JVT0dxUvyz@(bVKSeJbC1$Xsh8* z73=1`z#Lym+a%9flpVvqd z&vcC^?lT{r*C4w=xEAp4oG9@rH-(38CM_D2yIQ_o+VC#^->UhaUjDfjo5k1r%=_+0 Rpa|C?A3Aohc>gaK{|mksW;_4@ diff --git a/star/test_suite/accreted_material_j/docs/track1_000452.svg b/star/test_suite/accreted_material_j/docs/track1_000452.svg index 38926ebb7..3834ebefc 100644 --- a/star/test_suite/accreted_material_j/docs/track1_000452.svg +++ b/star/test_suite/accreted_material_j/docs/track1_000452.svg @@ -1,186 +1 @@ - - - - - - - - - - - - - + \ No newline at end of file diff --git a/star/test_suite/accreted_material_j/inlist_accreted_material_j b/star/test_suite/accreted_material_j/inlist_accreted_material_j index ec18219df..b7074fdfc 100644 --- a/star/test_suite/accreted_material_j/inlist_accreted_material_j +++ b/star/test_suite/accreted_material_j/inlist_accreted_material_j @@ -1,38 +1,38 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. - load_saved_model = .true. - load_model_filename = 'zams.mod' + load_saved_model = .true. + load_model_filename = 'zams.mod' - new_rotation_flag = .true. - change_rotation_flag = .true. - !relax_initial_omega_div_omega_crit = .true. - set_initial_omega_div_omega_crit = .true. - new_omega_div_omega_crit = 0.1 + new_rotation_flag = .true. + change_rotation_flag = .true. + !relax_initial_omega_div_omega_crit = .true. + set_initial_omega_div_omega_crit = .true. + new_omega_div_omega_crit = 0.1 - set_initial_dt = .true. - years_for_initial_dt = 1 + set_initial_dt = .true. + years_for_initial_dt = 1 - set_initial_model_number = .true. - initial_model_number = 0 + set_initial_model_number = .true. + initial_model_number = 0 - set_initial_age = .true. - initial_age = 0 + set_initial_age = .true. + initial_age = 0 - set_initial_cumulative_energy_error = .true. - new_cumulative_energy_error = 0d0 + set_initial_cumulative_energy_error = .true. + new_cumulative_energy_error = 0d0 - !change_D_omega_flag = .true. - !new_D_omega_flag = .true. + !change_D_omega_flag = .true. + !new_D_omega_flag = .true. - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - !required_termination_code_string = 'xa_central_lower_limit' - required_termination_code_string = 'star_mass_max_limit' + save_model_when_terminate = .true. + save_model_filename = 'final.mod' + !required_termination_code_string = 'xa_central_lower_limit' + required_termination_code_string = 'star_mass_max_limit' - pgstar_flag = .true. - save_pgstar_files_when_terminate = .true. + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / !end of star_job @@ -42,74 +42,74 @@ &kap - Zbase = 0.02 + Zbase = 0.02 / ! end of kap namelist &controls - scale_max_correction = 0.1d0 - ignore_species_in_max_correction = .true. + scale_max_correction = 0.1d0 + ignore_species_in_max_correction = .true. - energy_eqn_option = 'dedt' - use_gold2_tolerances = .true. + energy_eqn_option = 'dedt' + use_gold2_tolerances = .true. - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' - ! limit max_model_number as part of test_suite - max_model_number = 1000 + ! limit max_model_number as part of test_suite + max_model_number = 1000 - premix_omega = .true. + premix_omega = .true. - am_nu_visc_factor = 0 - am_D_mix_factor = 0.0333333333333333d00 - D_DSI_factor = 1 - D_SH_factor = 1 - D_SSI_factor = 1 - D_ES_factor = 1 - D_GSF_factor = 1 - D_ST_factor = 1 + am_nu_visc_factor = 0 + am_D_mix_factor = 0.0333333333333333d00 + D_DSI_factor = 1 + D_SH_factor = 1 + D_SSI_factor = 1 + D_ES_factor = 1 + D_GSF_factor = 1 + D_ST_factor = 1 - !set_min_D_mix = .true. - !min_D_mix = 1d10 + !set_min_D_mix = .true. + !min_D_mix = 1d10 - ! starting specifications - initial_mass = 20 ! in Msun units - initial_Z = 0.02 + ! starting specifications + initial_mass = 20 ! in Msun units + initial_Z = 0.02 - max_mdot_redo_cnt = 200 - min_years_dt_for_redo_mdot = 1d-5 - surf_omega_div_omega_crit_limit = 0.999d0 - surf_omega_div_omega_crit_tol = 0.055 - rotational_mdot_boost_fac = 1d10 - rotational_mdot_kh_fac = 1d10 - mdot_revise_factor = 1.1 - implicit_mdot_boost = 0.1 + max_mdot_redo_cnt = 200 + min_years_dt_for_redo_mdot = 1d-5 + surf_omega_div_omega_crit_limit = 0.999d0 + surf_omega_div_omega_crit_tol = 0.055 + rotational_mdot_boost_fac = 1d10 + rotational_mdot_kh_fac = 1d10 + mdot_revise_factor = 1.1 + implicit_mdot_boost = 0.1 - use_accreted_material_j = .true. - use_other_adjust_mdot = .true. + use_accreted_material_j = .true. + use_other_adjust_mdot = .true. - ! ratio of accreted am to keplerian - x_ctrl(1) = 0.1d0 - ! log10 accretion rate in msun/secyer - x_ctrl(2) = -3d0 + ! ratio of accreted am to keplerian + x_ctrl(1) = 0.1d0 + ! log10 accretion rate in msun/secyer + x_ctrl(2) = -3d0 - star_mass_max_limit = 25d0 + star_mass_max_limit = 25d0 - !varcontrol_target = 5d-4 - delta_lg_star_mass_limit = 2d-4 - delta_lg_star_mass_hard_limit = 4d-4 + !varcontrol_target = 5d-4 + delta_lg_star_mass_limit = 2d-4 + delta_lg_star_mass_hard_limit = 4d-4 ! output to files and terminal - photo_interval = 50 - profile_interval = 100 - max_num_profile_models = 3000 - history_interval = 10 - terminal_interval = 10 + photo_interval = 50 + profile_interval = 100 + max_num_profile_models = 3000 + history_interval = 10 + terminal_interval = 10 - write_header_frequency = 10 + write_header_frequency = 10 - !report_solver_progress = .true. + !report_solver_progress = .true. / diff --git a/star/test_suite/accreted_material_j/inlist_accreted_material_j_header b/star/test_suite/accreted_material_j/inlist_accreted_material_j_header index 2008891f8..dd7b8bc6f 100644 --- a/star/test_suite/accreted_material_j/inlist_accreted_material_j_header +++ b/star/test_suite/accreted_material_j/inlist_accreted_material_j_header @@ -2,24 +2,24 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_accreted_material_j' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_accreted_material_j' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_accreted_material_j' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_accreted_material_j' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_accreted_material_j' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_accreted_material_j' / ! end of kap namelist @@ -27,15 +27,15 @@ &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_accreted_material_j' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_accreted_material_j' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_pgstar' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_pgstar' / ! end of pgstar namelist diff --git a/star/test_suite/accreted_material_j/inlist_pgstar b/star/test_suite/accreted_material_j/inlist_pgstar index 5c3005611..29252822c 100644 --- a/star/test_suite/accreted_material_j/inlist_pgstar +++ b/star/test_suite/accreted_material_j/inlist_pgstar @@ -1,15 +1,11 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - - !file_device = 'vcps' ! postscript - !file_extension = 'ps' + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'vcps' ! postscript + file_extension = 'ps' pgstar_interval = 10 - History_Track1_win_flag = .true. History_Track1_win_width = 12 History_Track1_title = 'accreted_material_j' diff --git a/star/test_suite/accreted_material_j/inlist_zams b/star/test_suite/accreted_material_j/inlist_zams index 24c5b390d..95fd18487 100644 --- a/star/test_suite/accreted_material_j/inlist_zams +++ b/star/test_suite/accreted_material_j/inlist_zams @@ -2,16 +2,16 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. - create_pre_main_sequence_model = .true. + create_pre_main_sequence_model = .true. - save_model_when_terminate = .true. - save_model_filename = 'zams.mod' - required_termination_code_string = 'Lnuc_div_L_zams_limit' + save_model_when_terminate = .true. + save_model_filename = 'zams.mod' + required_termination_code_string = 'Lnuc_div_L_zams_limit' - !pgstar_flag = .true. + !pgstar_flag = .true. / ! end of star_job namelist @@ -21,31 +21,31 @@ &kap - kap_file_prefix = 'gs98' - Zbase = 0.02 + kap_file_prefix = 'gs98' + Zbase = 0.02 / ! end of kap namelist &controls - initial_mass = 20 ! in Msun units - initial_Z = 0.02 - - stop_near_zams = .true. - Lnuc_div_L_zams_limit = 0.9d0 - - ! limit max_model_number as part of test_suite - max_model_number = 10000 - use_gold2_tolerances = .true. - - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' - - photo_interval = 100 - profile_interval = 100 - history_interval = 5 - terminal_interval = 50 - + initial_mass = 20 ! in Msun units + initial_Z = 0.02 + + stop_near_zams = .true. + Lnuc_div_L_zams_limit = 0.9d0 + + ! limit max_model_number as part of test_suite + max_model_number = 10000 + use_gold2_tolerances = .true. + + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' + + photo_interval = 100 + profile_interval = 100 + history_interval = 5 + terminal_interval = 50 + / ! end of controls namelist diff --git a/star/test_suite/accreted_material_j/inlist_zams_header b/star/test_suite/accreted_material_j/inlist_zams_header index 83e825c58..3de76b840 100644 --- a/star/test_suite/accreted_material_j/inlist_zams_header +++ b/star/test_suite/accreted_material_j/inlist_zams_header @@ -2,24 +2,24 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_zams' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_zams' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_zams' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_zams' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_zams' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_zams' / ! end of kap namelist @@ -27,15 +27,15 @@ &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_zams' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_zams' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_zams' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_zams' / ! end of pgstar namelist From 0643737e90503ac7549cf3490ab838e84d7b7947 Mon Sep 17 00:00:00 2001 From: EbF Date: Tue, 6 Aug 2024 13:29:33 -0400 Subject: [PATCH 11/66] [ci skip] update conductive flame test_suite --- star/test_suite/conductive_flame/README.rst | 9 ++++++++- .../conductive_flame/docs/grid1000597.png | Bin 0 -> 28477 bytes star/test_suite/conductive_flame/inlist_pgstar | 8 ++++++++ 3 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 star/test_suite/conductive_flame/docs/grid1000597.png diff --git a/star/test_suite/conductive_flame/README.rst b/star/test_suite/conductive_flame/README.rst index a029494ca..39e701244 100644 --- a/star/test_suite/conductive_flame/README.rst +++ b/star/test_suite/conductive_flame/README.rst @@ -47,7 +47,13 @@ routine ``flame_properties`` in the ``run_star_extras.f90``. -.. image:: ../../../star/test_suite/conductive_flame/docs/grid1000427.png +.. image:: ../../../star/test_suite/conductive_flame/docs/grid1000597.png + :width: 100% + +pgstar commands used for the plots above: +.. literalinclude:: ../../../star/test_suite/conductive_flame/inlist_pgstar + :language: console + .. |Timmes1992| replace:: `Timmes & Woosley (1992) `__ @@ -58,3 +64,4 @@ routine ``flame_properties`` in the ``run_star_extras.f90``. 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zlYbptPt}QcpqI|?E7w)jUx7osMPj!}6JMifqeE~wr7tGVpMD}UM<$HuqTy30l1(v= zJfONGFmT_pmi97^tUYfYcmRBNLeVU0Z6Nt_X3sN25(yBAV$PvR z5_CA%z9bOqR&4=iU*380xLOk7XoddF4Xb^x9UN5MqCga)X<^K)PcOiin2!uU1+v6vA^mpok3X_OYtmIq`EBxd-ysoF ziGkXpJJsnlAzAj)L75CEtvwNEXt)5Hl{{h>uQHcNm literal 0 HcmV?d00001 diff --git a/star/test_suite/conductive_flame/inlist_pgstar b/star/test_suite/conductive_flame/inlist_pgstar index adf6a72c3..f9cac16d4 100644 --- a/star/test_suite/conductive_flame/inlist_pgstar +++ b/star/test_suite/conductive_flame/inlist_pgstar @@ -1,5 +1,13 @@ &pgstar + + ! device + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'png' ! png + file_extension = 'png' + !file_device = 'vcps' ! postscript + !file_extension = 'ps' + pgstar_interval = 1 pause = .false. From 39dc50f93c2ee48213e4bb80dc3e2da1a5f90010 Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Tue, 6 Aug 2024 11:45:46 -0600 Subject: [PATCH 12/66] [ci skip] change terminal age in starspots inlist --- star/test_suite/starspots/inlist_starspots | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 4ac93cd09..6c22a98b1 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -60,7 +60,7 @@ &controls star_history_name = 'history.data' - max_age = 0.8d9 + max_age = 12d9 !0.8d9 use_other_mlt_results = .true. !.true. use_other_surface_PT = .true. !.True. @@ -150,7 +150,7 @@ file_device = 'vcps' ! postscript file_extension = 'ps' - HR_win_flag = .false. ! switch to .true. to visualize in real-time + HR_win_flag = .true. ! switch to .true. to visualize in real-time HR_file_flag = .true. HR_file_dir = 'pgstar_out' HR_file_prefix = 'hr_starspots_' From 7890d3056491754ba678917a4beac70918dcdd81 Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Tue, 6 Aug 2024 12:15:34 -0600 Subject: [PATCH 13/66] [ci skip] adjust stopping condition and pgplot limits for starspots --- star/test_suite/starspots/inlist_starspots | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 0d18369ab..5f95343bc 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -60,7 +60,7 @@ &controls star_history_name = 'history.data' - max_age = 12d9 !0.8d9 + max_age = 24.63d9 !26d9 !0.8d9 use_other_mlt_results = .true. !.true. use_other_surface_PT = .true. !.True. @@ -83,7 +83,7 @@ photo_interval = 100 ! starting specifications - initial_mass = 1.0 ! in Msun units + initial_mass = 0.9 !1.0 ! in Msun units min_timestep_limit=0 max_model_number = -1 !1500 @@ -159,9 +159,9 @@ HR_title = 'HR' ! set static plot bounds - HR_logT_min = 3.0 - HR_logT_max = 6.5 - HR_logL_min = -2.0 + HR_logT_min = 3.55 + HR_logT_max = 3.78 + HR_logL_min = -0.7 HR_logL_max = 2.0 / ! end of pgstar namelist From 99960085491015fa992aa82c525ec7169b9b9f21 Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Tue, 6 Aug 2024 12:47:11 -0600 Subject: [PATCH 14/66] [ci skip] update rst --- star/test_suite/starspots/README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index e5bae4e7e..c63069c54 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -4,7 +4,7 @@ starspots ****************** -This test suite case evolves a 1.0 |Msun|, solar metallicity (Z=0.02) model +This test suite case evolves a 0.9 |Msun|, solar metallicity (Z=0.02) model to an age of 0.8 Gyr using MESA's implementation of the YREC (Yale Rotating Evolution Code) SPOTS formalism introduced by `Somers et al. (2020; ApJ) `__ @@ -28,7 +28,7 @@ Detailed discussion of this functionality can be found in A plot of the HR diagram for the problem is included below: -.. image:: ../../../star/test_suite/starspots/docs/hr_starspots_000794.svg +.. image:: ../../../star/test_suite/starspots/docs/hr_starspots_001496.svg :width: 100% Last-Updated: 23Jul2024 (MESA 6d0b0f29) by pmocz on C916PXT6XW in 207 seconds using 8 threads. From e2d6005aedefba0e057998a36b7f3549b917f1e6 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 14:51:16 -0400 Subject: [PATCH 15/66] [ci skip] add figure --- star/test_suite/starspots/README.rst | 4 ++-- star/test_suite/starspots/docs/hr_starspots_001496.svg | 1 + star/test_suite/starspots/inlist_starspots | 1 + 3 files changed, 4 insertions(+), 2 deletions(-) create mode 100644 star/test_suite/starspots/docs/hr_starspots_001496.svg diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index e5bae4e7e..18502ce0e 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -28,7 +28,7 @@ Detailed discussion of this functionality can be found in A plot of the HR diagram for the problem is included below: -.. image:: ../../../star/test_suite/starspots/docs/hr_starspots_000794.svg +.. image:: ../../../star/test_suite/starspots/docs/hr_starspots_001496.svg :width: 100% -Last-Updated: 23Jul2024 (MESA 6d0b0f29) by pmocz on C916PXT6XW in 207 seconds using 8 threads. +Last-Updated: 06Aug2024 (MESA 7890d305) by pmocz on C916PXT6XW in 629 seconds using 8 threads. diff --git a/star/test_suite/starspots/docs/hr_starspots_001496.svg b/star/test_suite/starspots/docs/hr_starspots_001496.svg new file mode 100644 index 000000000..ac9cbdbec --- /dev/null +++ b/star/test_suite/starspots/docs/hr_starspots_001496.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 5f95343bc..53929baa6 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -154,6 +154,7 @@ HR_file_flag = .true. HR_file_dir = 'pgstar_out' HR_file_prefix = 'hr_starspots_' + HR_file_interval = 50 HR_win_width = 9 HR_win_aspect_ratio = 1.0 HR_title = 'HR' From 2b5da8103ebec6941f9e68b166e0556ad905fdc2 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 14:55:26 -0400 Subject: [PATCH 16/66] [ci skip] remove old figure --- star/test_suite/starspots/docs/hr_starspots_000794.svg | 1 - 1 file changed, 1 deletion(-) delete mode 100644 star/test_suite/starspots/docs/hr_starspots_000794.svg diff --git a/star/test_suite/starspots/docs/hr_starspots_000794.svg b/star/test_suite/starspots/docs/hr_starspots_000794.svg deleted file mode 100644 index 7109c199f..000000000 --- a/star/test_suite/starspots/docs/hr_starspots_000794.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file From cf8664749a48ff685c814413a212bd320bc0f8db Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Tue, 6 Aug 2024 13:00:20 -0600 Subject: [PATCH 17/66] [ci skip] updates to readme --- star/test_suite/starspots/README.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index c63069c54..3357b93c7 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -5,7 +5,7 @@ starspots ****************** This test suite case evolves a 0.9 |Msun|, solar metallicity (Z=0.02) model -to an age of 0.8 Gyr using MESA's implementation of the +to an age of 24.63 Gyr using MESA's implementation of the YREC (Yale Rotating Evolution Code) SPOTS formalism introduced by `Somers et al. (2020; ApJ) `__ @@ -31,4 +31,5 @@ A plot of the HR diagram for the problem is included below: .. image:: ../../../star/test_suite/starspots/docs/hr_starspots_001496.svg :width: 100% +Last updated by Meridith Joyce on 08/06/2024 Last-Updated: 23Jul2024 (MESA 6d0b0f29) by pmocz on C916PXT6XW in 207 seconds using 8 threads. From 3611053ca2b2688bc3a7f473faab85e72f72d024 Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Tue, 6 Aug 2024 13:02:23 -0600 Subject: [PATCH 18/66] [ci skip] updates to README.rst --- star/test_suite/starspots/README.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index 3357b93c7..815d8188d 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -8,6 +8,8 @@ This test suite case evolves a 0.9 |Msun|, solar metallicity (Z=0.02) model to an age of 24.63 Gyr using MESA's implementation of the YREC (Yale Rotating Evolution Code) SPOTS formalism introduced by `Somers et al. (2020; ApJ) `__ +Compare to Figure 15 in Section 7 of MESA Instrument Paper VI. + The impedence of the surface flux due to magnetic pressure from starspots is parameterized in the style of an atmospheric boundary modification. As first described by From 87bfa6a9fc57d011bc75738157d23adc868aca28 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 15:26:49 -0400 Subject: [PATCH 19/66] [ci skip] Last-Run --- star/test_suite/1.3M_ms_high_Z/README.rst | 4 +++- star/test_suite/1.5M_with_diffusion/README.rst | 4 +++- star/test_suite/7M_prems_to_AGB/README.rst | 3 ++- star/test_suite/accreted_material_j/README.rst | 4 ++-- star/test_suite/conductive_flame/README.rst | 2 +- star/test_suite/conv_core_cpm/README.rst | 3 ++- star/test_suite/diffusion_smoothness/README.rst | 3 ++- star/test_suite/each_test_run | 8 ++++---- star/test_suite/high_mass/README.rst | 2 ++ 9 files changed, 21 insertions(+), 12 deletions(-) diff --git a/star/test_suite/1.3M_ms_high_Z/README.rst b/star/test_suite/1.3M_ms_high_Z/README.rst index 516d3e259..825b66871 100644 --- a/star/test_suite/1.3M_ms_high_Z/README.rst +++ b/star/test_suite/1.3M_ms_high_Z/README.rst @@ -45,4 +45,6 @@ The Python script used to create the figures above: :language: python -Last-Updated: 26Jul2024 (MESA afd04d7d) by pmocz on C916PXT6XW in 159 seconds using 8 threads. +Last-Updated: 27May2021 (MESA ebecc10) by fxt + +Last-Run: 26Jul2024 (MESA afd04d7d) by pmocz on C916PXT6XW in 159 seconds using 8 threads. diff --git a/star/test_suite/1.5M_with_diffusion/README.rst b/star/test_suite/1.5M_with_diffusion/README.rst index adf0f908f..79904265b 100644 --- a/star/test_suite/1.5M_with_diffusion/README.rst +++ b/star/test_suite/1.5M_with_diffusion/README.rst @@ -29,4 +29,6 @@ pgstar commands used for the plots above, e.g.: :end-at: ! end of pgstar namelist -Last-Updated: 17Jul2024 (MESA 0cc374fa) by pmocz on C916PXT6XW in 423 seconds using 8 threads. +Last-Updated: 27May2021 (MESA ebecc10) by fxt + +Last-Run: 17Jul2024 (MESA 0cc374fa) by pmocz on C916PXT6XW in 423 seconds using 8 threads. diff --git a/star/test_suite/7M_prems_to_AGB/README.rst b/star/test_suite/7M_prems_to_AGB/README.rst index dd63a4d53..ebc97e00f 100644 --- a/star/test_suite/7M_prems_to_AGB/README.rst +++ b/star/test_suite/7M_prems_to_AGB/README.rst @@ -23,5 +23,6 @@ pgstar commands used: :end-at: ! end of pgstar namelist +Last-Updated: 29May2021 (MESA e37f76f) by fxt -Last-Updated: 06Aug2024 (MESA f50b3763) by pmocz on C916PXT6XW in 410 seconds using 8 threads. +Last-Run: 06Aug2024 (MESA f50b3763) by pmocz on C916PXT6XW in 410 seconds using 8 threads. diff --git a/star/test_suite/accreted_material_j/README.rst b/star/test_suite/accreted_material_j/README.rst index 5ebf013fa..a743f35ac 100644 --- a/star/test_suite/accreted_material_j/README.rst +++ b/star/test_suite/accreted_material_j/README.rst @@ -25,6 +25,6 @@ pgstar commands used for the plots above: :end-at: ! end of pgstar namelist +Last-Updated: 30May2021 (MESA e37f76f) by fxt - -Last-Updated: 06Aug2024 (MESA ba042c9d) by pmocz on C916PXT6XW in 178 seconds using 8 threads. +Last-Run: 06Aug2024 (MESA ba042c9d) by pmocz on C916PXT6XW in 178 seconds using 8 threads. diff --git a/star/test_suite/conductive_flame/README.rst b/star/test_suite/conductive_flame/README.rst index 39e701244..5699b67b9 100644 --- a/star/test_suite/conductive_flame/README.rst +++ b/star/test_suite/conductive_flame/README.rst @@ -64,4 +64,4 @@ pgstar commands used for the plots above: Last-Updated: 2021-06-21 (mesa b2364463) by Josiah Schwab, + documentation 2024-01-22 EbF -Last-Updated: 06Aug2024 (MESA 7a3e4ee4) by EbF in 497 seconds using 10 threads. +Last-Run: 06Aug2024 (MESA 7a3e4ee4) by EbF in 497 seconds using 10 threads. diff --git a/star/test_suite/conv_core_cpm/README.rst b/star/test_suite/conv_core_cpm/README.rst index 37d3885be..df42d8f28 100644 --- a/star/test_suite/conv_core_cpm/README.rst +++ b/star/test_suite/conv_core_cpm/README.rst @@ -18,5 +18,6 @@ core if the model continued to evolve beyond its stopping condition. .. image:: ../../../star/test_suite/conv_core_cpm/docs/grid_000092.svg :width: 100% +Last-Updated: 2023-03-14 (MESA d6bbdf4) by Evan Bauer -Last-Updated: 17Jul2024 (MESA 5ef2ffac) by pmocz on C916PXT6XW in 125 seconds using 8 threads. +Last-Run: 17Jul2024 (MESA 5ef2ffac) by pmocz on C916PXT6XW in 125 seconds using 8 threads. diff --git a/star/test_suite/diffusion_smoothness/README.rst b/star/test_suite/diffusion_smoothness/README.rst index 409b5f6f4..c188eb447 100644 --- a/star/test_suite/diffusion_smoothness/README.rst +++ b/star/test_suite/diffusion_smoothness/README.rst @@ -22,5 +22,6 @@ pgstar commands used for the plot: :start-at: &pgstar :end-at: ! end of pgstar namelist +Last-Updated: 06Jun2021 (MESA 5be9e57) by fxt -Last-Updated: 06Aug2024 (MESA 8b152605) by pmocz on C916PXT6XW in 82 seconds using 8 threads. +Last-Run: 06Aug2024 (MESA 8b152605) by pmocz on C916PXT6XW in 82 seconds using 8 threads. diff --git a/star/test_suite/each_test_run b/star/test_suite/each_test_run index 4d53778a6..fcd26c6e1 100755 --- a/star/test_suite/each_test_run +++ b/star/test_suite/each_test_run @@ -92,11 +92,11 @@ function update_docs { if [ -e "$image_to_copy" ]; then cp "$image_to_copy" docs/ echo "Updated image $filename.$extension in the docs" - # replace the line "Last-Updated: ..." in README.rst - LAST_UPDATED="Last-Updated: $(date '+%d%b%Y') (MESA $(git rev-parse --short HEAD)) by $USER on $(hostname) in $(expr `date +%s` - $start_time) seconds using $OMP_NUM_THREADS threads." + # replace the line "Last-Run: ..." in README.rst + LAST_RUN="Last-Run: $(date '+%d%b%Y') (MESA $(git rev-parse --short HEAD)) by $USER on $(hostname) in $(expr `date +%s` - $start_time) seconds using $OMP_NUM_THREADS threads." # print name of - sed -i "" "/Last-Updated: .*/d" README.rst - echo $LAST_UPDATED >> README.rst + sed -i "" "/Last-Run: .*/d" README.rst + echo $LAST_RUN >> README.rst else echo "Error: $image_to_copy not found. Test may no longer be producing this file or may now be producing a different final snapshot number! Update test and README.rst accordingly." fi diff --git a/star/test_suite/high_mass/README.rst b/star/test_suite/high_mass/README.rst index d19299039..5e13c2cb8 100644 --- a/star/test_suite/high_mass/README.rst +++ b/star/test_suite/high_mass/README.rst @@ -23,4 +23,6 @@ pgstar commands used for the plots above: :language: console +Last-Updated: 12Jun2021 (MESA 5be9e57) by fxt. + Last-Updated: 17Jul2024 (MESA beef2c3b) by pmocz on C916PXT6XW in 67 seconds using 8 threads. 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z!)+(Jikdu39;O7Ee67>35$12s)*IzqI<(1piG9JVT0dxUvyz@(bVKSeJbC1$Xsh8* z73=1`z#Lym+a%9flpVvqd z&vcC^?lT{r*C4w=xEAp4oG9@rH-(38CM_D2yIQ_o+VC#^->UhaUjDfjo5k1r%=_+0 Rpa|C?A3Aohc>gaK{|mksW;_4@ literal 0 HcmV?d00001 diff --git a/star/test_suite/accreted_material_j/history_columns.list b/star/test_suite/accreted_material_j/history_columns.list new file mode 100644 index 000000000..56a1961d6 --- /dev/null +++ b/star/test_suite/accreted_material_j/history_columns.list @@ -0,0 +1,1067 @@ +! 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 a few items: + + ! version_number -- for the version of mesa being used + ! burn_min1 -- 1st limit for reported burning, in erg/g/s + ! burn_min2 -- 2nd limit for reported burning, in erg/g/s + + +!# other files + +! 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 + +!---------------------------------------------------------------------------------------------- + +!# general info about the model + + model_number ! counting from the start of the run + num_zones ! number of zones in the model + + !## age + + star_age ! elapsed simulated time in years since the start of the run + !star_age_sec ! elapsed simulated time in seconds since the start of the run + !star_age_min ! elapsed simulated time in minutes since the start of the run + !star_age_hr ! elapsed simulated time in hours since the start of the run + !star_age_day ! elapsed simulated time in days since the start of the run + !day ! elapsed simulated time in days since the start of the run + + !log_star_age + !log_star_age_sec + + !## timestep + + !time_step ! timestep in years since previous model + !time_step_sec ! timestep in seconds since previous model + !time_step_days + log_dt ! log10 time_step in years + !log_dt_sec ! log10 time_step in seconds + !log_dt_days ! log10 time_step in days + + !## mass + + star_mass ! in Msun units + !log_star_mass + + !star_gravitational_mass ! star_mass is baryonic mass + !star_mass_grav_div_mass + + !delta_mass ! star_mass - initial_mass in Msun units + log_xmstar ! log10 mass exterior to M_center (grams) + + !## mass change + + !star_mdot ! d(star_mass)/dt (in msolar per year) + log_abs_mdot ! log10(abs(star_mdot)) (in msolar per year) + + !## imposed surface conditions + !Tsurf_factor + !tau_factor + !tau_surface + + !## imposed center conditions + !m_center + !m_center_gm + !r_center + !r_center_cm + !r_center_km + !L_center + !log_L_center + !log_L_center_ergs_s + !v_center + !v_center_kms + + !logt_max + +!---------------------------------------------------------------------------------------------- + +!# mixing and convection + + !max_conv_vel_div_csound + !max_gradT_div_grada + !max_gradT_sub_grada + !min_log_mlt_Gamma + + + !## mixing regions + + mass_conv_core ! (Msun) mass coord of top of convective core. 0 if core is not convective + + ! 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. + + ! values are m/Mstar + conv_mx1_top + conv_mx1_bot + conv_mx2_top + conv_mx2_bot + mx1_top + mx1_bot + mx2_top + mx2_bot + + ! radius -- values are radii in Rsun units + !conv_mx1_top_r + !conv_mx1_bot_r + !conv_mx2_top_r + !conv_mx2_bot_r + !mx1_top_r + !mx1_bot_r + !mx2_top_r + !mx2_bot_r + + ! you might want to get a more complete list of mixing regions by using the following + + !mixing_regions ! note: this includes regions where the mixing type is no_mixing. + + ! the is the number of regions to report + ! there will be 2* columns for this in the log file, 2 for each region. + ! the first column for a region gives the mixing type as defined in const/public/const_def.f90. + + ! the second column for a region gives the m/mstar location of the top of the region + ! entries for extra columns after the last region in the star will have an invalid mixing_type value of -1. + ! 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' + + ! if the star has too many regions to report them all, + ! the smallest regions will be merged with neighbors for reporting purposes only. + + + !mix_relr_regions + ! same as above, but locations given as r/rstar instead of m/mstar. + ! the columns in the log file will have names like 'mix_relr_type_1' and 'mix_relr_top_1' + + + !## conditions at base of largest convection zone (by mass) + !cz_bot_mass ! mass coordinate of base (Msun) + !cz_mass ! mass coordinate of base (Msun) -- same as cz_bot_mass + !cz_log_xmass ! mass exterior to base (g) + !cz_log_xmsun ! mass exterior to base (Msun) + !cz_xm ! mass exterior to base (Msun) + !cz_logT + !cz_logRho + !cz_logP + !cz_bot_radius ! Rsun + !cz_log_column_depth + !cz_log_radial_depth + !cz_luminosity ! Lsun + !cz_opacity + !cz_log_tau + !cz_eta + !cz_log_eps_nuc ! log10(ergs/g/s) + !cz_t_heat ! Cp*T/eps_nuc (seconds) + + !cz_csound + !cz_scale_height + !cz_grav + + !cz_omega + !cz_omega_div_omega_crit + + !cz_zone + + ! mass fractions at base of largest convection zone (by mass) + !cz_log_xa h1 + !cz_log_xa he4 + + !## conditions at top of largest convection zone (by mass) + !cz_top_mass ! mass coordinate of top (Msun) + !cz_top_log_xmass ! mass exterior to top (g) + !cz_top_log_xmsun ! mass exterior to top (Msun) + !cz_top_xm ! mass exterior to top (Msun) + !cz_top_logT + !cz_top_logRho + !cz_top_logP + !cz_top_radius ! Rsun + !cz_top_log_column_depth + !cz_top_log_radial_depth + !cz_top_luminosity ! Lsun + !cz_top_opacity + !cz_top_log_tau + !cz_top_eta + !cz_top_log_eps_nuc ! log10(ergs/g/s) + !cz_top_t_heat ! Cp*T/eps_nuc (seconds) + + !cz_top_csound + !cz_top_scale_height + !cz_top_grav + + !cz_top_omega + !cz_top_omega_div_omega_crit + + !cz_top_zone + !cz_top_zone_logdq + + ! mass fractions at top of largest convection zone (by mass) + !cz_top_log_xa h1 + !cz_top_log_xa he4 + +!---------------------------------------------------------------------------------------------- + +!# nuclear reactions + + !## integrated quantities + + !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) + !power_photo + !power_z_burn + !log_power_nuc_burn ! total thermal power from all burning, excluding photodisintegrations + log_LH ! log10 power_h_burn + log_LHe ! log10 power_he_burn + log_LZ ! log10 total burning power including LC, but excluding LH and LHe and photodisintegrations + log_Lnuc ! log(LH + LHe + LZ) + !log_Lnuc_ergs_s + !log_Lnuc_sub_log_L + !lnuc_photo + + !extra_L ! integral of extra_heat in Lsun units + !log_extra_L ! log10 extra_L + + !## neutrino losses + !log_Lneu ! log10 power emitted in neutrinos, nuclear and thermal (in Lsun units) + !log_Lneu_nuc ! log10 power emitted in neutrinos, nuclear sources only (in Lsun units) + !log_Lneu_nonnuc ! log10 power emitted in neutrinos, thermal sources only (in Lsun units) + + !mass_loc_of_max_eps_nuc ! (in Msun units) + !mass_ext_to_max_eps_nuc ! (in Msun units) + !eps_grav_integral ! (in Lsun units) + !log_abs_Lgrav ! log10 abs(eps_grav_integral) (in Lsun units) + + !## information about reactions (by category) + + ! log10 total luminosity for reaction categories (Lsun units) + + pp + cno + tri_alpha + !c_alpha + !n_alpha + !o_alpha + !ne_alpha + !na_alpha + !mg_alpha + !si_alpha + !s_alpha + !ar_alpha + !ca_alpha + !ti_alpha + !fe_co_ni + !c12_c12 + !c12_o16 + !o16_o16 + !photo + !pnhe4 + !other + + !## information about individual reactions + + ! adds columns for all of the reactions that are in the current net + ! Note that if using op_split_burn=.true. then zones which have been split will report 0 for thier rates + !add_raw_rates ! raw reaction rates, reactions/second + !add_screened_rates ! screened reaction rates reactions/second + !add_eps_nuc_rates ! Nuclear energy (minus neutrino losses) released erg/s + !add_eps_neu_rates ! Neutrino losses erg/s + + ! individual reactions (as many as desired) + ! use list_net_reactions = .true. in star_job to list all reactions in the current net + ! reactions/second + !raw_rate r_h1_h1_ec_h2 + !raw_rate r_h1_h1_wk_h2 + + + + !## nuclear reactions at center + + ! center log10 burn erg/g/s for reaction categories + + !c_log_eps_burn cno + !c_log_eps_burn tri_alfa + + ! center d_eps_nuc_dlnd for reaction categories + + !c_d_eps_dlnd cno + !c_d_eps_dlnd tri_alfa + + ! center d_eps_nuc_dlnT for reaction categories + + !c_d_eps_dlnT cno + !c_d_eps_dlnT tri_alfa + + !## 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 + + + ! you might want to get a more complete list of burning regions by using the following + + !burning_regions + ! the is the number of regions to report + ! there will be 2* columns for this in the log file, 2 for each region. + ! the first column for a region gives int(sign(val)*log10(max(1,abs(val)))) + ! where val = ergs/gm/sec nuclear energy minus all neutrino losses. + ! the second column for a region gives the q location of the top of the region + ! entries for extra columns after the last region in the star will have a value of -9999 + ! all regions are included 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 q=0 and top of last is q=1. + + ! the columns in the log file will have names like 'burn_type_1' and 'burn_qtop_1' + + !burn_relr_regions + ! same as above, but locations given as r/rstar instead of m/mstar. + ! the columns in the log file will have names like 'burn_relr_type_1' and 'burn_relr_top_1' + + + ! if the star has too many regions to report them all, + ! the smallest regions will be merged with neighbors for reporting purposes only. + +!---------------------------------------------------------------------------------------------- + +!# information about core and envelope + + !## helium core + he_core_mass + !he_core_radius + !he_core_lgT + !he_core_lgRho + !he_core_L + !he_core_v + !he_core_omega + !he_core_omega_div_omega_crit + !he_core_k + + !## CO core + co_core_mass + !CO_core + !co_core_radius + !co_core_lgT + !co_core_lgRho + !co_core_L + !co_core_v + !co_core_omega + !co_core_omega_div_omega_crit + !co_core_k + + !## ONe core + one_core_mass + !one_core_radius + !one_core_lgT + !one_core_lgRho + !one_core_L + !one_core_v + !one_core_omega + !one_core_omega_div_omega_crit + !one_core_k + + !## iron core + fe_core_mass + !fe_core_radius + !fe_core_lgT + !fe_core_lgRho + !fe_core_L + !fe_core_v + !fe_core_omega + !fe_core_omega_div_omega_crit + !fe_core_k + + !## neuton rich core + neutron_rich_core_mass + !neutron_rich_core_radius + !neutron_rich_core_lgT + !neutron_rich_core_lgRho + !neutron_rich_core_L + !neutron_rich_core_v + !neutron_rich_core_omega + !neutron_rich_core_omega_div_omega_crit + !neutron_rich_core_k + + !## envelope + + !envelope_mass ! = star_mass - he_core_mass + !envelope_fraction_left ! = envelope_mass / (initial_mass - he_core_mass) + + !h_rich_layer_mass ! = star_mass - he_core_mass + !he_rich_layer_mass ! = he_core_mass - c_core_mass + !co_rich_layer_mass + +!---------------------------------------------------------------------------------------------- + +!# timescales + + !dynamic_timescale ! dynamic timescale (seconds) -- estimated by 2*pi*sqrt(r^3/(G*m)) + !kh_timescale ! kelvin-helmholtz timescale (years) + !mdot_timescale ! star_mass/abs(star_mdot) (years) + !kh_div_mdot_timescales ! kh_timescale/mdot_timescale + !nuc_timescale ! nuclear timescale (years) -- proportional to mass divided by luminosity + + !dt_cell_collapse ! min time for any cell to collapse at current velocities + !dt_div_dt_cell_collapse + + !dt_div_max_tau_conv ! dt/ maximum conv timescale + !dt_div_min_tau_conv ! dt/ minimum conv timescale + + + !min_dr_div_cs ! min over all cells of dr/csound (seconds) + !min_dr_div_cs_k ! location of min + !log_min_dr_div_cs ! log10 min dr_div_csound (seconds) + !min_dr_div_cs_yr ! min over all cells of dr/csound (years) + !log_min_dr_div_cs_yr ! log10 min dr_div_csound (years) + !dt_div_min_dr_div_cs + !log_dt_div_min_dr_div_cs + + !min_t_eddy ! minimum value of scale_height/conv_velocity + +!---------------------------------------------------------------------------------------------- + +!# conditions at or near the surface of the model + + !## conditions at the photosphere + !effective_T + !Teff + log_Teff ! log10 effective temperature + ! Teff is calculated using Stefan-Boltzmann relation L = 4 pi R^2 sigma Teff^4, + ! where L and R are evaluated at the photosphere (tau_factor < 1) + ! or surface of the model (tau_factor >= 1) when photosphere is not inside the model. + + !photosphere_black_body_T + !photosphere_cell_T ! temperature at model location closest to the photosphere, not necessarily Teff + !photosphere_cell_log_T + !photosphere_cell_density + !photosphere_cell_log_density + !photosphere_cell_opacity + !photosphere_cell_log_opacity + !photosphere_L ! Lsun units + !photosphere_log_L ! Lsun units + !photosphere_r ! Rsun units + !photosphere_log_r ! Rsun units + !photosphere_m ! Msun units + !photosphere_v_km_s + !photosphere_cell_k + !photosphere_column_density + !photosphere_csound + !photosphere_log_column_density + !photosphere_opacity + !photosphere_v_div_cs + !photosphere_xm + !photosphere_cell_free_e + !photosphere_cell_log_free_e + !photosphere_logg + !photosphere_T + + !## conditions at or near the surface of the model (outer edge of outer cell) + + !luminosity ! luminosity in Lsun units + !luminosity_ergs_s ! luminosity in cgs units + log_L ! log10 luminosity in Lsun units + !log_L_ergs_s ! log10 luminosity in cgs units + !radius ! Rsun + log_R ! log10 radius in Rsun units + !radius_cm + !log_R_cm + + log_g ! log10 gravity + !gravity + !log_Ledd + !log_L_div_Ledd ! log10(L/Leddington) + !lum_div_Ledd + !log_surf_optical_depth + !surface_optical_depth + + !log_surf_cell_opacity ! old name was log_surf_opacity + !log_surf_cell_P ! old name was log_surf_P + !log_surf_cell_pressure ! old name was log_surf_pressure + !log_surf_cell_density ! old name was log_surf_density + !log_surf_cell_temperature ! old name was log_surf_temperature + !surface_cell_temperature ! old name was surface_temperature + !log_surf_cell_z ! old name was log_surf_z + !surface_cell_entropy ! in units of kerg per baryon + ! old name was surface_entropy + + !v_surf ! (cm/s) + !v_surf_km_s ! (km/s) + v_div_csound_surf ! velocity divided by sound speed at outermost grid point + !v_div_csound_max ! max value of velocity divided by sound speed at face + !v_div_vesc + !v_phot_km_s + !v_surf_div_escape_v + + !v_surf_div_v_kh ! v_surf/(photosphere_r/kh_timescale) + + !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_Lrad_div_Ledd + !surf_avg_logT + !surf_avg_logRho + !surf_avg_opacity + + ! Gravity Darkening, reports the surface averaged L/Lsun and Teff (K) caused by + ! gravity darkening in rotating stars. Based on the model of Espinosa Lara & Rieutord (2011) + ! 'polar' refers to the line of sight being directed along the rotation axis of the star + ! 'equatorial' refers to the line of sight coincident with the stellar equator + !grav_dark_L_polar !Lsun + !grav_dark_Teff_polar !K + !grav_dark_L_equatorial !Lsun + !grav_dark_Teff_equatorial !K + + !surf_escape_v ! cm/s + + !v_wind_Km_per_s ! Km/s + ! = 1d-5*s% opacity(1)*max(0d0,-s% mstar_dot)/ & + ! (4*pi*s% photosphere_r*Rsun*s% tau_base) + ! Lars says: + ! wind_mdot = 4*pi*R^2*rho*v_wind + ! tau = integral(opacity*rho*dr) from R to infinity + ! so tau = opacity*wind_mdot/(4*pi*R*v_wind) at photosphere + ! or v_wind = opacity*wind_mdot/(4*pi*R*tau) at photosphere + + !rotational_mdot_boost ! factor for increase in mass loss mdot due to rotation + !log_rotational_mdot_boost ! log factor for increase in mass loss mdot due to rotation + !surf_r_equatorial_div_r_polar + !surf_r_equatorial_div_r + !surf_r_polar_div_r + +!---------------------------------------------------------------------------------------------- + +!# conditions near center + + !log_center_T ! temperature + !log_center_Rho ! density + !log_center_P ! pressure + + ! shorter names for above + log_cntr_P + log_cntr_Rho + log_cntr_T + + !center_T ! temperature + !center_Rho ! density + !center_P ! pressure + + !center_degeneracy ! the electron chemical potential in units of k*T + !center_gamma ! plasma interaction parameter + center_mu + center_ye + center_abar + !center_zbar + + !center_eps_grav + + !center_non_nuc_neu + !center_eps_nuc + !d_center_eps_nuc_dlnT + !d_center_eps_nuc_dlnd + !log_center_eps_nuc + + !center_entropy ! in units of kerg per baryon + !max_entropy ! in units of kerg per baryon + !fe_core_infall + !non_fe_core_infall + !non_fe_core_rebound + !max_infall_speed + + !compactness_parameter ! (m/Msun)/(R(m)/1000km) for m = 2.5 Msun + !compactness + !m4 ! Mass co-ordinate where entropy=4 + ! mu4 is sensitive to the choice of how much dm/dr you average over, thus we average dm and dr over M(entropy=4) and M(entropy=4)+0.3Msun + !mu4 ! dM(Msun)/dr(1000km) where entropy=4 + + + !center_omega + !center_omega_div_omega_crit + +!---------------------------------------------------------------------------------------------- + +!# abundances + + !species ! size of net + + !## mass fractions near center + + ! the following controls automatically add columns for all of the isos that are in the current net + !add_center_abundances + !add_log_center_abundances + + ! individual central mass fractions (as many as desired) + center h1 + center he4 + center c12 + center o16 + + ! individual log10 central mass fractions (as many as desired) + !log_center h1 + !log_center he4 + ! etc. + + + !## mass fractions near surface + + ! the following controls automatically add columns for all of the isos that are in the current net + !add_surface_abundances + !add_log_surface_abundances + + ! individual surface mass fractions (as many as desired) + !surface h1 + !surface he4 + surface c12 + surface o16 + ! etc. + + ! individual log10 surface mass fractions (as many as desired) + + !log_surface h1 + !log_surface he4 + + + !## mass fractions for entire star + + ! the following controls automatically add columns for all of the isos that are in the current net + !add_average_abundances + !add_log_average_abundances + + ! individual average mass fractions (as many as desired) + !average h1 + !average he4 + ! etc. + + ! individual log10 average mass fractions (as many as desired) + !log_average h1 + !log_average he4 + ! etc. + + + !## mass totals for entire star (in Msun units) + + ! the following controls automatically add columns for all of the isos that are in the current net + !add_total_mass + !add_log_total_mass + + ! individual mass totals for entire star (as many as desired) + total_mass h1 + total_mass he4 + ! etc. + + ! individial log10 mass totals for entire star (in Msun units) + !log_total_mass h1 + !log_total_mass he4 + ! etc. + +!---------------------------------------------------------------------------------------------- + +!# info at specific locations + + !## info at location of max temperature + !max_T + !log_max_T + + +!---------------------------------------------------------------------------------------------- + +!# information about shocks + + !## info about outermost outward moving shock + ! excluding locations with q > max_q_for_outer_mach1_location + ! returns values at location of max velocity + !shock_mass ! baryonic (Msun) + !shock_mass_gm ! baryonic (grams) + !shock_q + !shock_radius ! (Rsun) + !shock_radius_cm ! (cm) + !shock_velocity + !shock_csound + !shock_v_div_cs + !shock_lgT + !shock_lgRho + !shock_lgP + !shock_gamma1 + !shock_entropy + !shock_tau + !shock_k + !shock_pre_lgRho + +!---------------------------------------------------------------------------------------------- + +!# asteroseismology + + !delta_nu ! large frequency separation for p-modes (microHz) + ! 1e6/(seconds for sound to cross diameter of star) + !delta_Pg ! g-mode period spacing for l=1 (seconds) + ! sqrt(2) pi^2/(integral of brunt_N/r dr) + !log_delta_Pg + !nu_max ! estimate from scaling relation (microHz) + ! nu_max = nu_max_sun * M/Msun / ((R/Rsun)^2 (Teff/astero_Teff_sun)^0.5) + !nu_max_3_4th_div_delta_nu ! nu_max^0.75/delta_nu + !acoustic_cutoff ! 0.5*g*sqrt(gamma1*rho/P) at surface + !acoustic_radius ! integral of dr/csound (seconds) + !ng_for_nu_max ! = 1 / (nu_max*delta_Pg) + ! period for g-mode with frequency nu_max = nu_max_ng*delta_Pg + !gs_per_delta_nu ! delta_nu / (nu_max**2*delta_Pg) + ! number of g-modes per delta_nu at nu_max + + !int_k_r_dr_nu_max_Sl1 ! integral of k_r*dr where nu < N < Sl for nu = nu_max, l=1 + !int_k_r_dr_2pt0_nu_max_Sl1 ! integral of k_r*dr where nu < N < Sl for nu = nu_max*2, l=1 + !int_k_r_dr_0pt5_nu_max_Sl1 ! integral of k_r*dr where nu < N < Sl for nu = nu_max/2, l=1 + !int_k_r_dr_nu_max_Sl2 ! integral of k_r*dr where nu < N < Sl for nu = nu_max, l=2 + !int_k_r_dr_2pt0_nu_max_Sl2 ! integral of k_r*dr where nu < N < Sl for nu = nu_max*2, l=2 + !int_k_r_dr_0pt5_nu_max_Sl2 ! integral of k_r*dr where nu < N < Sl for nu = nu_max/2, l=2 + !int_k_r_dr_nu_max_Sl3 ! integral of k_r*dr where nu < N < Sl for nu = nu_max, l=3 + !int_k_r_dr_2pt0_nu_max_Sl3 ! integral of k_r*dr where nu < N < Sl for nu = nu_max*2, l=3 + !int_k_r_dr_0pt5_nu_max_Sl3 ! integral of k_r*dr where nu < N < Sl for nu = nu_max/2, l=3 + +!---------------------------------------------------------------------------------------------- + +!# energy information + + !total_energy ! at end of step + !log_total_energy ! log(abs(total_energy)) + !total_energy_after_adjust_mass ! after mass adjustments + + ! shorter versions of above + !tot_E + !log_tot_E + + + !total_gravitational_energy + !log_total_gravitational_energy ! log(abs(total_gravitational_energy)) + !total_gravitational_energy_after_adjust_mass + + ! shorter versions of above + !tot_PE + !log_tot_PE + + !total_internal_energy + !log_total_internal_energy + !total_internal_energy_after_adjust_mass + + ! shorter versions of above + !tot_IE + !log_tot_IE + + !total_radial_kinetic_energy + !log_total_radial_kinetic_energy + !total_radial_kinetic_energy_after_adjust_mass + + ! shorter versions of above (does not include rot KE) + !tot_KE + !log_tot_KE + + !total_turbulent_energy + !log_total_turbulent_energy + !total_turbulent_energy_after_adjust_mass + !tot_Et + !log_tot_Et + + !total_energy_foe + + !tot_IE_div_IE_plus_KE + !total_IE_div_IE_plus_KE + + !total_entropy + !total_eps_grav + + !total_energy_sources_and_sinks ! for this step + !total_nuclear_heating + !total_non_nuc_neu_cooling + !total_irradiation_heating + !total_extra_heating ! extra heat integrated over the model times dt (erg) + !total_WD_sedimentation_heating + + !rel_run_E_err + + !rel_E_err + !abs_rel_E_err + !log_rel_E_err + + !tot_e_equ_err + !tot_e_err + + + !error_in_energy_conservation ! for this step + ! = total_energy - (total_energy_start + total_energy_sources_and_sinks) + !cumulative_energy_error ! = sum over all steps of abs(error_in_energy_conservation) + !rel_cumulative_energy_error ! = cumulative_energy_error/total_energy + !log_rel_cumulative_energy_error ! = log10 of rel_cumulative_energy_error + !log_rel_run_E_err ! shorter name for rel_cumulative_energy_error + + !rel_error_in_energy_conservation ! = error_in_energy_conservation/total_energy + !log_rel_error_in_energy_conservation + + !virial_thm_P_avg + !virial_thm_rel_err + !work_inward_at_center + !work_outward_at_surface + + +!---------------------------------------------------------------------------------------------- + + !# rotation + + !total_angular_momentum + log_total_angular_momentum + !i_rot_total ! moment of inertia + + !total_rotational_kinetic_energy + !log_total_rotational_kinetic_energy + !total_rotational_kinetic_energy_after_adjust_mass + +!---------------------------------------------------------------------------------------------- + +!# velocities + + !avg_abs_v_div_cs + !log_avg_abs_v_div_cs + !max_abs_v_div_cs + !log_max_abs_v_div_cs + + !avg_abs_v + !log_avg_abs_v + !max_abs_v + !log_max_abs_v + + !u_surf + !u_surf_km_s + !u_div_csound_surf + !u_div_csound_max + + !infall_div_cs + +!---------------------------------------------------------------------------------------------- + +!# misc + + !e_thermal ! sum over all zones of Cp*T*dm + + !## eos + !logQ_max ! logQ = logRho - 2*logT + 12 + !logQ_min + !gamma1_min + + !## core mixing + !mass_semiconv_core + + !## H-He boundary + + !diffusion_time_H_He_bdy + !temperature_H_He_bdy + + + !## optical depth and opacity + + !one_div_yphot + !log_one_div_yphot + + !log_min_opacity + !min_opacity + + !log_tau_center + + !log_max_tau_conv + !max_tau_conv + !log_min_tau_conv + !min_tau_conv + + !tau_qhse_yrs + + !## other + + !Lsurf_m + !dlnR_dlnM + !h1_czb_mass ! location (in Msun units) of base of 1st convection zone above he core + !kh_mdot_limit + !log_cntr_dr_cm + !min_Pgas_div_P + !surf_c12_minus_o16 ! this is useful for seeing effects of dredge up on AGB + !surf_num_c12_div_num_o16 + + !phase_of_evolution ! Integer mapping to the type of evolution see star_data/public/star_data_def.inc for definitions + + !## MLT++ + !gradT_excess_alpha + !gradT_excess_min_beta + !gradT_excess_max_lambda + + !max_L_rad_div_Ledd + !max_L_rad_div_Ledd_div_phi_Joss + + + !## RTI + !rti_regions + + !## Ni & Co + !total_ni_co_56 + + + !## internal structure constants + + ! this is evaluated assuming a spherical star and does not account for rotation + !apsidal_constant_k2 + + +!---------------------------------------------------------------------------------------------- + +!# accretion + + !k_below_const_q + !q_below_const_q + !logxq_below_const_q + + !k_const_mass + !q_const_mass + !logxq_const_mass + + !k_below_just_added + !q_below_just_added + !logxq_below_just_added + + !k_for_test_CpT_absMdot_div_L + !q_for_test_CpT_absMdot_div_L + !logxq_for_test_CpT_absMdot_div_L + +!---------------------------------------------------------------------------------------------- + +!# Color output + + ! Outputs the bolometric correction (bc) for the star in filter band ``filter'' (case sensitive) + !bc filter + + ! Outputs the absolute magnitude for the star in filter band ``filter'' (case sensitive) + !abs_mag filter + + ! Adds all the bc's to the output + !add_bc + + ! Adds all the absolute magnitudes to the output + !add_abs_mag + + ! Outputs luminosity in filter band ``filter'' (erg s^-1) (case sensitive) + ! lum_band filter + + ! Adds all the filter band luminosities to the output (erg s^-1) + ! add_lum_band + + ! Outputs log luminosity in filter band ``filter'' (log erg s^-1) (case sensitive) + ! log_lum_band filter + + ! Adds all the filter band luminosities to the output (log erg s^-1) + ! add_log_lum_band + +!---------------------------------------------------------------------------------------------- + +!# RSP + + !rsp_DeltaMag ! absolute magnitude difference between minimum and maximum light (mag) + !rsp_DeltaR ! R_max - R_min difference in the max and min radius (Rsun) + !rsp_GREKM ! fractional growth of the kinetic energy per pulsation period ("nonlinear growth rate") - see equation 5 in MESA5 + !rsp_num_periods ! Count of the number of pulsation cycles completed + !rsp_period_in_days ! Running period, ie., period between two consecutive values of R_max (days) + !rsp_phase ! Running pulsation phase for a cycle + +!---------------------------------------------------------------------------------------------- +!# debugging + + !## retries + num_retries ! total during the run + + !## solver iterations + + num_iters ! same as num_solver_iterations + !num_solver_iterations ! iterations at this step + !total_num_solver_iterations ! total iterations during the run + !avg_num_solver_iters + + !rotation_solver_steps + + !diffusion_solver_steps + !diffusion_solver_iters + + !avg_setvars_per_step + !avg_skipped_setvars_per_step + !avg_solver_setvars_per_step + + !burn_solver_maxsteps + + !total_num_solver_calls_converged + !total_num_solver_calls_failed + !total_num_solver_calls_made + !total_num_solver_relax_calls_converged + !total_num_solver_relax_calls_failed + !total_num_solver_relax_calls_made + !total_num_solver_relax_iterations + + !total_step_attempts + !total_step_redos + !total_step_retries + !total_steps_finished + !total_steps_taken + + !TDC_num_cells + + !## Relaxation steps + !total_relax_step_attempts + !total_relax_step_redos + !total_relax_step_retries + !total_relax_steps_finished + !total_relax_steps_taken + + !## conservation during mesh adjust + !log_mesh_adjust_IE_conservation + !log_mesh_adjust_KE_conservation + !log_mesh_adjust_PE_conservation + + !## amr + !num_hydro_merges + !num_hydro_splits + + !## timing + !elapsed_time ! time since start of run (seconds) diff --git a/star/test_suite/accreted_material_j/inlist_accreted_material_j b/star/test_suite/accreted_material_j/inlist_accreted_material_j index ab0f3db53..ec18219df 100644 --- a/star/test_suite/accreted_material_j/inlist_accreted_material_j +++ b/star/test_suite/accreted_material_j/inlist_accreted_material_j @@ -1,6 +1,6 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. load_saved_model = .true. load_model_filename = 'zams.mod' @@ -31,6 +31,9 @@ !required_termination_code_string = 'xa_central_lower_limit' required_termination_code_string = 'star_mass_max_limit' + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. + / !end of star_job &eos @@ -55,9 +58,9 @@ ! limit max_model_number as part of test_suite max_model_number = 1000 - + premix_omega = .true. - + am_nu_visc_factor = 0 am_D_mix_factor = 0.0333333333333333d00 D_DSI_factor = 1 @@ -69,7 +72,7 @@ !set_min_D_mix = .true. !min_D_mix = 1d10 - + ! starting specifications initial_mass = 20 ! in Msun units initial_Z = 0.02 @@ -96,23 +99,23 @@ !varcontrol_target = 5d-4 delta_lg_star_mass_limit = 2d-4 delta_lg_star_mass_hard_limit = 4d-4 - + ! output to files and terminal photo_interval = 50 profile_interval = 100 max_num_profile_models = 3000 history_interval = 10 terminal_interval = 10 - + write_header_frequency = 10 - + !report_solver_progress = .true. / &pgstar - + / ! end of pgstar namelist diff --git a/star/test_suite/accreted_material_j/inlist_accreted_material_j_header b/star/test_suite/accreted_material_j/inlist_accreted_material_j_header index 54bd3ff57..2008891f8 100644 --- a/star/test_suite/accreted_material_j/inlist_accreted_material_j_header +++ b/star/test_suite/accreted_material_j/inlist_accreted_material_j_header @@ -36,6 +36,6 @@ &pgstar read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_accreted_material_j' + extra_pgstar_inlist_name(1)= 'inlist_pgstar' / ! end of pgstar namelist diff --git a/star/test_suite/accreted_material_j/inlist_pgstar b/star/test_suite/accreted_material_j/inlist_pgstar new file mode 100644 index 000000000..5c3005611 --- /dev/null +++ b/star/test_suite/accreted_material_j/inlist_pgstar @@ -0,0 +1,36 @@ +&pgstar + + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'png' ! png + file_extension = 'png' + + !file_device = 'vcps' ! postscript + !file_extension = 'ps' + + pgstar_interval = 10 + + + History_Track1_win_flag = .true. + History_Track1_win_width = 12 + History_Track1_title = 'accreted_material_j' + History_Track1_xname = 'star_mass' + History_Track1_yname = 'log_total_angular_momentum' + History_Track1_yaxis_label = 'log J' + History_Track1_xaxis_label = 'M\d\(2281)' + History_Track1_reverse_xaxis = .false. + History_Track1_reverse_yaxis = .false. + + History_Track1_xmin = 20.0 + History_Track1_xmax = 25.0 + History_Track1_ymin = 51.9 + History_Track1_ymax = 52.7 + +! file output + History_Track1_file_flag = .true. + History_Track1_file_dir = 'pgstar_out' + History_Track1_file_prefix = 'track1_' + History_Track1_file_interval = 10 + History_Track1_file_width =12 + History_Track1_file_aspect_ratio = -1 + +/ ! end of pgstar namelist From 8f6092f67241a2c579908b8d09a30a690b096a84 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 10:39:28 -0400 Subject: [PATCH 22/66] updating TP 32 --- .../diffusion_smoothness/README.rst | 44 +--- .../docs/brunt_000036.svg | 243 +----------------- .../inlist_diffusion_smoothness | 39 ++- .../inlist_diffusion_smoothness_header | 2 - .../diffusion_smoothness/inlist_zams | 2 - .../diffusion_smoothness/inlist_zams_header | 1 - 6 files changed, 37 insertions(+), 294 deletions(-) diff --git a/star/test_suite/diffusion_smoothness/README.rst b/star/test_suite/diffusion_smoothness/README.rst index 46bf4dbdb..409b5f6f4 100644 --- a/star/test_suite/diffusion_smoothness/README.rst +++ b/star/test_suite/diffusion_smoothness/README.rst @@ -17,44 +17,10 @@ This test case has 2 part2. Click to see a larger view of a plot. pgstar commands used for the plot: -.. code-block:: console +.. literalinclude:: ../../../star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness + :language: console + :start-at: &pgstar + :end-at: ! end of pgstar namelist - &pgstar - - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - - !file_device = 'vcps' ! postscript - !file_extension = 'ps' - - pgstar_interval = 1 - - ! Brunt B profile - Profile_Panels1_win_flag = .true. - Profile_Panels1_win_width = 14 - Profile_Panels1_show_grid = .false - Profile_Panels1_title = 'diffusion_smoothness' - - Profile_Panels1_xaxis_name = 'zone' - Profile_Panels1_xmin = -101d0 - Profile_Panels1_xmax = -101d0 - Profile_Panels1_xaxis_reversed = .true. - Profile_Panels1_show_mix_regions_on_xaxis = .true. - - Profile_Panels1_num_panels = 1 - Profile_Panels1_yaxis_name(1) = 'brunt_B' - Profile_Panels1_ymin(:) = -101d0 - Profile_Panels1_ymax(:) = -101d0 - Profile_Panels1_other_yaxis_name(1) = '' - - Profile_Panels1_file_flag = .true. - Profile_Panels1_file_dir = 'png' - Profile_Panels1_file_prefix = 'brunt_' - Profile_Panels1_file_interval = 10000 - Profile_Panels1_file_width = 14 - - / ! end of pgstar namelist - -Last-Updated: 06Jun2021 (MESA 5be9e57) by fxt +Last-Updated: 06Aug2024 (MESA 8b152605) by pmocz on C916PXT6XW in 82 seconds using 8 threads. diff --git a/star/test_suite/diffusion_smoothness/docs/brunt_000036.svg b/star/test_suite/diffusion_smoothness/docs/brunt_000036.svg index b872075e7..715714029 100644 --- a/star/test_suite/diffusion_smoothness/docs/brunt_000036.svg +++ b/star/test_suite/diffusion_smoothness/docs/brunt_000036.svg @@ -1,242 +1 @@ - - - - - - - - - - - - - - - - - - - - - + \ No newline at end of file diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness index a6b192683..ef39217c5 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness @@ -26,8 +26,8 @@ set_initial_cumulative_energy_error = .true. new_cumulative_energy_error = 0d0 - !pgstar_flag = .true. - + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / ! end of star_job namelist @@ -116,13 +116,36 @@ / ! end of controls namelist - &pgstar - - ! top level controls - !pause = .true. - ! if true, the code waits for user to enter a RETURN on the command line - + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'vcps' ! postscript + file_extension = 'ps' + + pgstar_interval = 1 + + ! Brunt B profile + Profile_Panels1_win_flag = .true. + Profile_Panels1_win_width = 14 + Profile_Panels1_show_grid = .false + Profile_Panels1_title = 'diffusion_smoothness' + + Profile_Panels1_xaxis_name = 'zone' + Profile_Panels1_xmin = -101d0 + Profile_Panels1_xmax = -101d0 + Profile_Panels1_xaxis_reversed = .true. + Profile_Panels1_show_mix_regions_on_xaxis = .true. + + Profile_Panels1_num_panels = 1 + Profile_Panels1_yaxis_name(1) = 'brunt_B' + Profile_Panels1_ymin(:) = -101d0 + Profile_Panels1_ymax(:) = -101d0 + Profile_Panels1_other_yaxis_name(1) = '' + + Profile_Panels1_file_flag = .true. + Profile_Panels1_file_dir = 'pgstar_out' + Profile_Panels1_file_prefix = 'brunt_' + Profile_Panels1_file_interval = 10000 + Profile_Panels1_file_width = 14 / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header index 90d444869..af5d6b624 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header @@ -1,7 +1,6 @@ &star_job - read_extra_star_job_inlist(1) = .true. extra_star_job_inlist_name(1) = 'inlist_diffusion_smoothness' @@ -24,7 +23,6 @@ / ! end of kap namelist - &controls read_extra_controls_inlist(1) = .true. diff --git a/star/test_suite/diffusion_smoothness/inlist_zams b/star/test_suite/diffusion_smoothness/inlist_zams index 8bfa87a5f..cccd02ef5 100644 --- a/star/test_suite/diffusion_smoothness/inlist_zams +++ b/star/test_suite/diffusion_smoothness/inlist_zams @@ -65,7 +65,6 @@ / ! end of controls namelist - &pgstar ! top level controls @@ -73,5 +72,4 @@ !pause = .true. ! if true, the code waits for user to enter a RETURN on the command line - / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_zams_header b/star/test_suite/diffusion_smoothness/inlist_zams_header index 9b647ddf7..a387c02e0 100644 --- a/star/test_suite/diffusion_smoothness/inlist_zams_header +++ b/star/test_suite/diffusion_smoothness/inlist_zams_header @@ -1,7 +1,6 @@ &star_job - read_extra_star_job_inlist(1) = .true. extra_star_job_inlist_name(1) = 'inlist_zams' From 84cadcd89ca827fbcc06cc419c8f03b8a888240d Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 10:52:11 -0400 Subject: [PATCH 23/66] TP 17. change png to svg --- star/test_suite/7M_prems_to_AGB/README.rst | 43 +++--------------- .../7M_prems_to_AGB/docs/hr000785.png | Bin 16960 -> 0 bytes .../7M_prems_to_AGB/docs/hr000785.svg | 1 + .../inlist_7M_prems_to_AGB_header | 1 - star/test_suite/7M_prems_to_AGB/inlist_pgstar | 6 +-- .../7M_prems_to_AGB/inlist_start_header | 1 - 6 files changed, 11 insertions(+), 41 deletions(-) delete mode 100644 star/test_suite/7M_prems_to_AGB/docs/hr000785.png create mode 100644 star/test_suite/7M_prems_to_AGB/docs/hr000785.svg diff --git a/star/test_suite/7M_prems_to_AGB/README.rst b/star/test_suite/7M_prems_to_AGB/README.rst index 8a1ffc48f..dd63a4d53 100644 --- a/star/test_suite/7M_prems_to_AGB/README.rst +++ b/star/test_suite/7M_prems_to_AGB/README.rst @@ -4,7 +4,7 @@ 7M_prems_to_AGB *************** -This test case checks that the evolution of a 7 Msun, metal-poor Z = 0.001, model reaches the AGB. +This test case checks that the evolution of a 7 |Msun|, metal-poor Z = 0.001, model reaches the AGB. This test case has two parts. Click to see a larger view of a plot. @@ -12,45 +12,16 @@ This test case has two parts. Click to see a larger view of a plot. * Part 2 (``inlist_7M_prems_to_AGB``) continues the evolution as core hydrogen and helium burning proceed, terminating when log10(L/Lsun)=4.3 is reached. The model executes a blue loop as helium depletes, with the red edge and blue edge of the classical Cepheid instability strip boundaries shown in the HR diagram: -.. image:: ../../../star/test_suite/7M_prems_to_AGB/docs/hr000794.svg +.. image:: ../../../star/test_suite/7M_prems_to_AGB/docs/hr000785.svg :width: 100% pgstar commands used: -.. code-block:: console +.. literalinclude:: ../../../star/test_suite/7M_prems_to_AGB/inlist_pgstar + :language: console + :start-at: &pgstar + :end-at: ! end of pgstar namelist - &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - - !file_device = 'vcps' ! postscript - !file_extension = 'ps' - - pgstar_interval = 10 - - HR_win_flag = .true. - HR_win_width = 12 - HR_win_aspect_ratio = 1.2 ! aspect_ratio = height/width - - HR_logT_min = 3.5 - HR_logT_max = 4.5 - HR_logL_min = 2.7 - HR_logL_max = 4.4 - - ! file output - HR_file_flag = .true. - HR_file_dir = 'pgstar_out' - HR_file_prefix = 'hr' - HR_file_interval = 100 ! output when mod(model_number,HR_file_interval)==0 - HR_file_width = 15 ! negative means use same value as for window - HR_file_aspect_ratio = -1 ! negative means use same value as for window - - / ! end of pgstar namelist - - - - -Last-Updated: 29May2021 (MESA e37f76f) by fxt +Last-Updated: 06Aug2024 (MESA f50b3763) by pmocz on C916PXT6XW in 410 seconds using 8 threads. diff --git a/star/test_suite/7M_prems_to_AGB/docs/hr000785.png b/star/test_suite/7M_prems_to_AGB/docs/hr000785.png deleted file mode 100644 index df1fe2ed008d159d5ec00924f39b33fddecd55c5..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16960 zcmeIZ3piBW+c2(!r-M)=l~5r$PG`wso{|)0DxngioGNLGL@|3h$te^$RZLMyV$w;H z*&T*SPLC)>*%=|nF$S~8Y%|~5TRrdZ`rh~Vz2E!(|KIPrzW?>FtJPljy3gxgYp+@N zy`#4~+9^(-KV42vPI1fTjXUM!CS!7P@{*~O0Oa}==XY{)ljOE<-DL~9GVllgkNAf_ 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b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header index 1cc9ef4c0..d496188f4 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header +++ b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header @@ -1,7 +1,6 @@ &star_job - read_extra_star_job_inlist(2) = .true. extra_star_job_inlist_name(2) = 'inlist_7M_prems_to_AGB' diff --git a/star/test_suite/7M_prems_to_AGB/inlist_pgstar b/star/test_suite/7M_prems_to_AGB/inlist_pgstar index 10359a49f..9e82833e9 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_pgstar +++ b/star/test_suite/7M_prems_to_AGB/inlist_pgstar @@ -2,10 +2,10 @@ file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! postscript - file_extension = 'png' + file_device = 'vcps' ! postscript + file_extension = 'ps' - pgstar_interval = 10 + pgstar_interval = 10 HR_win_flag = .true. HR_win_width = 12 diff --git a/star/test_suite/7M_prems_to_AGB/inlist_start_header b/star/test_suite/7M_prems_to_AGB/inlist_start_header index 8852b908a..687756114 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_start_header +++ b/star/test_suite/7M_prems_to_AGB/inlist_start_header @@ -1,7 +1,6 @@ &star_job - read_extra_star_job_inlist(2) = .true. extra_star_job_inlist_name(2) = 'inlist_start' From 283b1c9993d84bed0877684c3cedc60c8655c341 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 11:07:38 -0400 Subject: [PATCH 24/66] format inlists --- .../7M_prems_to_AGB/inlist_7M_prems_to_AGB | 92 +++---- .../inlist_7M_prems_to_AGB_header | 20 +- star/test_suite/7M_prems_to_AGB/inlist_pgstar | 40 +-- star/test_suite/7M_prems_to_AGB/inlist_start | 40 +-- .../7M_prems_to_AGB/inlist_start_header | 20 +- .../inlist_diffusion_smoothness | 242 +++++++++--------- .../inlist_diffusion_smoothness_header | 20 +- .../diffusion_smoothness/inlist_zams | 100 ++++---- .../diffusion_smoothness/inlist_zams_header | 20 +- 9 files changed, 297 insertions(+), 297 deletions(-) diff --git a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB index 9baf6422d..976cdabaa 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB +++ b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB @@ -2,20 +2,20 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. - load_saved_model = .true. - load_model_filename = 'start.mod' + load_saved_model = .true. + load_model_filename = 'start.mod' - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - required_termination_code_string = 'log_L_upper_limit' + save_model_when_terminate = .true. + save_model_filename = 'final.mod' + required_termination_code_string = 'log_L_upper_limit' - set_initial_cumulative_energy_error = .true. - new_cumulative_energy_error = 0d0 + set_initial_cumulative_energy_error = .true. + new_cumulative_energy_error = 0d0 - pgstar_flag = .true. - save_pgstar_files_when_terminate = .true. + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / ! end of star_job namelist @@ -25,7 +25,7 @@ / ! end of eos namelist &kap - Zbase = 0.001 + Zbase = 0.001 use_Type2_opacities = .true. @@ -33,50 +33,50 @@ &controls - energy_eqn_option = 'dedt' - use_gold2_tolerances = .true. - max_abs_rel_run_E_err = 1d-2 + energy_eqn_option = 'dedt' + use_gold2_tolerances = .true. + max_abs_rel_run_E_err = 1d-2 - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' - ! limit max_model_number as part of test_suite - max_model_number = 3000 + ! limit max_model_number as part of test_suite + max_model_number = 3000 - initial_mass = 7.00 - initial_z = 0.001 + initial_mass = 7.00 + initial_z = 0.001 - mixing_length_alpha = 1.73 + mixing_length_alpha = 1.73 - log_L_upper_limit = 4.3 + log_L_upper_limit = 4.3 - overshoot_scheme(1) = 'exponential' - overshoot_zone_type(1) = 'any' - overshoot_zone_loc(1) = 'any' - overshoot_bdy_loc(1) = 'any' - overshoot_f(1) = 0.014 - overshoot_f0(1) = 0.004 + overshoot_scheme(1) = 'exponential' + overshoot_zone_type(1) = 'any' + overshoot_zone_loc(1) = 'any' + overshoot_bdy_loc(1) = 'any' + overshoot_f(1) = 0.014 + overshoot_f0(1) = 0.004 - atm_option = 'T_tau' - atm_T_tau_relation = 'Eddington' - atm_T_tau_opacity = 'fixed' + atm_option = 'T_tau' + atm_T_tau_relation = 'Eddington' + atm_T_tau_opacity = 'fixed' ! mass loss - cool_wind_full_on_T = 9.99d9 - hot_wind_full_on_T = 1d10 - cool_wind_RGB_scheme = 'Reimers' - cool_wind_AGB_scheme = 'Blocker' - RGB_to_AGB_wind_switch = 1d-4 - Reimers_scaling_factor = 0.5d0 - Blocker_scaling_factor = 0.0003d0 - - - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 - write_header_frequency = 10 + cool_wind_full_on_T = 9.99d9 + hot_wind_full_on_T = 1d10 + cool_wind_RGB_scheme = 'Reimers' + cool_wind_AGB_scheme = 'Blocker' + RGB_to_AGB_wind_switch = 1d-4 + Reimers_scaling_factor = 0.5d0 + Blocker_scaling_factor = 0.0003d0 + + + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 + write_header_frequency = 10 / ! end of controls namelist diff --git a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header index d496188f4..0f6e5d9a4 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header +++ b/star/test_suite/7M_prems_to_AGB/inlist_7M_prems_to_AGB_header @@ -1,39 +1,39 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_7M_prems_to_AGB' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_7M_prems_to_AGB' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_7M_prems_to_AGB' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_7M_prems_to_AGB' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_7M_prems_to_AGB' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_7M_prems_to_AGB' / ! end of kap namelist &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_7M_prems_to_AGB' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_7M_prems_to_AGB' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_pgstar' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_pgstar' / ! end of pgstar namelist diff --git a/star/test_suite/7M_prems_to_AGB/inlist_pgstar b/star/test_suite/7M_prems_to_AGB/inlist_pgstar index 9e82833e9..c2c0cbe65 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_pgstar +++ b/star/test_suite/7M_prems_to_AGB/inlist_pgstar @@ -1,30 +1,30 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'vcps' ! postscript - file_extension = 'ps' + file_device = 'vcps' ! postscript + file_extension = 'ps' - pgstar_interval = 10 + pgstar_interval = 10 - HR_win_flag = .true. - HR_win_width = 12 - HR_win_aspect_ratio = 1.2 ! aspect_ratio = height/width + HR_win_flag = .true. + HR_win_width = 12 + HR_win_aspect_ratio = 1.2 ! aspect_ratio = height/width - HR_logT_min = 3.5 - HR_logT_max = 4.5 - HR_logL_min = 2.7 - HR_logL_max = 4.4 + HR_logT_min = 3.5 + HR_logT_max = 4.5 + HR_logL_min = 2.7 + HR_logL_max = 4.4 - ! file output - HR_file_flag = .true. - HR_file_dir = 'pgstar_out' - HR_file_prefix = 'hr' - HR_file_interval = 100 ! output when mod(model_number,HR_file_interval)==0 - HR_file_width = 15 ! negative means use same value as for window - HR_file_aspect_ratio = -1 ! negative means use same value as for window + ! file output + HR_file_flag = .true. + HR_file_dir = 'pgstar_out' + HR_file_prefix = 'hr' + HR_file_interval = 100 ! output when mod(model_number,HR_file_interval)==0 + HR_file_width = 15 ! negative means use same value as for window + HR_file_aspect_ratio = -1 ! negative means use same value as for window - show_HR_classical_instability_strip = .true. - show_HR_Mira_instability_region = .false. + show_HR_classical_instability_strip = .true. + show_HR_Mira_instability_region = .false. / ! end of pgstar namelist diff --git a/star/test_suite/7M_prems_to_AGB/inlist_start b/star/test_suite/7M_prems_to_AGB/inlist_start index 4c75cbdf4..d1055e923 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_start +++ b/star/test_suite/7M_prems_to_AGB/inlist_start @@ -1,24 +1,24 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. - create_pre_main_sequence_model = .true. + create_pre_main_sequence_model = .true. - save_model_when_terminate = .true. - save_model_filename = 'start.mod' - required_termination_code_string = 'max_age' + save_model_when_terminate = .true. + save_model_filename = 'start.mod' + required_termination_code_string = 'max_age' - change_initial_net = .true. - new_net_name = 'o18_and_ne22.net' + change_initial_net = .true. + new_net_name = 'o18_and_ne22.net' / ! end of star_job namelist &kap - Zbase = 0.001 - use_Type2_opacities = .true. + Zbase = 0.001 + use_Type2_opacities = .true. / !end of kap namelist &eos @@ -27,20 +27,20 @@ &controls - ! limit max_model_number as part of test_suite - max_model_number = 150 - use_gold2_tolerances = .true. + ! limit max_model_number as part of test_suite + max_model_number = 150 + use_gold2_tolerances = .true. - max_age = 0.5d0 + max_age = 0.5d0 - initial_mass = 7.00 - initial_z = 0.001 + initial_mass = 7.00 + initial_z = 0.001 - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 - write_header_frequency = 10 + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 + write_header_frequency = 10 / ! end of controls namelist diff --git a/star/test_suite/7M_prems_to_AGB/inlist_start_header b/star/test_suite/7M_prems_to_AGB/inlist_start_header index 687756114..3a86b4deb 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_start_header +++ b/star/test_suite/7M_prems_to_AGB/inlist_start_header @@ -1,24 +1,24 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_start' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_start' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_start' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_start' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_start' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_start' / ! end of kap namelist @@ -26,15 +26,15 @@ &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_start' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_start' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_start' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_start' / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness index ef39217c5..262a63ea6 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness @@ -1,33 +1,33 @@ &star_job - show_log_description_at_start = .false. - - !show_net_species_info = .true. - !show_net_reactions_info = .true. + show_log_description_at_start = .false. - load_saved_model = .true. - load_model_filename = 'zams.mod' - - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - required_termination_code_string = 'max_age' + !show_net_species_info = .true. + !show_net_reactions_info = .true. + load_saved_model = .true. + load_model_filename = 'zams.mod' - change_initial_net = .true. - new_net_name = 'o18_and_ne22.net' - - set_initial_age = .true. - initial_age = 0 + save_model_when_terminate = .true. + save_model_filename = 'final.mod' + required_termination_code_string = 'max_age' - set_initial_model_number = .true. - initial_model_number = 0 - set_initial_cumulative_energy_error = .true. - new_cumulative_energy_error = 0d0 + change_initial_net = .true. + new_net_name = 'o18_and_ne22.net' - pgstar_flag = .true. - save_pgstar_files_when_terminate = .true. + set_initial_age = .true. + initial_age = 0 + + set_initial_model_number = .true. + initial_model_number = 0 + + set_initial_cumulative_energy_error = .true. + new_cumulative_energy_error = 0d0 + + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / ! end of star_job namelist @@ -35,117 +35,117 @@ / ! end of eos namelist &kap - Zbase = 0.02d0 - kap_file_prefix = 'gs98' + Zbase = 0.02d0 + kap_file_prefix = 'gs98' / ! end of kap namelist &controls - energy_eqn_option = 'dedt' - calculate_Brunt_N2 = .true. - use_gold2_tolerances = .true. - - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' - - ! limit max_model_number as part of test_suite - max_model_number = 100 - - x_integer_ctrl(1) = 1 ! part number - - max_age = 3d9 - - initial_mass = 1.0 - initial_z = 0.02d0 - - varcontrol_target = 1d-3 - mesh_delta_coeff = 0.7 - - limit_for_rel_error_in_energy_conservation = 1d-6 ! this makes d2N2 too large. takes 63 steps. log_rel_run_E_err -3.5859393528096946 - limit_for_rel_error_in_energy_conservation = 1d-5 ! this is smooth enough. takes 58 steps. log_rel_run_E_err -3.4820705862368895 - hard_limit_for_rel_error_in_energy_conservation = 1d-4 - - convective_bdy_weight = 1 - - cool_wind_RGB_scheme = 'Reimers' - cool_wind_AGB_scheme = 'Blocker' - RGB_to_AGB_wind_switch = 1d-4 - Reimers_scaling_factor = 0.7d0 - Blocker_scaling_factor = 0.7d0 + energy_eqn_option = 'dedt' + calculate_Brunt_N2 = .true. + use_gold2_tolerances = .true. + + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' + + ! limit max_model_number as part of test_suite + max_model_number = 100 + + x_integer_ctrl(1) = 1 ! part number + + max_age = 3d9 + + initial_mass = 1.0 + initial_z = 0.02d0 + + varcontrol_target = 1d-3 + mesh_delta_coeff = 0.7 + + limit_for_rel_error_in_energy_conservation = 1d-6 ! this makes d2N2 too large. takes 63 steps. log_rel_run_E_err -3.5859393528096946 + limit_for_rel_error_in_energy_conservation = 1d-5 ! this is smooth enough. takes 58 steps. log_rel_run_E_err -3.4820705862368895 + hard_limit_for_rel_error_in_energy_conservation = 1d-4 + + convective_bdy_weight = 1 + + cool_wind_RGB_scheme = 'Reimers' + cool_wind_AGB_scheme = 'Blocker' + RGB_to_AGB_wind_switch = 1d-4 + Reimers_scaling_factor = 0.7d0 + Blocker_scaling_factor = 0.7d0 ! set_min_D_mix = .true. - min_D_mix = 1d2 ! D_mix will be at least this large - min_center_Ye_for_min_D_mix = 0.47 ! min_D_mix is only used when center Ye >= this - ! i.e., when center Ye drops below this, min_D_mix is 0 - - - num_cells_for_smooth_brunt_B = 0 - - !show_diffusion_info = .true. ! terminal output for diffusion - !show_diffusion_substep_info = .true. - !show_diffusion_timing = .true. - - do_element_diffusion = .true. ! determines whether or not we do diffusion - - diffusion_calculates_ionization = .true. - - diffusion_num_classes = 4 ! number of classes of species for diffusion calculations - diffusion_class_representative(1) = 'h1' - diffusion_class_representative(2) = 'he4' - diffusion_class_representative(3) = 'o16' - diffusion_class_representative(4) = 'fe56' - - ! in ascending order. species goes into 1st class with A_max >= species A - diffusion_class_A_max(1) = 2 - diffusion_class_A_max(2) = 4 - diffusion_class_A_max(3) = 16 - diffusion_class_A_max(4) = 10000 - - diffusion_use_isolve = .true. - diffusion_rtol_for_isolve = 1d-4 - diffusion_atol_for_isolve = 1d-5 - diffusion_maxsteps_for_isolve = 1000 - diffusion_isolve_solver = 'ros2_solver' - - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 + min_D_mix = 1d2 ! D_mix will be at least this large + min_center_Ye_for_min_D_mix = 0.47 ! min_D_mix is only used when center Ye >= this + ! i.e., when center Ye drops below this, min_D_mix is 0 + + + num_cells_for_smooth_brunt_B = 0 + + !show_diffusion_info = .true. ! terminal output for diffusion + !show_diffusion_substep_info = .true. + !show_diffusion_timing = .true. + + do_element_diffusion = .true. ! determines whether or not we do diffusion + + diffusion_calculates_ionization = .true. + + diffusion_num_classes = 4 ! number of classes of species for diffusion calculations + diffusion_class_representative(1) = 'h1' + diffusion_class_representative(2) = 'he4' + diffusion_class_representative(3) = 'o16' + diffusion_class_representative(4) = 'fe56' + + ! in ascending order. species goes into 1st class with A_max >= species A + diffusion_class_A_max(1) = 2 + diffusion_class_A_max(2) = 4 + diffusion_class_A_max(3) = 16 + diffusion_class_A_max(4) = 10000 + + diffusion_use_isolve = .true. + diffusion_rtol_for_isolve = 1d-4 + diffusion_atol_for_isolve = 1d-5 + diffusion_maxsteps_for_isolve = 1000 + diffusion_isolve_solver = 'ros2_solver' + + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 / ! end of controls namelist &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'vcps' ! postscript - file_extension = 'ps' - - pgstar_interval = 1 - - ! Brunt B profile - Profile_Panels1_win_flag = .true. - Profile_Panels1_win_width = 14 - Profile_Panels1_show_grid = .false - Profile_Panels1_title = 'diffusion_smoothness' - - Profile_Panels1_xaxis_name = 'zone' - Profile_Panels1_xmin = -101d0 - Profile_Panels1_xmax = -101d0 - Profile_Panels1_xaxis_reversed = .true. - Profile_Panels1_show_mix_regions_on_xaxis = .true. - - Profile_Panels1_num_panels = 1 - Profile_Panels1_yaxis_name(1) = 'brunt_B' - Profile_Panels1_ymin(:) = -101d0 - Profile_Panels1_ymax(:) = -101d0 - Profile_Panels1_other_yaxis_name(1) = '' - - Profile_Panels1_file_flag = .true. - Profile_Panels1_file_dir = 'pgstar_out' - Profile_Panels1_file_prefix = 'brunt_' - Profile_Panels1_file_interval = 10000 - Profile_Panels1_file_width = 14 + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'vcps' ! postscript + file_extension = 'ps' + + pgstar_interval = 1 + + ! Brunt B profile + Profile_Panels1_win_flag = .true. + Profile_Panels1_win_width = 14 + Profile_Panels1_show_grid = .false + Profile_Panels1_title = 'diffusion_smoothness' + + Profile_Panels1_xaxis_name = 'zone' + Profile_Panels1_xmin = -101d0 + Profile_Panels1_xmax = -101d0 + Profile_Panels1_xaxis_reversed = .true. + Profile_Panels1_show_mix_regions_on_xaxis = .true. + + Profile_Panels1_num_panels = 1 + Profile_Panels1_yaxis_name(1) = 'brunt_B' + Profile_Panels1_ymin(:) = -101d0 + Profile_Panels1_ymax(:) = -101d0 + Profile_Panels1_other_yaxis_name(1) = '' + + Profile_Panels1_file_flag = .true. + Profile_Panels1_file_dir = 'pgstar_out' + Profile_Panels1_file_prefix = 'brunt_' + Profile_Panels1_file_interval = 10000 + Profile_Panels1_file_width = 14 / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header index af5d6b624..aaf43854c 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness_header @@ -1,39 +1,39 @@ &star_job - read_extra_star_job_inlist(1) = .true. - extra_star_job_inlist_name(1) = 'inlist_diffusion_smoothness' + read_extra_star_job_inlist(1) = .true. + extra_star_job_inlist_name(1) = 'inlist_diffusion_smoothness' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_diffusion_smoothness' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_diffusion_smoothness' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_diffusion_smoothness' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_diffusion_smoothness' / ! end of kap namelist &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_diffusion_smoothness' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_diffusion_smoothness' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_diffusion_smoothness' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_diffusion_smoothness' / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_zams b/star/test_suite/diffusion_smoothness/inlist_zams index cccd02ef5..fda0c5e76 100644 --- a/star/test_suite/diffusion_smoothness/inlist_zams +++ b/star/test_suite/diffusion_smoothness/inlist_zams @@ -1,75 +1,75 @@ &star_job - show_log_description_at_start = .false. - - !show_net_species_info = .true. - !show_net_reactions_info = .true. + show_log_description_at_start = .false. - create_pre_main_sequence_model = .true. - - save_model_when_terminate = .true. - save_model_filename = 'zams.mod' - required_termination_code_string = 'Lnuc_div_L_zams_limit' + !show_net_species_info = .true. + !show_net_reactions_info = .true. + create_pre_main_sequence_model = .true. - change_initial_net = .true. - new_net_name = 'o18_and_ne22.net' - - !pgstar_flag = .true. + save_model_when_terminate = .true. + save_model_filename = 'zams.mod' + required_termination_code_string = 'Lnuc_div_L_zams_limit' + + + change_initial_net = .true. + new_net_name = 'o18_and_ne22.net' + + !pgstar_flag = .true. / ! end of star_job namelist &kap - Zbase = 0.02d0 + Zbase = 0.02d0 - kap_file_prefix = 'gs98' + kap_file_prefix = 'gs98' / ! end of kap namelist &controls - stop_near_zams = .true. - Lnuc_div_L_zams_limit = 0.98d0 - - ! limit max_model_number as part of test_suite - max_model_number = 10000 - use_gold2_tolerances = .true. - - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' - - x_integer_ctrl(1) = 0 ! part number - - initial_mass = 1.0 - initial_z = 0.02d0 - - varcontrol_target = 1d-3 - mesh_delta_coeff = 0.7 - + stop_near_zams = .true. + Lnuc_div_L_zams_limit = 0.98d0 + + ! limit max_model_number as part of test_suite + max_model_number = 10000 + use_gold2_tolerances = .true. + + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' + + x_integer_ctrl(1) = 0 ! part number + + initial_mass = 1.0 + initial_z = 0.02d0 + + varcontrol_target = 1d-3 + mesh_delta_coeff = 0.7 + ! set_min_D_mix = .true. - min_D_mix = 1d2 ! D_mix will be at least this large - min_center_Ye_for_min_D_mix = 0.47 ! min_D_mix is only used when center Ye >= this - ! i.e., when center Ye drops below this, min_D_mix is 0 - - - num_cells_for_smooth_brunt_B = 0 - - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 + min_D_mix = 1d2 ! D_mix will be at least this large + min_center_Ye_for_min_D_mix = 0.47 ! min_D_mix is only used when center Ye >= this + ! i.e., when center Ye drops below this, min_D_mix is 0 + + + num_cells_for_smooth_brunt_B = 0 + + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 / ! end of controls namelist &pgstar - - ! top level controls - !pause = .true. - ! if true, the code waits for user to enter a RETURN on the command line - + ! top level controls + + !pause = .true. + ! if true, the code waits for user to enter a RETURN on the command line + / ! end of pgstar namelist diff --git a/star/test_suite/diffusion_smoothness/inlist_zams_header b/star/test_suite/diffusion_smoothness/inlist_zams_header index a387c02e0..f855a2d43 100644 --- a/star/test_suite/diffusion_smoothness/inlist_zams_header +++ b/star/test_suite/diffusion_smoothness/inlist_zams_header @@ -1,24 +1,24 @@ &star_job - read_extra_star_job_inlist(1) = .true. - extra_star_job_inlist_name(1) = 'inlist_zams' + read_extra_star_job_inlist(1) = .true. + extra_star_job_inlist_name(1) = 'inlist_zams' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_zams' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_zams' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_zams' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_zams' / ! end of kap namelist @@ -26,15 +26,15 @@ &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_zams' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_zams' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_zams' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_zams' / ! end of pgstar namelist From b2aed385faac54570232b3fc7f2a2f951c4e70f2 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 11:36:01 -0400 Subject: [PATCH 25/66] changing file to svg --- .../test_suite/accreted_material_j/README.rst | 44 +---- .../docs/track1_000452.png | Bin 8085 -> 0 bytes .../docs/track1_000452.svg | 187 +----------------- .../inlist_accreted_material_j | 146 +++++++------- .../inlist_accreted_material_j_header | 20 +- .../accreted_material_j/inlist_pgstar | 10 +- .../accreted_material_j/inlist_zams | 54 ++--- .../accreted_material_j/inlist_zams_header | 20 +- 8 files changed, 129 insertions(+), 352 deletions(-) delete mode 100644 star/test_suite/accreted_material_j/docs/track1_000452.png diff --git a/star/test_suite/accreted_material_j/README.rst b/star/test_suite/accreted_material_j/README.rst index f952de46c..5ebf013fa 100644 --- a/star/test_suite/accreted_material_j/README.rst +++ b/star/test_suite/accreted_material_j/README.rst @@ -19,46 +19,12 @@ This test case has two parts. Click to see a larger view of a plot. pgstar commands used for the plots above: -.. code-block:: console +.. literalinclude:: ../../../star/test_suite/accreted_material_j/inlist_pgstar + :language: console + :start-at: &pgstar + :end-at: ! end of pgstar namelist - &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - !file_device = 'vcps' ! postscript - !file_extension = 'ps' - - pgstar_interval = 10 - - - History_Track1_win_flag = .true. - History_Track1_win_width = 12 - History_Track1_title = 'accreted_material_j' - History_Track1_xname = 'star_mass' - History_Track1_yname = 'log_total_angular_momentum' - History_Track1_yaxis_label = 'log J' - History_Track1_xaxis_label = 'M\d\(2281)' - History_Track1_reverse_xaxis = .false. - History_Track1_reverse_yaxis = .false. - - History_Track1_xmin = 20.0 - History_Track1_xmax = 25.0 - History_Track1_ymin = 51.9 - History_Track1_ymax = 52.7 - - ! file output - History_Track1_file_flag = .true. - History_Track1_file_dir = 'png' - History_Track1_file_prefix = 'track1_' - History_Track1_file_interval = 10 - History_Track1_file_width =12 - History_Track1_file_aspect_ratio = -1 - - / ! end of pgstar namelist - - - -Last-Updated: 30May2021 (MESA e37f76f) by fxt +Last-Updated: 06Aug2024 (MESA ba042c9d) by pmocz on C916PXT6XW in 178 seconds using 8 threads. diff --git a/star/test_suite/accreted_material_j/docs/track1_000452.png b/star/test_suite/accreted_material_j/docs/track1_000452.png deleted file mode 100644 index 3ce3eb0b0f9a8d7652a0a6f33e784cde10f7589c..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8085 zcmeHLX;c&0wnn|Jw&POU0a2nYkQNnM5D*pOj1e#@lT4;%o+Gmeq`VH$f{F$O!xU|l zfCwmq$QW%}5eWo|hy((y5F$f}21p2%s(PnF_j-5Tb>E-&^R35P@Kw&9_x|=t$kpS= ztQId=yFf!jV=?*2!IK&qa}W)U+35T^;N;Eh%SXV0#&H|_L*OL_esEC#;?L^ehZ;sL 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z!)+(Jikdu39;O7Ee67>35$12s)*IzqI<(1piG9JVT0dxUvyz@(bVKSeJbC1$Xsh8* z73=1`z#Lym+a%9flpVvqd z&vcC^?lT{r*C4w=xEAp4oG9@rH-(38CM_D2yIQ_o+VC#^->UhaUjDfjo5k1r%=_+0 Rpa|C?A3Aohc>gaK{|mksW;_4@ diff --git a/star/test_suite/accreted_material_j/docs/track1_000452.svg b/star/test_suite/accreted_material_j/docs/track1_000452.svg index 38926ebb7..3834ebefc 100644 --- a/star/test_suite/accreted_material_j/docs/track1_000452.svg +++ b/star/test_suite/accreted_material_j/docs/track1_000452.svg @@ -1,186 +1 @@ - - - - - - - - - - - - - + \ No newline at end of file diff --git a/star/test_suite/accreted_material_j/inlist_accreted_material_j b/star/test_suite/accreted_material_j/inlist_accreted_material_j index ec18219df..b7074fdfc 100644 --- a/star/test_suite/accreted_material_j/inlist_accreted_material_j +++ b/star/test_suite/accreted_material_j/inlist_accreted_material_j @@ -1,38 +1,38 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. - load_saved_model = .true. - load_model_filename = 'zams.mod' + load_saved_model = .true. + load_model_filename = 'zams.mod' - new_rotation_flag = .true. - change_rotation_flag = .true. - !relax_initial_omega_div_omega_crit = .true. - set_initial_omega_div_omega_crit = .true. - new_omega_div_omega_crit = 0.1 + new_rotation_flag = .true. + change_rotation_flag = .true. + !relax_initial_omega_div_omega_crit = .true. + set_initial_omega_div_omega_crit = .true. + new_omega_div_omega_crit = 0.1 - set_initial_dt = .true. - years_for_initial_dt = 1 + set_initial_dt = .true. + years_for_initial_dt = 1 - set_initial_model_number = .true. - initial_model_number = 0 + set_initial_model_number = .true. + initial_model_number = 0 - set_initial_age = .true. - initial_age = 0 + set_initial_age = .true. + initial_age = 0 - set_initial_cumulative_energy_error = .true. - new_cumulative_energy_error = 0d0 + set_initial_cumulative_energy_error = .true. + new_cumulative_energy_error = 0d0 - !change_D_omega_flag = .true. - !new_D_omega_flag = .true. + !change_D_omega_flag = .true. + !new_D_omega_flag = .true. - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - !required_termination_code_string = 'xa_central_lower_limit' - required_termination_code_string = 'star_mass_max_limit' + save_model_when_terminate = .true. + save_model_filename = 'final.mod' + !required_termination_code_string = 'xa_central_lower_limit' + required_termination_code_string = 'star_mass_max_limit' - pgstar_flag = .true. - save_pgstar_files_when_terminate = .true. + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / !end of star_job @@ -42,74 +42,74 @@ &kap - Zbase = 0.02 + Zbase = 0.02 / ! end of kap namelist &controls - scale_max_correction = 0.1d0 - ignore_species_in_max_correction = .true. + scale_max_correction = 0.1d0 + ignore_species_in_max_correction = .true. - energy_eqn_option = 'dedt' - use_gold2_tolerances = .true. + energy_eqn_option = 'dedt' + use_gold2_tolerances = .true. - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' - ! limit max_model_number as part of test_suite - max_model_number = 1000 + ! limit max_model_number as part of test_suite + max_model_number = 1000 - premix_omega = .true. + premix_omega = .true. - am_nu_visc_factor = 0 - am_D_mix_factor = 0.0333333333333333d00 - D_DSI_factor = 1 - D_SH_factor = 1 - D_SSI_factor = 1 - D_ES_factor = 1 - D_GSF_factor = 1 - D_ST_factor = 1 + am_nu_visc_factor = 0 + am_D_mix_factor = 0.0333333333333333d00 + D_DSI_factor = 1 + D_SH_factor = 1 + D_SSI_factor = 1 + D_ES_factor = 1 + D_GSF_factor = 1 + D_ST_factor = 1 - !set_min_D_mix = .true. - !min_D_mix = 1d10 + !set_min_D_mix = .true. + !min_D_mix = 1d10 - ! starting specifications - initial_mass = 20 ! in Msun units - initial_Z = 0.02 + ! starting specifications + initial_mass = 20 ! in Msun units + initial_Z = 0.02 - max_mdot_redo_cnt = 200 - min_years_dt_for_redo_mdot = 1d-5 - surf_omega_div_omega_crit_limit = 0.999d0 - surf_omega_div_omega_crit_tol = 0.055 - rotational_mdot_boost_fac = 1d10 - rotational_mdot_kh_fac = 1d10 - mdot_revise_factor = 1.1 - implicit_mdot_boost = 0.1 + max_mdot_redo_cnt = 200 + min_years_dt_for_redo_mdot = 1d-5 + surf_omega_div_omega_crit_limit = 0.999d0 + surf_omega_div_omega_crit_tol = 0.055 + rotational_mdot_boost_fac = 1d10 + rotational_mdot_kh_fac = 1d10 + mdot_revise_factor = 1.1 + implicit_mdot_boost = 0.1 - use_accreted_material_j = .true. - use_other_adjust_mdot = .true. + use_accreted_material_j = .true. + use_other_adjust_mdot = .true. - ! ratio of accreted am to keplerian - x_ctrl(1) = 0.1d0 - ! log10 accretion rate in msun/secyer - x_ctrl(2) = -3d0 + ! ratio of accreted am to keplerian + x_ctrl(1) = 0.1d0 + ! log10 accretion rate in msun/secyer + x_ctrl(2) = -3d0 - star_mass_max_limit = 25d0 + star_mass_max_limit = 25d0 - !varcontrol_target = 5d-4 - delta_lg_star_mass_limit = 2d-4 - delta_lg_star_mass_hard_limit = 4d-4 + !varcontrol_target = 5d-4 + delta_lg_star_mass_limit = 2d-4 + delta_lg_star_mass_hard_limit = 4d-4 ! output to files and terminal - photo_interval = 50 - profile_interval = 100 - max_num_profile_models = 3000 - history_interval = 10 - terminal_interval = 10 + photo_interval = 50 + profile_interval = 100 + max_num_profile_models = 3000 + history_interval = 10 + terminal_interval = 10 - write_header_frequency = 10 + write_header_frequency = 10 - !report_solver_progress = .true. + !report_solver_progress = .true. / diff --git a/star/test_suite/accreted_material_j/inlist_accreted_material_j_header b/star/test_suite/accreted_material_j/inlist_accreted_material_j_header index 2008891f8..dd7b8bc6f 100644 --- a/star/test_suite/accreted_material_j/inlist_accreted_material_j_header +++ b/star/test_suite/accreted_material_j/inlist_accreted_material_j_header @@ -2,24 +2,24 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_accreted_material_j' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_accreted_material_j' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_accreted_material_j' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_accreted_material_j' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_accreted_material_j' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_accreted_material_j' / ! end of kap namelist @@ -27,15 +27,15 @@ &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_accreted_material_j' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_accreted_material_j' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_pgstar' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_pgstar' / ! end of pgstar namelist diff --git a/star/test_suite/accreted_material_j/inlist_pgstar b/star/test_suite/accreted_material_j/inlist_pgstar index 5c3005611..29252822c 100644 --- a/star/test_suite/accreted_material_j/inlist_pgstar +++ b/star/test_suite/accreted_material_j/inlist_pgstar @@ -1,15 +1,11 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - - !file_device = 'vcps' ! postscript - !file_extension = 'ps' + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'vcps' ! postscript + file_extension = 'ps' pgstar_interval = 10 - History_Track1_win_flag = .true. History_Track1_win_width = 12 History_Track1_title = 'accreted_material_j' diff --git a/star/test_suite/accreted_material_j/inlist_zams b/star/test_suite/accreted_material_j/inlist_zams index 24c5b390d..95fd18487 100644 --- a/star/test_suite/accreted_material_j/inlist_zams +++ b/star/test_suite/accreted_material_j/inlist_zams @@ -2,16 +2,16 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. - create_pre_main_sequence_model = .true. + create_pre_main_sequence_model = .true. - save_model_when_terminate = .true. - save_model_filename = 'zams.mod' - required_termination_code_string = 'Lnuc_div_L_zams_limit' + save_model_when_terminate = .true. + save_model_filename = 'zams.mod' + required_termination_code_string = 'Lnuc_div_L_zams_limit' - !pgstar_flag = .true. + !pgstar_flag = .true. / ! end of star_job namelist @@ -21,31 +21,31 @@ &kap - kap_file_prefix = 'gs98' - Zbase = 0.02 + kap_file_prefix = 'gs98' + Zbase = 0.02 / ! end of kap namelist &controls - initial_mass = 20 ! in Msun units - initial_Z = 0.02 - - stop_near_zams = .true. - Lnuc_div_L_zams_limit = 0.9d0 - - ! limit max_model_number as part of test_suite - max_model_number = 10000 - use_gold2_tolerances = .true. - - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' - - photo_interval = 100 - profile_interval = 100 - history_interval = 5 - terminal_interval = 50 - + initial_mass = 20 ! in Msun units + initial_Z = 0.02 + + stop_near_zams = .true. + Lnuc_div_L_zams_limit = 0.9d0 + + ! limit max_model_number as part of test_suite + max_model_number = 10000 + use_gold2_tolerances = .true. + + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' + + photo_interval = 100 + profile_interval = 100 + history_interval = 5 + terminal_interval = 50 + / ! end of controls namelist diff --git a/star/test_suite/accreted_material_j/inlist_zams_header b/star/test_suite/accreted_material_j/inlist_zams_header index 83e825c58..3de76b840 100644 --- a/star/test_suite/accreted_material_j/inlist_zams_header +++ b/star/test_suite/accreted_material_j/inlist_zams_header @@ -2,24 +2,24 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_zams' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_zams' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_zams' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_zams' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_zams' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_zams' / ! end of kap namelist @@ -27,15 +27,15 @@ &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_zams' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_zams' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_zams' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_zams' / ! end of pgstar namelist From 8f47f3d4b4ad21364e95393fc3cb19a27de28577 Mon Sep 17 00:00:00 2001 From: EbF Date: Tue, 6 Aug 2024 13:29:33 -0400 Subject: [PATCH 26/66] [ci skip] update conductive flame test_suite --- star/test_suite/conductive_flame/README.rst | 9 ++++++++- .../conductive_flame/docs/grid1000597.png | Bin 0 -> 28477 bytes star/test_suite/conductive_flame/inlist_pgstar | 8 ++++++++ 3 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 star/test_suite/conductive_flame/docs/grid1000597.png diff --git a/star/test_suite/conductive_flame/README.rst b/star/test_suite/conductive_flame/README.rst index a029494ca..39e701244 100644 --- a/star/test_suite/conductive_flame/README.rst +++ b/star/test_suite/conductive_flame/README.rst @@ -47,7 +47,13 @@ routine ``flame_properties`` in the ``run_star_extras.f90``. -.. image:: ../../../star/test_suite/conductive_flame/docs/grid1000427.png +.. image:: ../../../star/test_suite/conductive_flame/docs/grid1000597.png + :width: 100% + +pgstar commands used for the plots above: +.. literalinclude:: ../../../star/test_suite/conductive_flame/inlist_pgstar + :language: console + .. |Timmes1992| replace:: `Timmes & Woosley (1992) `__ @@ -58,3 +64,4 @@ routine ``flame_properties`` in the ``run_star_extras.f90``. 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zlYbptPt}QcpqI|?E7w)jUx7osMPj!}6JMifqeE~wr7tGVpMD}UM<$HuqTy30l1(v= zJfONGFmT_pmi97^tUYfYcmRBNLeVU0Z6Nt_X3sN25(yBAV$PvR z5_CA%z9bOqR&4=iU*380xLOk7XoddF4Xb^x9UN5MqCga)X<^K)PcOiin2!uU1+v6vA^mpok3X_OYtmIq`EBxd-ysoF ziGkXpJJsnlAzAj)L75CEtvwNEXt)5Hl{{h>uQHcNm literal 0 HcmV?d00001 diff --git a/star/test_suite/conductive_flame/inlist_pgstar b/star/test_suite/conductive_flame/inlist_pgstar index adf6a72c3..f9cac16d4 100644 --- a/star/test_suite/conductive_flame/inlist_pgstar +++ b/star/test_suite/conductive_flame/inlist_pgstar @@ -1,5 +1,13 @@ &pgstar + + ! device + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + file_device = 'png' ! png + file_extension = 'png' + !file_device = 'vcps' ! postscript + !file_extension = 'ps' + pgstar_interval = 1 pause = .false. From 1adbf1aacb613ca96d356ed8cf53b606a5cf9727 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 15:26:49 -0400 Subject: [PATCH 27/66] [ci skip] Last-Run --- star/test_suite/1.3M_ms_high_Z/README.rst | 4 +++- star/test_suite/1.5M_with_diffusion/README.rst | 4 +++- star/test_suite/7M_prems_to_AGB/README.rst | 3 ++- star/test_suite/accreted_material_j/README.rst | 4 ++-- star/test_suite/conductive_flame/README.rst | 2 +- star/test_suite/conv_core_cpm/README.rst | 3 ++- star/test_suite/diffusion_smoothness/README.rst | 3 ++- star/test_suite/each_test_run | 8 ++++---- star/test_suite/high_mass/README.rst | 2 ++ 9 files changed, 21 insertions(+), 12 deletions(-) diff --git a/star/test_suite/1.3M_ms_high_Z/README.rst b/star/test_suite/1.3M_ms_high_Z/README.rst index 516d3e259..825b66871 100644 --- a/star/test_suite/1.3M_ms_high_Z/README.rst +++ b/star/test_suite/1.3M_ms_high_Z/README.rst @@ -45,4 +45,6 @@ The Python script used to create the figures above: :language: python -Last-Updated: 26Jul2024 (MESA afd04d7d) by pmocz on C916PXT6XW in 159 seconds using 8 threads. +Last-Updated: 27May2021 (MESA ebecc10) by fxt + +Last-Run: 26Jul2024 (MESA afd04d7d) by pmocz on C916PXT6XW in 159 seconds using 8 threads. diff --git a/star/test_suite/1.5M_with_diffusion/README.rst b/star/test_suite/1.5M_with_diffusion/README.rst index adf0f908f..79904265b 100644 --- a/star/test_suite/1.5M_with_diffusion/README.rst +++ b/star/test_suite/1.5M_with_diffusion/README.rst @@ -29,4 +29,6 @@ pgstar commands used for the plots above, e.g.: :end-at: ! end of pgstar namelist -Last-Updated: 17Jul2024 (MESA 0cc374fa) by pmocz on C916PXT6XW in 423 seconds using 8 threads. +Last-Updated: 27May2021 (MESA ebecc10) by fxt + +Last-Run: 17Jul2024 (MESA 0cc374fa) by pmocz on C916PXT6XW in 423 seconds using 8 threads. diff --git a/star/test_suite/7M_prems_to_AGB/README.rst b/star/test_suite/7M_prems_to_AGB/README.rst index dd63a4d53..ebc97e00f 100644 --- a/star/test_suite/7M_prems_to_AGB/README.rst +++ b/star/test_suite/7M_prems_to_AGB/README.rst @@ -23,5 +23,6 @@ pgstar commands used: :end-at: ! end of pgstar namelist +Last-Updated: 29May2021 (MESA e37f76f) by fxt -Last-Updated: 06Aug2024 (MESA f50b3763) by pmocz on C916PXT6XW in 410 seconds using 8 threads. +Last-Run: 06Aug2024 (MESA f50b3763) by pmocz on C916PXT6XW in 410 seconds using 8 threads. diff --git a/star/test_suite/accreted_material_j/README.rst b/star/test_suite/accreted_material_j/README.rst index 5ebf013fa..a743f35ac 100644 --- a/star/test_suite/accreted_material_j/README.rst +++ b/star/test_suite/accreted_material_j/README.rst @@ -25,6 +25,6 @@ pgstar commands used for the plots above: :end-at: ! end of pgstar namelist +Last-Updated: 30May2021 (MESA e37f76f) by fxt - -Last-Updated: 06Aug2024 (MESA ba042c9d) by pmocz on C916PXT6XW in 178 seconds using 8 threads. +Last-Run: 06Aug2024 (MESA ba042c9d) by pmocz on C916PXT6XW in 178 seconds using 8 threads. diff --git a/star/test_suite/conductive_flame/README.rst b/star/test_suite/conductive_flame/README.rst index 39e701244..5699b67b9 100644 --- a/star/test_suite/conductive_flame/README.rst +++ b/star/test_suite/conductive_flame/README.rst @@ -64,4 +64,4 @@ pgstar commands used for the plots above: Last-Updated: 2021-06-21 (mesa b2364463) by Josiah Schwab, + documentation 2024-01-22 EbF -Last-Updated: 06Aug2024 (MESA 7a3e4ee4) by EbF in 497 seconds using 10 threads. +Last-Run: 06Aug2024 (MESA 7a3e4ee4) by EbF in 497 seconds using 10 threads. diff --git a/star/test_suite/conv_core_cpm/README.rst b/star/test_suite/conv_core_cpm/README.rst index 37d3885be..df42d8f28 100644 --- a/star/test_suite/conv_core_cpm/README.rst +++ b/star/test_suite/conv_core_cpm/README.rst @@ -18,5 +18,6 @@ core if the model continued to evolve beyond its stopping condition. .. image:: ../../../star/test_suite/conv_core_cpm/docs/grid_000092.svg :width: 100% +Last-Updated: 2023-03-14 (MESA d6bbdf4) by Evan Bauer -Last-Updated: 17Jul2024 (MESA 5ef2ffac) by pmocz on C916PXT6XW in 125 seconds using 8 threads. +Last-Run: 17Jul2024 (MESA 5ef2ffac) by pmocz on C916PXT6XW in 125 seconds using 8 threads. diff --git a/star/test_suite/diffusion_smoothness/README.rst b/star/test_suite/diffusion_smoothness/README.rst index 409b5f6f4..c188eb447 100644 --- a/star/test_suite/diffusion_smoothness/README.rst +++ b/star/test_suite/diffusion_smoothness/README.rst @@ -22,5 +22,6 @@ pgstar commands used for the plot: :start-at: &pgstar :end-at: ! end of pgstar namelist +Last-Updated: 06Jun2021 (MESA 5be9e57) by fxt -Last-Updated: 06Aug2024 (MESA 8b152605) by pmocz on C916PXT6XW in 82 seconds using 8 threads. +Last-Run: 06Aug2024 (MESA 8b152605) by pmocz on C916PXT6XW in 82 seconds using 8 threads. diff --git a/star/test_suite/each_test_run b/star/test_suite/each_test_run index 4d53778a6..fcd26c6e1 100755 --- a/star/test_suite/each_test_run +++ b/star/test_suite/each_test_run @@ -92,11 +92,11 @@ function update_docs { if [ -e "$image_to_copy" ]; then cp "$image_to_copy" docs/ echo "Updated image $filename.$extension in the docs" - # replace the line "Last-Updated: ..." in README.rst - LAST_UPDATED="Last-Updated: $(date '+%d%b%Y') (MESA $(git rev-parse --short HEAD)) by $USER on $(hostname) in $(expr `date +%s` - $start_time) seconds using $OMP_NUM_THREADS threads." + # replace the line "Last-Run: ..." in README.rst + LAST_RUN="Last-Run: $(date '+%d%b%Y') (MESA $(git rev-parse --short HEAD)) by $USER on $(hostname) in $(expr `date +%s` - $start_time) seconds using $OMP_NUM_THREADS threads." # print name of - sed -i "" "/Last-Updated: .*/d" README.rst - echo $LAST_UPDATED >> README.rst + sed -i "" "/Last-Run: .*/d" README.rst + echo $LAST_RUN >> README.rst else echo "Error: $image_to_copy not found. Test may no longer be producing this file or may now be producing a different final snapshot number! Update test and README.rst accordingly." fi diff --git a/star/test_suite/high_mass/README.rst b/star/test_suite/high_mass/README.rst index d19299039..5e13c2cb8 100644 --- a/star/test_suite/high_mass/README.rst +++ b/star/test_suite/high_mass/README.rst @@ -23,4 +23,6 @@ pgstar commands used for the plots above: :language: console +Last-Updated: 12Jun2021 (MESA 5be9e57) by fxt. + Last-Updated: 17Jul2024 (MESA beef2c3b) by pmocz on C916PXT6XW in 67 seconds using 8 threads. From 6ce126d527f14487d7ac3028e891ad53b04a3f13 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 15:41:27 -0400 Subject: [PATCH 28/66] [ci skip] cond flame --- star/test_suite/conductive_flame/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/star/test_suite/conductive_flame/README.rst b/star/test_suite/conductive_flame/README.rst index 5699b67b9..65f60ba40 100644 --- a/star/test_suite/conductive_flame/README.rst +++ b/star/test_suite/conductive_flame/README.rst @@ -64,4 +64,4 @@ pgstar commands used for the plots above: Last-Updated: 2021-06-21 (mesa b2364463) by Josiah Schwab, + documentation 2024-01-22 EbF -Last-Run: 06Aug2024 (MESA 7a3e4ee4) by EbF in 497 seconds using 10 threads. +Last-Run: 06Aug2024 (MESA 1adbf1aa) by pmocz on C916PXT6XW in 327 seconds using 8 threads. From 76b223b5fd16f7c50ecf902caccbd5186f5de21d Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 15:42:44 -0400 Subject: [PATCH 29/66] update readme, lets test everything --- star/test_suite/starspots/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index c8082d3b6..990c0f06a 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -34,6 +34,6 @@ A plot of the HR diagram for the problem is included below: :width: 100% -Last updated by Meridith Joyce on 08/06/2024 +Last-Updated: 06Aug2024 by Meridith Joyce Last-Run: 06Aug2024 (MESA 7890d305) by pmocz on C916PXT6XW in 629 seconds using 8 threads. From 7d219a29650b6f2b84854b7036cdd10e2475f3a3 Mon Sep 17 00:00:00 2001 From: Jared Goldberg Date: Tue, 6 Aug 2024 16:27:37 -0400 Subject: [PATCH 30/66] Update CODEOWNERS Claiming co-ownership of ccsn_IIp --- CODEOWNERS | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CODEOWNERS b/CODEOWNERS index b2c27780c..3b4ac5903 100644 --- a/CODEOWNERS +++ b/CODEOWNERS @@ -56,7 +56,7 @@ star/test_suite/adjust_net star/test_suite/c13_pocket @fxt44 star/test_suite/carbon_kh @evbauer star/test_suite/cburn_inward -star/test_suite/ccsn_IIp @fxt44 +star/test_suite/ccsn_IIp @fxt44 @aurimontem star/test_suite/check_redo @fxt44 star/test_suite/check_pulse_atm @warrickball star/test_suite/conductive_flame @fxt44 @@ -89,7 +89,7 @@ star/test_suite/make_he_wd @evbauer @fxt44 star/test_suite/make_metals @fxt44 star/test_suite/make_o_ne_wd @fxt44 @evbauer star/test_suite/make_planets @fxt44 -star/test_suite/make_pre_ccsn_13bvn @Debraheem +star/test_suite/make_pre_ccsn_13bvn @Debraheem @aurimontem star/test_suite/make_sdb @evbauer star/test_suite/make_zams @fxt44 star/test_suite/make_zams_low_mass @fxt44 From 6fd47b39ca023dc0788b02ba71c5f2cc5eb2a39f Mon Sep 17 00:00:00 2001 From: aurimontem Date: Tue, 6 Aug 2024 16:54:24 -0400 Subject: [PATCH 31/66] [ci skip] update make_zams to include plot output --- star/test_suite/make_zams/README.rst | 2 + .../test_suite/make_zams/docs/grid_000192.svg | 477 +----------------- star/test_suite/make_zams/inlist_zams | 148 +++++- 3 files changed, 150 insertions(+), 477 deletions(-) diff --git a/star/test_suite/make_zams/README.rst b/star/test_suite/make_zams/README.rst index 37abfcce1..d79439608 100644 --- a/star/test_suite/make_zams/README.rst +++ b/star/test_suite/make_zams/README.rst @@ -168,3 +168,5 @@ pgstar commands used for the plot above: Last-Updated: 20Jun2021 (MESA e2acbc2) by fxt. + +Last-Run: 06Aug2024 (MESA 76b223b5) by aurimontem on MWKMFHK9LH in 65 seconds using 8 threads. diff --git a/star/test_suite/make_zams/docs/grid_000192.svg b/star/test_suite/make_zams/docs/grid_000192.svg index 27c9e4408..f9378b4e7 100644 --- a/star/test_suite/make_zams/docs/grid_000192.svg +++ b/star/test_suite/make_zams/docs/grid_000192.svg @@ -1,476 +1 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + \ No newline at end of file diff --git a/star/test_suite/make_zams/inlist_zams b/star/test_suite/make_zams/inlist_zams index 0061b07db..037803e28 100644 --- a/star/test_suite/make_zams/inlist_zams +++ b/star/test_suite/make_zams/inlist_zams @@ -10,6 +10,9 @@ save_model_filename = 'zams.mod' required_termination_code_string = 'Lnuc_div_L_zams_limit' + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. + / ! end of star_job namelist &eos @@ -18,7 +21,6 @@ &kap Zbase = 0.01d0 - kap_file_prefix = 'gs98' / ! end of kap namelist @@ -46,3 +48,147 @@ / ! end of controls namelist +&pgstar + + + file_device = 'vcps' ! postscript + file_extension = 'ps' + + pgstar_interval = 10 + + Abundance_win_flag = .false. + Abundance_win_width = 15 + Abundance_win_aspect_ratio = 0.75 + + Abundance_title = '' + Abundance_num_isos_to_show = 6 + + Abundance_which_isos_to_show(1) = 'h1' + Abundance_which_isos_to_show(2) = 'he3' + Abundance_which_isos_to_show(3) = 'he4' + Abundance_which_isos_to_show(4) = 'c12' + Abundance_which_isos_to_show(5) = 'n14' + Abundance_which_isos_to_show(6) = 'o16' + + num_abundance_line_labels = 4 + Abundance_line_txt_scale_factor = 1.0 + Abundance_legend_max_cnt = 0 + + Abundance_xaxis_name = 'mass' + Abundance_xaxis_reversed = .false. + Abundance_xmin = 0.0 + Abundance_xmax = 1.0 + + Abundance_log_mass_frac_min = -3.0 + Abundance_log_mass_frac_max = 0.3 + + + HR_win_flag = .false. + HR_win_width = 12 + HR_win_aspect_ratio = 1.2 ! aspect_ratio = height/width + HR_title = '' + + HR_logT_min = 3.5 + HR_logT_max = 4.5 + HR_logL_min = 1.0 + HR_logL_max = 3.0 + + + Text_Summary1_win_flag = .false. + Text_Summary1_win_width = 10 + Text_Summary1_win_aspect_ratio = 0.15 + + Text_Summary1_xleft = 0.01 + Text_Summary1_xright = 0.99 + Text_Summary1_ybot = 0.0 + Text_Summary1_ytop = 1.0 + Text_Summary1_txt_scale = 1.0 + + Text_Summary1_num_rows = 1 ! <= 20 + Text_Summary1_num_cols = 3 ! <= 20 + Text_Summary1_name(:,:) = '' + + Text_Summary1_name(1,1) = 'star_mass' + Text_Summary1_name(1,2) = 'log_LH' + Text_Summary1_name(1,3) = 'num_zones' + + Grid1_title = 'make_zams' + Grid1_win_flag = .false. + Grid1_win_width = 15 + Grid1_win_aspect_ratio = 0.6 + + Grid1_plot_name(:) = '' + Grid1_plot_row(:) = 1 ! number from 1 at top + Grid1_plot_rowspan(:) = 1 ! plot spans this number of rows + Grid1_plot_col(:) = 1 ! number from 1 at left + Grid1_plot_colspan(:) = 1 ! plot spans this number of columns + Grid1_plot_pad_left(:) = 0.0 ! fraction of full window width for padding on left + Grid1_plot_pad_right(:) = 0.0 ! fraction of full window width for padding on right + Grid1_plot_pad_top(:) = 0.0 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(:) = 0.0 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(:) = 0.7 ! multiply txt_scale for subplot by this + + Grid1_num_cols = 6 ! divide plotting region into this many equal width cols + Grid1_num_rows = 2 ! divide plotting region into this many equal height rows + Grid1_num_plots = 10 ! <= 10 + + pgstar_show_model_number = .true. + pgstar_model_scale = 1.0 + pgstar_model_lw = 3 + pgstar_model_disp = 2.0 + pgstar_model_coord = 0.92 + pgstar_model_fjust = 1.0 + + pgstar_show_age = .true. + pgstar_age_scale = 1.0 + pgstar_age_lw = 3 + pgstar_age_disp = 2.0 + pgstar_age_coord = -0.10 + pgstar_age_fjust = 0.0 + + Grid1_plot_name(1) = 'Text_Summary1' + Grid1_plot_row(1) = 1 ! number from 1 at top + Grid1_plot_rowspan(1) = 1 ! plot spans this number of rows + Grid1_plot_col(1) = 1 ! number from 1 at left + Grid1_plot_colspan(1) = 6 ! plot spans this number of columns + + Grid1_plot_pad_left(1) = -0.06 ! fraction of full window width for padding on left + Grid1_plot_pad_right(1) = 0.05 ! fraction of full window width for padding on right + Grid1_plot_pad_top(1) = -0.02 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(1) = 0.39 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(1) = 1.2 ! multiply txt_scale for subplot by this + + + Grid1_plot_name(2) = 'Abundance' + Grid1_plot_row(2) = 1 ! number from 1 at top + Grid1_plot_rowspan(2) = 2 ! plot spans this number of rows + Grid1_plot_col(2) = 1 ! number from 1 at left + Grid1_plot_colspan(2) = 3 ! plot spans this number of columns + + Grid1_plot_pad_left(2) = -0.05 ! fraction of full window width for padding on left + Grid1_plot_pad_right(2) = 0.10 ! fraction of full window width for padding on right + Grid1_plot_pad_top(2) = 0.03 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(2) = 0.03 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(2) = 0.7 ! multiply txt_scale for subplot by this + + + Grid1_plot_name(3) = 'HR' + Grid1_plot_row(3) = 1 ! number from 1 at top + Grid1_plot_rowspan(3) = 2 ! plot spans this number of rows + Grid1_plot_col(3) = 5 ! Number from 1 at left + Grid1_plot_colspan(3) = 3 ! plot spans this number of columns + + Grid1_plot_pad_left(3) = -0.15 ! fraction of full window width for padding on left + Grid1_plot_pad_right(3) = 0.20 ! fraction of full window width for padding on right + Grid1_plot_pad_top(3) = 0.03 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(3) = 0.03 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(3) = 0.7 ! multiply txt_scale for subplot by this + + + Grid1_file_flag = .true. + Grid1_file_dir = 'pgstar_out' + Grid1_file_prefix = 'grid_' + Grid1_file_interval = 10000 + Grid1_file_width = -1 ! (inches) negative means use same value as for window + + / ! end of pgstar namelist From 6f3dbc0aaf9451f1dc04739c8c45ea15053683a8 Mon Sep 17 00:00:00 2001 From: aurimontem Date: Tue, 6 Aug 2024 16:58:58 -0400 Subject: [PATCH 32/66] [ci skip] update readme --- star/test_suite/make_zams/README.rst | 151 +-------------------------- 1 file changed, 2 insertions(+), 149 deletions(-) diff --git a/star/test_suite/make_zams/README.rst b/star/test_suite/make_zams/README.rst index d79439608..d964fd65c 100644 --- a/star/test_suite/make_zams/README.rst +++ b/star/test_suite/make_zams/README.rst @@ -16,155 +16,8 @@ This test case has 1 part. Click to see a larger version of a plot. pgstar commands used for the plot above: -.. code-block:: console - - &pgstar - - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - !file_device = 'png' ! png - !file_extension = 'png' - - file_device = 'vcps' ! postscript - file_extension = 'ps' - - pgstar_interval = 10 - - Abundance_win_flag = .false. - Abundance_win_width = 15 - Abundance_win_aspect_ratio = 0.75 - - Abundance_title = '' - Abundance_num_isos_to_show = 6 - - Abundance_which_isos_to_show(1) = 'h1' - Abundance_which_isos_to_show(2) = 'he3' - Abundance_which_isos_to_show(3) = 'he4' - Abundance_which_isos_to_show(4) = 'c12' - Abundance_which_isos_to_show(5) = 'n14' - Abundance_which_isos_to_show(6) = 'o16' - - num_abundance_line_labels = 4 - Abundance_line_txt_scale_factor = 1.0 - Abundance_legend_max_cnt = 0 - - Abundance_xaxis_name = 'mass' - Abundance_xaxis_reversed = .false. - Abundance_xmin = 0.0 - Abundance_xmax = 1.0 - - Abundance_log_mass_frac_min = -3.0 - Abundance_log_mass_frac_max = 0.3 - - - HR_win_flag = .false. - HR_win_width = 12 - HR_win_aspect_ratio = 1.2 ! aspect_ratio = height/width - HR_title = '' - - HR_logT_min = 3.5 - HR_logT_max = 4.5 - HR_logL_min = 1.0 - HR_logL_max = 3.0 - - - Text_Summary1_win_flag = .false. - Text_Summary1_win_width = 10 - Text_Summary1_win_aspect_ratio = 0.15 - - Text_Summary1_xleft = 0.01 - Text_Summary1_xright = 0.99 - Text_Summary1_ybot = 0.0 - Text_Summary1_ytop = 1.0 - Text_Summary1_txt_scale = 1.0 - - Text_Summary1_num_rows = 1 ! <= 20 - Text_Summary1_num_cols = 3 ! <= 20 - Text_Summary1_name(:,:) = '' - - Text_Summary1_name(1,1) = 'star_mass' - Text_Summary1_name(1,2) = 'log_LH' - Text_Summary1_name(1,3) = 'num_zones' - - Grid1_title = 'make_zams' - Grid1_win_flag = .true. - Grid1_win_width = 15 - Grid1_win_aspect_ratio = 0.6 - - Grid1_plot_name(:) = '' - Grid1_plot_row(:) = 1 ! number from 1 at top - Grid1_plot_rowspan(:) = 1 ! plot spans this number of rows - Grid1_plot_col(:) = 1 ! number from 1 at left - Grid1_plot_colspan(:) = 1 ! plot spans this number of columns - Grid1_plot_pad_left(:) = 0.0 ! fraction of full window width for padding on left - Grid1_plot_pad_right(:) = 0.0 ! fraction of full window width for padding on right - Grid1_plot_pad_top(:) = 0.0 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(:) = 0.0 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(:) = 0.7 ! multiply txt_scale for subplot by this - - Grid1_num_cols = 6 ! divide plotting region into this many equal width cols - Grid1_num_rows = 2 ! divide plotting region into this many equal height rows - Grid1_num_plots = 10 ! <= 10 - - pgstar_show_model_number = .true. - pgstar_model_scale = 1.0 - pgstar_model_lw = 3 - pgstar_model_disp = 2.0 - pgstar_model_coord = 0.92 - pgstar_model_fjust = 1.0 - - pgstar_show_age = .true. - pgstar_age_scale = 1.0 - pgstar_age_lw = 3 - pgstar_age_disp = 2.0 - pgstar_age_coord = -0.10 - pgstar_age_fjust = 0.0 - - Grid1_plot_name(1) = 'Text_Summary1' - Grid1_plot_row(1) = 1 ! number from 1 at top - Grid1_plot_rowspan(1) = 1 ! plot spans this number of rows - Grid1_plot_col(1) = 1 ! number from 1 at left - Grid1_plot_colspan(1) = 6 ! plot spans this number of columns - - Grid1_plot_pad_left(1) = -0.06 ! fraction of full window width for padding on left - Grid1_plot_pad_right(1) = 0.05 ! fraction of full window width for padding on right - Grid1_plot_pad_top(1) = -0.02 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(1) = 0.39 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(1) = 1.2 ! multiply txt_scale for subplot by this - - - Grid1_plot_name(2) = 'Abundance' - Grid1_plot_row(2) = 1 ! number from 1 at top - Grid1_plot_rowspan(2) = 2 ! plot spans this number of rows - Grid1_plot_col(2) = 1 ! number from 1 at left - Grid1_plot_colspan(2) = 3 ! plot spans this number of columns - - Grid1_plot_pad_left(2) = -0.05 ! fraction of full window width for padding on left - Grid1_plot_pad_right(2) = 0.10 ! fraction of full window width for padding on right - Grid1_plot_pad_top(2) = 0.03 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(2) = 0.03 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(2) = 0.7 ! multiply txt_scale for subplot by this - - - Grid1_plot_name(3) = 'HR' - Grid1_plot_row(3) = 1 ! number from 1 at top - Grid1_plot_rowspan(3) = 2 ! plot spans this number of rows - Grid1_plot_col(3) = 5 ! Number from 1 at left - Grid1_plot_colspan(3) = 3 ! plot spans this number of columns - - Grid1_plot_pad_left(3) = -0.15 ! fraction of full window width for padding on left - Grid1_plot_pad_right(3) = 0.20 ! fraction of full window width for padding on right - Grid1_plot_pad_top(3) = 0.03 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(3) = 0.03 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(3) = 0.7 ! multiply txt_scale for subplot by this - - - Grid1_file_flag = .true. - Grid1_file_dir = 'pgstar_out' - Grid1_file_prefix = 'grid_' - Grid1_file_interval = 10000 - Grid1_file_width = -1 ! (inches) negative means use same value as for window - - / ! end of pgstar namelist +.. literalinclude:: ../../../star/test_suite/high_mass/inlist_pgstar +:language: console Last-Updated: 20Jun2021 (MESA e2acbc2) by fxt. From 4beba1c4e5040f2f7d49ac4b8fc5ddd2bdc727f3 Mon Sep 17 00:00:00 2001 From: aurimontem Date: Tue, 6 Aug 2024 17:02:31 -0400 Subject: [PATCH 33/66] [ci skip] update readme again --- star/test_suite/make_zams/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/star/test_suite/make_zams/README.rst b/star/test_suite/make_zams/README.rst index d964fd65c..705f1280d 100644 --- a/star/test_suite/make_zams/README.rst +++ b/star/test_suite/make_zams/README.rst @@ -16,7 +16,7 @@ This test case has 1 part. Click to see a larger version of a plot. pgstar commands used for the plot above: -.. literalinclude:: ../../../star/test_suite/high_mass/inlist_pgstar +.. literalinclude:: ../../../star/test_suite/make_zams/inlist_zams :language: console From ed8c74d727cd12f8ab01209e413e98745b9635aa Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 18:02:48 -0400 Subject: [PATCH 34/66] [ci skip] doc fizes --- star/test_suite/conductive_flame/README.rst | 1 + star/test_suite/make_zams/README.rst | 4 +++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/star/test_suite/conductive_flame/README.rst b/star/test_suite/conductive_flame/README.rst index 65f60ba40..b42d5f4f4 100644 --- a/star/test_suite/conductive_flame/README.rst +++ b/star/test_suite/conductive_flame/README.rst @@ -51,6 +51,7 @@ routine ``flame_properties`` in the ``run_star_extras.f90``. :width: 100% pgstar commands used for the plots above: + .. literalinclude:: ../../../star/test_suite/conductive_flame/inlist_pgstar :language: console diff --git a/star/test_suite/make_zams/README.rst b/star/test_suite/make_zams/README.rst index 705f1280d..38d225508 100644 --- a/star/test_suite/make_zams/README.rst +++ b/star/test_suite/make_zams/README.rst @@ -17,7 +17,9 @@ This test case has 1 part. Click to see a larger version of a plot. pgstar commands used for the plot above: .. literalinclude:: ../../../star/test_suite/make_zams/inlist_zams -:language: console + :language: console + :start-at: &pgstar + :end-at: ! end of pgstar namelist Last-Updated: 20Jun2021 (MESA e2acbc2) by fxt. From 0b40398bde0f09d44acc72beee80774046d98867 Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 6 Aug 2024 18:16:41 -0400 Subject: [PATCH 35/66] [ci skip] spelling --- docs/source/test_suite.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/test_suite.rst b/docs/source/test_suite.rst index b00038a8f..33e0367ce 100644 --- a/docs/source/test_suite.rst +++ b/docs/source/test_suite.rst @@ -309,7 +309,7 @@ on the horizontal branch (HB) through core helium burning. :ref:`high_mass` ^^^^^^^^^^^^^^^^ -This test case checks the evolution of a 300 |Msun|, Z = 1e-4 metallicity, model through core hydrogen depletion. +This test case checks the evolution of a 300 |Msun|, Z = 1e-5 metallicity, model through core hydrogen depletion. :ref:`high_z` ^^^^^^^^^^^^^ @@ -713,7 +713,7 @@ optimise model parameters using the ``astero`` module. ^^^^^^^^^^^^^^^^^^^ Each of these test cases runs a handful of iterations of a crude -optimisation, principally to increase test coverage across the +optimization, principally to increase test coverage across the ``astero`` module. :ref:`surface_effects` From 731b288e6f7a6e0f098c65a3e14bf6ba768cd292 Mon Sep 17 00:00:00 2001 From: Bill Wolf Date: Wed, 7 Aug 2024 10:40:07 -0500 Subject: [PATCH 36/66] [ci skip] Update documentation for wd_nova_burst. * Add python plot script for new plot. * Add new plot for wd_nova_burst. * Remove pgstar plot and code from README.rst. * Add new plot to README.rst. --- star/test_suite/wd_nova_burst/README.rst | 76 +- .../wd_nova_burst/docs/wd_nova_burst_grid.svg | 8443 +++++++++++++++++ star/test_suite/wd_nova_burst/plot.py | 209 + 3 files changed, 8658 insertions(+), 70 deletions(-) create mode 100644 star/test_suite/wd_nova_burst/docs/wd_nova_burst_grid.svg create mode 100644 star/test_suite/wd_nova_burst/plot.py diff --git a/star/test_suite/wd_nova_burst/README.rst b/star/test_suite/wd_nova_burst/README.rst index b0caf99d2..142305d90 100644 --- a/star/test_suite/wd_nova_burst/README.rst +++ b/star/test_suite/wd_nova_burst/README.rst @@ -36,86 +36,22 @@ and when the luminosity falls below 1e3 Lsun a nova cycle is considered finished have finished burst -.. image:: ../../../star/test_suite/wd_nova_burst/docs/grid8_000586.svg +.. image:: ../../../star/test_suite/wd_nova_burst/docs/wd_nova_burst_grid.svg :width: 100% |br| -pgstar commands used for the plots above: - -.. code-block:: console - - &pgstar - - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - !file_device = 'png' ! png - !file_extension = 'png' - - file_device = 'vcps' ! postscript - file_extension = 'ps' - - pgstar_interval = 1 - - Grid8_win_flag = .true. - Grid8_win_width = 12 - Grid8_title = 'wd_nova_burst' - - Summary_Burn_xaxis_name = 'logxq' - Summary_Burn_xaxis_reversed = .true. - Summary_Burn_xmin = -14 ! -101d0 ! only used if /= -101d0 - Summary_Burn_xmax = -3 ! -101d0 ! only used if /= -101d0 - Summary_Burn_title = ' ' - - - Abundance_title = ' ' - Abundance_xaxis_name = 'logxq' - Abundance_xaxis_reversed = .true. - Abundance_xmin = -14 ! -101d0 ! only used if /= -101d0 - Abundance_xmax = -3 ! -101d0 ! only used if /= -101d0 - Abundance_txt_scale = 0.8 - Abundance_legend_max_cnt = 0 - - HR_title = ' ' - HR_txt_scale = 0.8 - HR_logT_min = 4.5 - HR_logT_max = 6.0 - HR_logL_min = -1.0 - HR_logL_max = 5.0 - - - TRho_title = ' ' - TRho_txt_scale = 0.8 - TRho_logT_min = -101d0 - TRho_logT_max = -101d0 - TRho_logRho_min = -101d0 - TRho_logRho_max = -101d0 - - - TRho_Profile_title = ' ' - TRho_Profile_txt_scale = 0.7 - TRho_Profile_xmin = -8.0 - TRho_Profile_xmax = 9.0 - TRho_Profile_ymin = 5.0 - TRho_Profile_ymax = 9.0 - - Text_Summary1_name(5,2) = 'time_step_sec' - Text_Summary1_name(6,2) = 'max_tau_conv' - - Grid8_file_flag = .true. - Grid8_file_dir = 'pgstar_out' - Grid8_file_prefix = 'grid8_' - Grid8_file_interval = 10000 - Grid8_file_width = -1 - Grid8_file_aspect_ratio = -1 - - / ! end of pgstar namelist +The Python script used to create the figures above: +.. literalinclude:: ../../../star/test_suite/wd_nova_burst/plot.py + :language: python -Last-Updated: 08Jul2021 (MESA 094ff71) by fxt. +Last-Updated: 07Aug2024 (MESA 0b40398b) by wmwolf. .. # define a hard line break for HTML .. |br| raw:: html
+Last-Run: 07Aug2024 (MESA 0b40398b) by wmwolf on Hercules in 431 seconds using 20 threads. diff --git a/star/test_suite/wd_nova_burst/docs/wd_nova_burst_grid.svg b/star/test_suite/wd_nova_burst/docs/wd_nova_burst_grid.svg new file mode 100644 index 000000000..5ee57a994 --- /dev/null +++ b/star/test_suite/wd_nova_burst/docs/wd_nova_burst_grid.svg @@ -0,0 +1,8443 @@ + + + + + + + + 2024-08-07T10:36:47.644034 + image/svg+xml + + + Matplotlib v3.8.1, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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100644 index 000000000..9b72f1b30 --- /dev/null +++ b/star/test_suite/wd_nova_burst/plot.py @@ -0,0 +1,209 @@ +import matplotlib.pyplot as plt +import numpy as np +import os +import mesa_reader as mr + +# pip install git+https://github.com/wmwolf/py_mesa_reader.git + +# if the directory plt_out/ does not exits, make it +if not os.path.exists("plt_out"): + os.makedirs("plt_out") + +# "MESA" styles for plotting +# note that this requires having a LaTeX installation locally. +# If you don't have that, you can comment out the "text.usetex" line. +plt.rcParams['figure.figsize'] = (3.38, 2.535) +plt.rcParams['lines.markersize'] = 4 +plt.rcParams['lines.linewidth'] = 1.5 +plt.rcParams["text.usetex"] = True +plt.rcParams["font.size"] = 10 +plt.rcParams["font.family"] = "serif" +plt.rcParams["font.serif"] = "Computer Modern Roman" +plt.rcParams['axes.titlesize'] = 'medium' +plt.rcParams['axes.labelsize'] = 'medium' +plt.rcParams['legend.fontsize'] = 8 +plt.rcParams['legend.frameon'] = False +plt.rcParams['figure.dpi'] = 300 + +plt.rcParams['xtick.direction'] = 'in' +plt.rcParams['ytick.direction'] = 'in' +plt.rcParams['xtick.top'] = True +plt.rcParams['ytick.right'] = True +plt.rcParams['xtick.minor.visible'] = True +plt.rcParams['ytick.minor.visible'] = True + +plt.rcParams['savefig.bbox'] = 'tight' +plt.rcParams['savefig.pad_inches'] = 0.1 +plt.rcParams['savefig.dpi'] = 300 +plt.rcParams['savefig.format'] = 'svg' + +plt.rcParams['axes.formatter.use_mathtext'] = True + +# read in the history data from MESA +l = mr.MesaLogDir("LOGS") +h = l.history +p = l.profile_data() + +import matplotlib.pyplot as plt +from matplotlib.gridspec import GridSpec + +# Create a figure +fig = plt.figure(figsize=(10, 6)) + +# Create a GridSpec with 6 rows and 3 columns +gs_outer = fig.add_gridspec(1,2, width_ratios=[1, 2]) +gs_left = gs_outer[0].subgridspec(2, 1, hspace=0.3) +gs_right = gs_outer[1].subgridspec(3, 2, hspace=0, wspace=0.75) + +# First column: Two plots of roughly equal height +ax1 = fig.add_subplot(gs_left[0]) +ax2 = fig.add_subplot(gs_left[1]) + +# Second column: Three stacked axes sharing the same x-axis +ax3 = fig.add_subplot(gs_right[0, 0]) +ax4 = fig.add_subplot(gs_right[1, 0]) +ax5 = fig.add_subplot(gs_right[2, 0]) + +# Third column: Three stacked axes sharing a different x-axis +ax6 = fig.add_subplot(gs_right[0, 1]) +ax7 = fig.add_subplot(gs_right[1, 1]) +ax8 = fig.add_subplot(gs_right[2, 1]) + +# HR diagram +ax1.loglog(h.Teff, h.L) +ax1.set_xlabel(r"Effective Temperature [K]") +ax1.set_ylabel(r"Luminosity [$L_{\odot}$]") +ax1.invert_xaxis() +# add marker to last point +ax1.plot(h.Teff[-1], h.L[-1], 'o', color='C3') + +# T-Rho Profile +# load data from MESA_DIR and save to arrays in T-Rho space +plot_info_dir = os.path.join(os.environ['MESA_DIR'], 'data/star_data/plot_info') + +# degeneracy data +psi4_file = os.path.join(plot_info_dir, 'psi4.data') +psi4_data = np.genfromtxt(psi4_file) +psi4_xs = 10**np.array(psi4_data.T[0]) +psi4_ys = 10**np.array(psi4_data.T[1]) + +# hydrogen burn line +hydrogen_burn_file = os.path.join(plot_info_dir, 'hydrogen_burn.data') +hydrogen_burn_data = np.genfromtxt(hydrogen_burn_file) +hydrogen_burn_xs = 10**np.array(hydrogen_burn_data.T[0]) +hydrogen_burn_ys = 10**np.array(hydrogen_burn_data.T[1]) + +# helium burn line +helium_burn_file = os.path.join(plot_info_dir, 'helium_burn.data') +helium_burn_data = np.genfromtxt(helium_burn_file) +helium_burn_xs = 10**np.array(helium_burn_data.T[0]) +helium_burn_ys = 10**np.array(helium_burn_data.T[1]) + +# plot raw T-Rho data; sets limits for us +ax2.loglog(p.Rho, p.T) + +# plot psi4 and hydrogen burn lines +# preserve limits... shouldn't have to do it like this, but +# autoscale commands always seem to fail. +x_left, x_right = ax2.get_xlim() +y_bottom, y_top = ax2.get_ylim() +ax2.plot(psi4_xs, psi4_ys, color='lightgrey', ls=':', zorder=-5) +ax2.plot(hydrogen_burn_xs, hydrogen_burn_ys, ls='--', color='lightgrey', zorder=-5) +ax2.plot(helium_burn_xs, helium_burn_ys, ls='--', color='lightgrey', zorder=-5) +ax2.set_xlim(x_left, x_right) +ax2.set_ylim(y_bottom, y_top) +ax2.set_xlabel(r"Density [g/cm$^3$]") +ax2.set_ylabel(r"Temperature [K]") + +# plot strong burning zones +high_burning = np.where(p.eps_nuc > 1e7, True, False) +mid_burning = np.where((p.eps_nuc > 1e3) & (p.eps_nuc < 1e7), True, False) +low_burning = np.where((p.eps_nuc > 1) & (p.eps_nuc < 1e3), True, False) +# temporarily set butt style to round +save_capstyle = plt.rcParams['lines.solid_capstyle'] +plt.rcParams['lines.solid_capstyle'] = 'round' +ax2.plot(p.Rho[high_burning], p.T[high_burning], marker='o', ls='', ms=6, color='C3', zorder=-1) +ax2.plot([], [], lw=6, color='C3', label=r"$\epsilon_{\mathrm{nuc}} > 10^7\,\mathrm{erg/g/s}$") +ax2.plot(p.Rho[mid_burning], p.T[mid_burning], marker='o', ls='', ms=4.5, color='C1', zorder=-2) +ax2.plot([], [], color='C1', lw=4.5, label=r"$\epsilon_{\mathrm{nuc}} > 10^3\,\mathrm{erg/g/s}$") +ax2.plot(p.Rho[low_burning], p.T[low_burning], marker='o', ls='', ms=3, color='goldenrod', zorder=-3) +ax2.plot([], [], color='goldenrod', lw=3, label=r"$\epsilon_{\mathrm{nuc}} > 1\,\mathrm{erg/g/s}$") +ax2.legend(loc='lower right') +# restore capstyle +plt.rcParams['lines.solid_capstyle'] = save_capstyle + +# time series for last 5 years +window = 5 + +# top panel: photospheric and H-burning luminosities +mask = h.star_age > (max(h.star_age) - window) +ax3.set_title("Last 5 Years") +ax3.semilogy(h.star_age[mask], h.L[mask], label=r"$L$") +ax3.semilogy(h.star_age[mask], h.LH[mask], ls='--', label=r"$L_{\mathrm{H}}$") +ax3.set_ylabel(r"Luminosity [$L_{\odot}$]") +ax3.legend(loc='upper left') +ax3.set_xticklabels([]) + +# temperature and radius +ax4.semilogy(h.star_age[mask], h.Teff[mask], label=r'$T_{\mathrm{eff}}$') +ax4.semilogy([], [], label=r'$R$', ls='--', color='C1') +ax4.legend(loc='upper left') +ax4b = ax4.twinx() +ax4b.semilogy(h.star_age[mask], h.R[mask], ls='--', color='C1') +ax4.set_ylabel(r"Eff. Temp. [K]", color='C0') +ax4b.set_ylabel('Radius [$R_{\odot}$]', color='C1') +ax4.set_xticklabels([]) + +# mass loss and envelope mass +ax5.semilogy(h.star_age[mask], h.star_mass[mask] - h.he_core_mass[mask], label=r'$\Delta M_{\mathrm{H}}$') +ax5.semilogy([], [], ls='--', label=r'$|\dot{M}|$') +ax5.legend(loc='center left') +ax5.set_ylabel(r"Envelope Mass [$M_{\odot}$]", color='C0') +ax5b = ax5.twinx() +ax5b.semilogy(h.star_age[mask], h.abs_mdot[mask], ls='--', color='C1') +ax5b.set_ylabel(r"$\left\vert\dot{M}\right\vert$ [$M_{\odot}$/yr]", color='C1') + +ax5.set_xlabel(r"Star Age [yr]") + +# profile at the end of the simulation +# first up, common isotope mass fractions +xm = p.star_mass - p.mass +for iso in ['h1', 'he4', 'c12', 'n14', 'o16']: + element = ''.join([i for i in iso if not i.isdigit()]).capitalize() + mass_number = ''.join([i for i in iso if i.isdigit()]) + tex_iso = r"${}^{" + mass_number + r"}$" + element + ax6.loglog(xm, p.data(iso), label=tex_iso) + +ax6.set_title("Final Profile") +ax6.set_ylim(4e-5, 1.5) +ax6.legend(loc='lower left') +ax6.set_ylabel(r"Mass Fraction") +ax6.set_xticklabels([]) + +# nuclear energy generation rates +ax7.loglog(xm, p.eps_nuc, label=r"$\epsilon_{\mathrm{nuc}}$") +ax7.loglog(xm, p.pp, ls='--', label=r"$\epsilon_{\mathrm{pp}}$") +ax7.loglog(xm, p.cno, ls=':', label=r"$\epsilon_{\mathrm{CNO}}$") +ax7.legend(loc='upper right') +ax7.set_ylabel(r"Specific Power [erg/g/s]") +ax7.set_xticklabels([]) +ax7.set_ylim(1e-6, 1e10) + +# basic thermodynamic quantities +ax8.loglog(xm, p.Rho, label='$\\rho$') +ax8.loglog([], [], ls='--', label='$T$') +ax8.set_ylim(2e-3, 2e6) +ax8.set_ylabel(r"Density [g/cm$^3$]", color='C0') +ax8b = ax8.twinx() +ax8b.loglog(xm, p.T, ls='--', color='C1') +ax8b.set_ylim(2e6, 1.25e8) +ax8b.set_ylabel(r"Temperature [K]", color='C1') +ax8.legend(loc='upper right') + +for ax in [ax6, ax7, ax8]: + ax.set_xlim(8e-4, 1e-10) +ax8.set_xlabel(r"Exterior Mass Coordinate [M$_{\odot}$]") + + +fig.savefig("plt_out/wd_nova_burst_grid.svg") + From 02833a9d931b7496d4df08758dbda28dcbf9a2ff Mon Sep 17 00:00:00 2001 From: pmocz Date: Wed, 7 Aug 2024 14:42:41 -0400 Subject: [PATCH 37/66] [ci skip] line break was giving docs warning --- star/test_suite/wd_nova_burst/README.rst | 6 ------ 1 file changed, 6 deletions(-) diff --git a/star/test_suite/wd_nova_burst/README.rst b/star/test_suite/wd_nova_burst/README.rst index 142305d90..caed02106 100644 --- a/star/test_suite/wd_nova_burst/README.rst +++ b/star/test_suite/wd_nova_burst/README.rst @@ -40,7 +40,6 @@ and when the luminosity falls below 1e3 Lsun a nova cycle is considered finished :width: 100% -|br| The Python script used to create the figures above: .. literalinclude:: ../../../star/test_suite/wd_nova_burst/plot.py @@ -49,9 +48,4 @@ The Python script used to create the figures above: Last-Updated: 07Aug2024 (MESA 0b40398b) by wmwolf. - -.. # define a hard line break for HTML -.. |br| raw:: html - -
Last-Run: 07Aug2024 (MESA 0b40398b) by wmwolf on Hercules in 431 seconds using 20 threads. From 3b9e5bb140bf6af988c5eba224bb82819b3603c0 Mon Sep 17 00:00:00 2001 From: pmocz Date: Wed, 7 Aug 2024 15:00:00 -0400 Subject: [PATCH 38/66] [ci skip] autoformat inlists and add fxts old pgstar plotting routine as an inlist in wd_nova_burst --- star/test_suite/wd_nova_burst/inlist_pgstar | 64 +++++ star/test_suite/wd_nova_burst/inlist_setup | 212 +++++++-------- .../wd_nova_burst/inlist_setup_header | 20 +- .../wd_nova_burst/inlist_wd_nova_burst | 248 +++++++++--------- .../wd_nova_burst/inlist_wd_nova_burst_header | 20 +- 5 files changed, 314 insertions(+), 250 deletions(-) create mode 100644 star/test_suite/wd_nova_burst/inlist_pgstar diff --git a/star/test_suite/wd_nova_burst/inlist_pgstar b/star/test_suite/wd_nova_burst/inlist_pgstar new file mode 100644 index 000000000..5a8d914c3 --- /dev/null +++ b/star/test_suite/wd_nova_burst/inlist_pgstar @@ -0,0 +1,64 @@ +&pgstar + + file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background + !file_device = 'png' ! png + !file_extension = 'png' + + file_device = 'vcps' ! postscript + file_extension = 'ps' + + pgstar_interval = 1 + + Grid8_win_flag = .true. + Grid8_win_width = 12 + Grid8_title = 'wd_nova_burst' + + Summary_Burn_xaxis_name = 'logxq' + Summary_Burn_xaxis_reversed = .true. + Summary_Burn_xmin = -14 ! -101d0 ! only used if /= -101d0 + Summary_Burn_xmax = -3 ! -101d0 ! only used if /= -101d0 + Summary_Burn_title = ' ' + + + Abundance_title = ' ' + Abundance_xaxis_name = 'logxq' + Abundance_xaxis_reversed = .true. + Abundance_xmin = -14 ! -101d0 ! only used if /= -101d0 + Abundance_xmax = -3 ! -101d0 ! only used if /= -101d0 + Abundance_txt_scale = 0.8 + Abundance_legend_max_cnt = 0 + + HR_title = ' ' + HR_txt_scale = 0.8 + HR_logT_min = 4.5 + HR_logT_max = 6.0 + HR_logL_min = -1.0 + HR_logL_max = 5.0 + + + TRho_title = ' ' + TRho_txt_scale = 0.8 + TRho_logT_min = -101d0 + TRho_logT_max = -101d0 + TRho_logRho_min = -101d0 + TRho_logRho_max = -101d0 + + + TRho_Profile_title = ' ' + TRho_Profile_txt_scale = 0.7 + TRho_Profile_xmin = -8.0 + TRho_Profile_xmax = 9.0 + TRho_Profile_ymin = 5.0 + TRho_Profile_ymax = 9.0 + + Text_Summary1_name(5,2) = 'time_step_sec' + Text_Summary1_name(6,2) = 'max_tau_conv' + + Grid8_file_flag = .true. + Grid8_file_dir = 'pgstar_out' + Grid8_file_prefix = 'grid8_' + Grid8_file_interval = 10000 + Grid8_file_width = -1 + Grid8_file_aspect_ratio = -1 + +/ ! end of pgstar namelist diff --git a/star/test_suite/wd_nova_burst/inlist_setup b/star/test_suite/wd_nova_burst/inlist_setup index cb46aa22a..ee9e1c644 100644 --- a/star/test_suite/wd_nova_burst/inlist_setup +++ b/star/test_suite/wd_nova_burst/inlist_setup @@ -4,35 +4,35 @@ &star_job - show_log_description_at_start = .false. - - load_saved_model = .true. - load_model_filename = '1.1M_lgTc_7.7.mod' ! from make_o_ne_wd test case + show_log_description_at_start = .false. - save_model_when_terminate = .true. - save_model_filename = 'ready.mod' - required_termination_code_string = 'max_age' - - change_initial_net = .true. - new_net_name = 'cno_extras_o18_to_mg26_plus_fe56.net' - auto_extend_net = .false. + load_saved_model = .true. + load_model_filename = '1.1M_lgTc_7.7.mod' ! from make_o_ne_wd test case - change_v_flag = .true. - new_v_flag = .true. + save_model_when_terminate = .true. + save_model_filename = 'ready.mod' + required_termination_code_string = 'max_age' - set_tau_factor = .true. - set_to_this_tau_factor = 30 + change_initial_net = .true. + new_net_name = 'cno_extras_o18_to_mg26_plus_fe56.net' + auto_extend_net = .false. - set_initial_dt = .true. - years_for_initial_dt = 1d6 + change_v_flag = .true. + new_v_flag = .true. - set_initial_age = .true. - initial_age = 0 + set_tau_factor = .true. + set_to_this_tau_factor = 30 - set_initial_model_number = .true. - initial_model_number = 0 + set_initial_dt = .true. + years_for_initial_dt = 1d6 - !pgstar_flag = .true. + set_initial_age = .true. + initial_age = 0 + + set_initial_model_number = .true. + initial_model_number = 0 + + !pgstar_flag = .true. / ! end of star_job namelist @@ -42,126 +42,126 @@ / &kap - Zbase = 0.02d0 + Zbase = 0.02d0 - use_Type2_opacities = .true. + use_Type2_opacities = .true. / ! end of kap namelist &controls - ! limit max_model_number as part of test_suite - max_model_number = 1800 ! 1300 - - max_age = 1d7 - + ! limit max_model_number as part of test_suite + max_model_number = 1800 ! 1300 + + max_age = 1d7 + ! solver - energy_eqn_option = 'eps_grav' - use_gold2_tolerances = .true. + energy_eqn_option = 'eps_grav' + use_gold2_tolerances = .true. + + limit_for_rel_error_in_energy_conservation = 1d-5 + hard_limit_for_rel_error_in_energy_conservation = 1d-3 + + use_gold_tolerances = .false. + warning_limit_for_max_residual = 1d99 + convergence_ignore_equL_residuals = .true. + + + mass_change_full_on_dt = 1d-6 ! (seconds) + mass_change_full_off_dt = 1d-6 ! (seconds) - limit_for_rel_error_in_energy_conservation = 1d-5 - hard_limit_for_rel_error_in_energy_conservation = 1d-3 + ! NOTE: for super eddington wind, + ! we use Ledd averaged over mass to optical depth tau = 100 + super_eddington_scaling_factor = 1 + ! parameter for mass loss driven by super Eddington luminosity + super_eddington_wind_Ledd_factor = 1 + ! multiply Ledd by this factor when computing super Eddington wind + ! e.g., if this is 2, then only get wind when L > 2*Ledd - use_gold_tolerances = .false. - warning_limit_for_max_residual = 1d99 - convergence_ignore_equL_residuals = .true. + mixing_length_alpha = 1.9 + MLT_option = 'Henyey' + use_Ledoux_criterion = .true. + alpha_semiconvection = 1d-3 + thermohaline_coeff = 1d3 - mass_change_full_on_dt = 1d-6 ! (seconds) - mass_change_full_off_dt = 1d-6 ! (seconds) + star_mass_max_limit = 1.301d0 - ! NOTE: for super eddington wind, - ! we use Ledd averaged over mass to optical depth tau = 100 - super_eddington_scaling_factor = 1 - ! parameter for mass loss driven by super Eddington luminosity - super_eddington_wind_Ledd_factor = 1 - ! multiply Ledd by this factor when computing super Eddington wind - ! e.g., if this is 2, then only get wind when L > 2*Ledd + !mass_change = 1d-9 + accrete_same_as_surface = .false. + accretion_h1 = 0.7000 ! Estimate Nomoto 2007 + accretion_h2 = 0 + accretion_he3 = 0.292910D-04 + accretion_he4 = 0.279971 ! Estimated Nomoto 2007 + accretion_zfracs = 4 ! Lodders 03 - mixing_length_alpha = 1.9 - MLT_option = 'Henyey' + min_timestep_limit = 1d-12 - use_Ledoux_criterion = .true. - alpha_semiconvection = 1d-3 - thermohaline_coeff = 1d3 + xa_function_species(1) = 'h1' ! name of nuclide as defined in chem_def + xa_function_weight(1) = 20 + xa_function_param(1) = 1d-6 + xa_function_species(2) = 'he4' ! name of nuclide as defined in chem_def + xa_function_weight(2) = 20 + xa_function_param(2) = 1d-2 - star_mass_max_limit = 1.301d0 - - !mass_change = 1d-9 - accrete_same_as_surface = .false. - accretion_h1 = 0.7000 ! Estimate Nomoto 2007 - accretion_h2 = 0 - accretion_he3 = 0.292910D-04 - accretion_he4 = 0.279971 ! Estimated Nomoto 2007 - accretion_zfracs = 4 ! Lodders 03 - - min_timestep_limit = 1d-12 + delta_lgL_H_limit = 0.1 ! limit for magnitude of change in lgL_H + lgL_H_burn_min = -0.5 ! ignore changes in lgL_H if value is less than this - xa_function_species(1) = 'h1' ! name of nuclide as defined in chem_def - xa_function_weight(1) = 20 - xa_function_param(1) = 1d-6 - xa_function_species(2) = 'he4' ! name of nuclide as defined in chem_def - xa_function_weight(2) = 20 - xa_function_param(2) = 1d-2 + delta_lgL_He_limit = 0.25 ! limit for magnitude of change in lgL_He + lgL_He_burn_min = 2.5 ! ignore changes in lgL_He if value is less than this - delta_lgL_H_limit = 0.1 ! limit for magnitude of change in lgL_H - lgL_H_burn_min = -0.5 ! ignore changes in lgL_H if value is less than this + delta_lgRho_limit = 1 ! limit for magnitude of max change in log10 density at any point + delta_lgRho_hard_limit = -1 - delta_lgL_He_limit = 0.25 ! limit for magnitude of change in lgL_He - lgL_He_burn_min = 2.5 ! ignore changes in lgL_He if value is less than this - - delta_lgRho_limit = 1 ! limit for magnitude of max change in log10 density at any point - delta_lgRho_hard_limit = -1 + delta_lgT_limit = 0.5 + delta_lgL_limit = 0.05 + delta_lgTeff_limit = 0.10 - delta_lgT_limit = 0.5 - delta_lgL_limit = 0.05 - delta_lgTeff_limit = 0.10 - - delta_lgL_nuc_limit = 0.05 - delta_lgL_nuc_hard_limit = 0.10 - lgL_nuc_burn_min = -3d0 + delta_lgL_nuc_limit = 0.05 + delta_lgL_nuc_hard_limit = 0.10 + lgL_nuc_burn_min = -3d0 - atm_option = 'T_tau' - atm_T_tau_relation = 'Eddington' - atm_T_tau_opacity = 'fixed' - Pextra_factor = 4 + atm_option = 'T_tau' + atm_T_tau_relation = 'Eddington' + atm_T_tau_opacity = 'fixed' + Pextra_factor = 4 - !varcontrol_target = 3d-4 + !varcontrol_target = 3d-4 - mesh_delta_coeff = 1.0 - max_allowed_nz = 20000 + mesh_delta_coeff = 1.0 + max_allowed_nz = 20000 - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' - photo_interval = 50 - profile_interval = 50 - history_interval = 5 - terminal_interval = 10 - write_header_frequency = 10 + photo_interval = 50 + profile_interval = 50 + history_interval = 5 + terminal_interval = 10 + write_header_frequency = 10 / ! end of controls namelist &pgstar - Grid8_win_flag = .true. - Grid8_win_width = 7 - Summary_Burn_xaxis_name = 'logxq' - Summary_Burn_xaxis_reversed = .true. - Summary_Burn_xmin = -14 ! -101d0 ! only used if /= -101d0 - Summary_Burn_xmax = -3 ! -101d0 ! only used if /= -101d0 - Abundance_xaxis_name = 'logxq' - Abundance_xaxis_reversed = .true. - Abundance_xmin = -14 ! -101d0 ! only used if /= -101d0 - Abundance_xmax = -3 ! -101d0 ! only used if /= -101d0 + Grid8_win_flag = .true. + Grid8_win_width = 7 + Summary_Burn_xaxis_name = 'logxq' + Summary_Burn_xaxis_reversed = .true. + Summary_Burn_xmin = -14 ! -101d0 ! only used if /= -101d0 + Summary_Burn_xmax = -3 ! -101d0 ! only used if /= -101d0 + Abundance_xaxis_name = 'logxq' + Abundance_xaxis_reversed = .true. + Abundance_xmin = -14 ! -101d0 ! only used if /= -101d0 + Abundance_xmax = -3 ! -101d0 ! only used if /= -101d0 / ! end of pgstar namelist diff --git a/star/test_suite/wd_nova_burst/inlist_setup_header b/star/test_suite/wd_nova_burst/inlist_setup_header index 74cab97c4..c31f63313 100644 --- a/star/test_suite/wd_nova_burst/inlist_setup_header +++ b/star/test_suite/wd_nova_burst/inlist_setup_header @@ -2,24 +2,24 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_setup' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_setup' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_setup' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_setup' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_setup' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_setup' / ! end of kap namelist @@ -27,8 +27,8 @@ &controls - read_extra_controls_inlist(2) = .true. - extra_controls_inlist_name(2)= 'inlist_setup' + read_extra_controls_inlist(2) = .true. + extra_controls_inlist_name(2)= 'inlist_setup' / ! end of controls namelist @@ -36,7 +36,7 @@ &pgstar - read_extra_pgstar_inlist(2) = .true. - extra_pgstar_inlist_name(2)= 'inlist_setup' + read_extra_pgstar_inlist(2) = .true. + extra_pgstar_inlist_name(2)= 'inlist_setup' / ! end of pgstar namelist diff --git a/star/test_suite/wd_nova_burst/inlist_wd_nova_burst b/star/test_suite/wd_nova_burst/inlist_wd_nova_burst index b9a6219db..e354063b9 100644 --- a/star/test_suite/wd_nova_burst/inlist_wd_nova_burst +++ b/star/test_suite/wd_nova_burst/inlist_wd_nova_burst @@ -4,35 +4,35 @@ &star_job - show_log_description_at_start = .false. - - load_saved_model = .true. - load_model_filename = 'ready.mod' ! from running inlist_setup + show_log_description_at_start = .false. - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - required_termination_code_string = 'extras_check_model' + load_saved_model = .true. + load_model_filename = 'ready.mod' ! from running inlist_setup + + save_model_when_terminate = .true. + save_model_filename = 'final.mod' + required_termination_code_string = 'extras_check_model' ! save_model_when_terminate = .true. ! save_model_filename = 'start_of_wd_nova_burst.mod' ! required_termination_code_string = 'max_model_number' - set_initial_age = .true. - initial_age = 0 + set_initial_age = .true. + initial_age = 0 - set_initial_model_number = .true. - initial_model_number = 0 + set_initial_model_number = .true. + initial_model_number = 0 - set_tau_factor = .true. - set_to_this_tau_factor = 30 + set_tau_factor = .true. + set_to_this_tau_factor = 30 - set_initial_cumulative_energy_error = .true. - new_cumulative_energy_error = 0d0 + set_initial_cumulative_energy_error = .true. + new_cumulative_energy_error = 0d0 - set_initial_dt = .true. - years_for_initial_dt = 1d-5 + set_initial_dt = .true. + years_for_initial_dt = 1d-5 - !pgstar_flag = .true. + !pgstar_flag = .true. / ! end of star_job namelist @@ -42,127 +42,127 @@ &kap - Zbase = 0.02d0 + Zbase = 0.02d0 - use_Type2_opacities = .true. + use_Type2_opacities = .true. / ! end of kap namelist &controls - ! limit max_model_number as part of test_suite - !max_model_number = 223 - max_model_number = 2250 - + ! limit max_model_number as part of test_suite + !max_model_number = 223 + max_model_number = 2250 + ! solver - energy_eqn_option = 'eps_grav' - - use_gold2_tolerances = .false. - - limit_for_rel_error_in_energy_conservation = 1d-5 - hard_limit_for_rel_error_in_energy_conservation = 1d-3 - - warning_limit_for_max_residual = 1d99 - convergence_ignore_equL_residuals = .true. - - - mass_change_full_on_dt = 1d-6 ! (seconds) - mass_change_full_off_dt = 1d-6 ! (seconds) - - ! NOTE: for super eddington wind, - ! we use Ledd averaged over mass to optical depth tau = 100 - super_eddington_scaling_factor = 1 - ! parameter for mass loss driven by super Eddington luminosity - super_eddington_wind_Ledd_factor = 1 - ! multiply Ledd by this factor when computing super Eddington wind - ! e.g., if this is 2, then only get wind when L > 2*Ledd - - mixing_length_alpha = 1.9 - MLT_option = 'TDC' - - use_Ledoux_criterion = .true. - alpha_semiconvection = 1d-3 - thermohaline_coeff = 1d3 - - mass_change = 1d-9 - accrete_same_as_surface = .false. - accretion_h1 = 0.7000 ! Estimate Nomoto 2007 - accretion_h2 = 0 - accretion_he3 = 0.292910D-04 - accretion_he4 = 0.279971 ! Estimated Nomoto 2007 - accretion_zfracs = 4 ! Lodders 03 - - min_timestep_limit = 1d-12 - - xa_function_species(1) = 'h1' ! name of nuclide as defined in chem_def - xa_function_weight(1) = 20 - xa_function_param(1) = 1d-6 - xa_function_species(2) = 'he4' ! name of nuclide as defined in chem_def - xa_function_weight(2) = 20 - xa_function_param(2) = 1d-2 - - delta_lgL_H_limit = 0.1 ! limit for magnitude of change in lgL_H - lgL_H_burn_min = -0.5 ! ignore changes in lgL_H if value is less than this - - delta_lgL_He_limit = 0.25 ! limit for magnitude of change in lgL_He - lgL_He_burn_min = 2.5 ! ignore changes in lgL_He if value is less than this - - delta_lgRho_limit = 1 ! limit for magnitude of max change in log10 density at any point - delta_lgRho_hard_limit = -1 - - delta_lgT_limit = 0.5 - delta_lgL_limit = 0.05 - delta_lgTeff_limit = 0.10 - - delta_lgL_nuc_limit = 0.02 - delta_lgL_nuc_hard_limit = 0.20 - lgL_nuc_burn_min = -3d0 - - atm_option = 'T_tau' - atm_T_tau_relation = 'Eddington' - atm_T_tau_opacity = 'fixed' - Pextra_factor = 120 ! 4 * tau_factor - - !varcontrol_target = 3d-4 - - max_q_for_conv_timescale = 0.999999999d0 - - mesh_delta_coeff = 1.0 - max_allowed_nz = 20000 - - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' - - photo_interval = 50 - profile_interval = 50 - history_interval = 5 - terminal_interval = 10 - write_header_frequency = 10 - + energy_eqn_option = 'eps_grav' + + use_gold2_tolerances = .false. + + limit_for_rel_error_in_energy_conservation = 1d-5 + hard_limit_for_rel_error_in_energy_conservation = 1d-3 + + warning_limit_for_max_residual = 1d99 + convergence_ignore_equL_residuals = .true. + + + mass_change_full_on_dt = 1d-6 ! (seconds) + mass_change_full_off_dt = 1d-6 ! (seconds) + + ! NOTE: for super eddington wind, + ! we use Ledd averaged over mass to optical depth tau = 100 + super_eddington_scaling_factor = 1 + ! parameter for mass loss driven by super Eddington luminosity + super_eddington_wind_Ledd_factor = 1 + ! multiply Ledd by this factor when computing super Eddington wind + ! e.g., if this is 2, then only get wind when L > 2*Ledd + + mixing_length_alpha = 1.9 + MLT_option = 'TDC' + + use_Ledoux_criterion = .true. + alpha_semiconvection = 1d-3 + thermohaline_coeff = 1d3 + + mass_change = 1d-9 + accrete_same_as_surface = .false. + accretion_h1 = 0.7000 ! Estimate Nomoto 2007 + accretion_h2 = 0 + accretion_he3 = 0.292910D-04 + accretion_he4 = 0.279971 ! Estimated Nomoto 2007 + accretion_zfracs = 4 ! Lodders 03 + + min_timestep_limit = 1d-12 + + xa_function_species(1) = 'h1' ! name of nuclide as defined in chem_def + xa_function_weight(1) = 20 + xa_function_param(1) = 1d-6 + xa_function_species(2) = 'he4' ! name of nuclide as defined in chem_def + xa_function_weight(2) = 20 + xa_function_param(2) = 1d-2 + + delta_lgL_H_limit = 0.1 ! limit for magnitude of change in lgL_H + lgL_H_burn_min = -0.5 ! ignore changes in lgL_H if value is less than this + + delta_lgL_He_limit = 0.25 ! limit for magnitude of change in lgL_He + lgL_He_burn_min = 2.5 ! ignore changes in lgL_He if value is less than this + + delta_lgRho_limit = 1 ! limit for magnitude of max change in log10 density at any point + delta_lgRho_hard_limit = -1 + + delta_lgT_limit = 0.5 + delta_lgL_limit = 0.05 + delta_lgTeff_limit = 0.10 + + delta_lgL_nuc_limit = 0.02 + delta_lgL_nuc_hard_limit = 0.20 + lgL_nuc_burn_min = -3d0 + + atm_option = 'T_tau' + atm_T_tau_relation = 'Eddington' + atm_T_tau_opacity = 'fixed' + Pextra_factor = 120 ! 4 * tau_factor + + !varcontrol_target = 3d-4 + + max_q_for_conv_timescale = 0.999999999d0 + + mesh_delta_coeff = 1.0 + max_allowed_nz = 20000 + + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' + + photo_interval = 50 + profile_interval = 50 + history_interval = 5 + terminal_interval = 10 + write_header_frequency = 10 + / ! end of controls namelist &pgstar - Grid8_win_flag = .true. - Grid8_win_width = 7 - Summary_Burn_xaxis_name = 'logxq' - Summary_Burn_xaxis_reversed = .true. - Summary_Burn_xmin = -14 ! -101d0 ! only used if /= -101d0 - Summary_Burn_xmax = -3 ! -101d0 ! only used if /= -101d0 - Abundance_xaxis_name = 'logxq' - Abundance_xaxis_reversed = .true. - Abundance_xmin = -14 ! -101d0 ! only used if /= -101d0 - Abundance_xmax = -3 ! -101d0 ! only used if /= -101d0 - - Text_Summary1_name(5,2) = 'time_step_sec' - Text_Summary1_name(6,2) = 'max_tau_conv' - !Text_Summary1_name(7,2) = 'cz_bot_radius' - !Text_Summary1_name(8,2) = 'cz_top_radius' + Grid8_win_flag = .true. + Grid8_win_width = 7 + Summary_Burn_xaxis_name = 'logxq' + Summary_Burn_xaxis_reversed = .true. + Summary_Burn_xmin = -14 ! -101d0 ! only used if /= -101d0 + Summary_Burn_xmax = -3 ! -101d0 ! only used if /= -101d0 + Abundance_xaxis_name = 'logxq' + Abundance_xaxis_reversed = .true. + Abundance_xmin = -14 ! -101d0 ! only used if /= -101d0 + Abundance_xmax = -3 ! -101d0 ! only used if /= -101d0 + + Text_Summary1_name(5,2) = 'time_step_sec' + Text_Summary1_name(6,2) = 'max_tau_conv' + !Text_Summary1_name(7,2) = 'cz_bot_radius' + !Text_Summary1_name(8,2) = 'cz_top_radius' / ! end of pgstar namelist diff --git a/star/test_suite/wd_nova_burst/inlist_wd_nova_burst_header b/star/test_suite/wd_nova_burst/inlist_wd_nova_burst_header index d15b65c35..0a8fe6886 100644 --- a/star/test_suite/wd_nova_burst/inlist_wd_nova_burst_header +++ b/star/test_suite/wd_nova_burst/inlist_wd_nova_burst_header @@ -2,24 +2,24 @@ &star_job - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_wd_nova_burst' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_wd_nova_burst' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_wd_nova_burst' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_wd_nova_burst' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_wd_nova_burst' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_wd_nova_burst' / ! end of kap namelist @@ -27,8 +27,8 @@ &controls - read_extra_controls_inlist(2) = .true. - extra_controls_inlist_name(2)= 'inlist_wd_nova_burst' + read_extra_controls_inlist(2) = .true. + extra_controls_inlist_name(2)= 'inlist_wd_nova_burst' / ! end of controls namelist @@ -36,7 +36,7 @@ &pgstar - read_extra_pgstar_inlist(2) = .true. - extra_pgstar_inlist_name(2)= 'inlist_wd_nova_burst' + read_extra_pgstar_inlist(2) = .true. + extra_pgstar_inlist_name(2)= 'inlist_wd_nova_burst' / ! end of pgstar namelist From eacb4dbd2fc40243946811d647fa03f7da78585b Mon Sep 17 00:00:00 2001 From: pmocz Date: Wed, 7 Aug 2024 15:18:47 -0400 Subject: [PATCH 39/66] [ci skip] readme formating --- star/test_suite/1.3M_ms_high_Z/inlist_pgstar | 8 ++++---- star/test_suite/7M_prems_to_AGB/inlist_pgstar | 8 +++++--- star/test_suite/accreted_material_j/inlist_pgstar | 7 +++++-- star/test_suite/conductive_flame/inlist_pgstar | 12 ++++++------ .../diffusion_smoothness/inlist_diffusion_smoothness | 7 +++++-- star/test_suite/high_mass/inlist_pgstar | 9 +++++---- star/test_suite/wd_nova_burst/inlist_pgstar | 10 +++++----- 7 files changed, 35 insertions(+), 26 deletions(-) diff --git a/star/test_suite/1.3M_ms_high_Z/inlist_pgstar b/star/test_suite/1.3M_ms_high_Z/inlist_pgstar index 4e189de87..8ace39dcc 100644 --- a/star/test_suite/1.3M_ms_high_Z/inlist_pgstar +++ b/star/test_suite/1.3M_ms_high_Z/inlist_pgstar @@ -4,11 +4,11 @@ ! amount of control of the presentation of the information. ! device - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - !file_device = 'png' ! png - !file_extension = 'png' - file_device = 'vcps' ! postscript + file_white_on_black_flag = .true. + file_device = 'vcps' ! postscript file_extension = 'ps' + !file_device = 'png' ! png + !file_extension = 'png' pgstar_interval = 10 diff --git a/star/test_suite/7M_prems_to_AGB/inlist_pgstar b/star/test_suite/7M_prems_to_AGB/inlist_pgstar index c2c0cbe65..c80d425e1 100644 --- a/star/test_suite/7M_prems_to_AGB/inlist_pgstar +++ b/star/test_suite/7M_prems_to_AGB/inlist_pgstar @@ -1,9 +1,11 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - - file_device = 'vcps' ! postscript + ! device + file_white_on_black_flag = .true. + file_device = 'vcps' ! postscript file_extension = 'ps' + !file_device = 'png' ! png + !file_extension = 'png' pgstar_interval = 10 diff --git a/star/test_suite/accreted_material_j/inlist_pgstar b/star/test_suite/accreted_material_j/inlist_pgstar index 29252822c..9e1b2413c 100644 --- a/star/test_suite/accreted_material_j/inlist_pgstar +++ b/star/test_suite/accreted_material_j/inlist_pgstar @@ -1,8 +1,11 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'vcps' ! postscript + ! device + file_white_on_black_flag = .true. + file_device = 'vcps' ! postscript file_extension = 'ps' + !file_device = 'png' ! png + !file_extension = 'png' pgstar_interval = 10 diff --git a/star/test_suite/conductive_flame/inlist_pgstar b/star/test_suite/conductive_flame/inlist_pgstar index f9cac16d4..aef9926b6 100644 --- a/star/test_suite/conductive_flame/inlist_pgstar +++ b/star/test_suite/conductive_flame/inlist_pgstar @@ -1,12 +1,12 @@ &pgstar - ! device - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'png' ! png - file_extension = 'png' - !file_device = 'vcps' ! postscript - !file_extension = 'ps' + ! device + file_white_on_black_flag = .true. + !file_device = 'vcps' ! postscript + !file_extension = 'ps' + file_device = 'png' ! png + file_extension = 'png' pgstar_interval = 1 pause = .false. diff --git a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness index 262a63ea6..b61943f0a 100644 --- a/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness +++ b/star/test_suite/diffusion_smoothness/inlist_diffusion_smoothness @@ -118,9 +118,12 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - file_device = 'vcps' ! postscript + ! device + file_white_on_black_flag = .true. + file_device = 'vcps' ! postscript file_extension = 'ps' + !file_device = 'png' ! png + !file_extension = 'png' pgstar_interval = 1 diff --git a/star/test_suite/high_mass/inlist_pgstar b/star/test_suite/high_mass/inlist_pgstar index c2850001d..ecf511d13 100644 --- a/star/test_suite/high_mass/inlist_pgstar +++ b/star/test_suite/high_mass/inlist_pgstar @@ -1,10 +1,11 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - !file_device = 'png' ! png - !file_extension = 'png' - file_device = 'vcps' ! postscript + ! device + file_white_on_black_flag = .true. + file_device = 'vcps' ! postscript file_extension = 'ps' + !file_device = 'png' ! png + !file_extension = 'png' pgstar_interval = 10 diff --git a/star/test_suite/wd_nova_burst/inlist_pgstar b/star/test_suite/wd_nova_burst/inlist_pgstar index 5a8d914c3..d4cf93dbc 100644 --- a/star/test_suite/wd_nova_burst/inlist_pgstar +++ b/star/test_suite/wd_nova_burst/inlist_pgstar @@ -1,11 +1,11 @@ &pgstar - file_white_on_black_flag = .true. ! white_on_black flags -- true means white foreground color on black background - !file_device = 'png' ! png - !file_extension = 'png' - - file_device = 'vcps' ! postscript + ! device + file_white_on_black_flag = .true. + file_device = 'vcps' ! postscript file_extension = 'ps' + !file_device = 'png' ! png + !file_extension = 'png' pgstar_interval = 1 From 96341792bcb1a8394a180eb58ba7f6ee4f222229 Mon Sep 17 00:00:00 2001 From: pmocz Date: Wed, 7 Aug 2024 15:20:07 -0400 Subject: [PATCH 40/66] [ci skip] readme formating --- .../conductive_flame/inlist_conductive_flame | 157 ++++--- .../inlist_conductive_flame_header | 22 +- .../test_suite/conductive_flame/inlist_pgstar | 443 +++++++++--------- 3 files changed, 310 insertions(+), 312 deletions(-) diff --git a/star/test_suite/conductive_flame/inlist_conductive_flame b/star/test_suite/conductive_flame/inlist_conductive_flame index a9dfafdf4..550b42bcc 100644 --- a/star/test_suite/conductive_flame/inlist_conductive_flame +++ b/star/test_suite/conductive_flame/inlist_conductive_flame @@ -1,123 +1,124 @@ &star_job - show_log_description_at_start = .false. + show_log_description_at_start = .false. + ! build our own model + create_initial_model = .true. - ! build our own model - create_initial_model = .true. + save_model_when_terminate = .true. + save_model_filename = 'final.mod' + required_termination_code_string = 'flame reached halfway point' - save_model_when_terminate = .true. - save_model_filename = 'final.mod' - required_termination_code_string = 'flame reached halfway point' + ! pick the net + change_net = .true. + !new_net_name = 'mesa_204.net' + new_net_name = 'approx21.net' - ! pick the net - change_net = .true. - !new_net_name = 'mesa_204.net' - new_net_name = 'approx21.net' + ! need extremely small initial timestep + set_initial_dt = .true. + seconds_for_initial_dt = 1e-15 + initial_model_relax_num_steps = 0 - ! need extremely small initial timestep - set_initial_dt = .true. - seconds_for_initial_dt = 1e-15 - initial_model_relax_num_steps = 0 - - ! display on-screen plots - pgstar_flag = .true. - save_pgstar_files_when_terminate = .true. + ! display on-screen plots + pgstar_flag = .true. + save_pgstar_files_when_terminate = .true. / !end of star_job namelist &eos - ! use HELM EOS - use_Skye = .false. - use_PC = .false. + ! use HELM EOS + use_Skye = .false. + use_PC = .false. / !end of eos namelist &kap - ! specify base metallicity for Type2 opacities - ! unimportant since radiative opacities are irrelevant - Zbase = 0.02 + ! specify base metallicity for Type2 opacities + ! unimportant since radiative opacities are irrelevant + Zbase = 0.02 / ! end of kap namelist + &controls - ! test targets; 10% tolerance - x_ctrl(9) = 2.39e7 ! flame speed [cm/s] - x_ctrl(10) = 2.391e-5 ! flame width [cm] + ! test targets; 10% tolerance + x_ctrl(9) = 2.39e7 ! flame speed [cm/s] + x_ctrl(10) = 2.391e-5 ! flame width [cm] + + warn_when_large_virial_thm_rel_err = 1d99 ! doesn't apply - warn_when_large_virial_thm_rel_err = 1d99 ! doesn't apply + num_trace_history_values = 2 + trace_history_value_name(1) = 'rel_E_err' + trace_history_value_name(2) = 'log_rel_run_E_err' - num_trace_history_values = 2 - trace_history_value_name(1) = 'rel_E_err' - trace_history_value_name(2) = 'log_rel_run_E_err' + ! limit max_model_number as part of test_suite + max_model_number = 3000 ! 1800 - ! limit max_model_number as part of test_suite - max_model_number = 3000 ! 1800 + ! use our own routine to build the model + use_other_build_initial_model = .true. + x_integer_ctrl(1) = 300 ! number of points + x_ctrl(1) = 10 ! mass (in g) + x_ctrl(2) = 1d10 ! initial density (cgs) + x_ctrl(3) = 2d8 ! initial temperature (cgs) - ! use our own routine to build the model - use_other_build_initial_model = .true. - x_integer_ctrl(1) = 300 ! number of points - x_ctrl(1) = 10 ! mass (in g) - x_ctrl(2) = 1d10 ! initial density (cgs) - x_ctrl(3) = 2d8 ! initial temperature (cgs) + x_ctrl(4) = 0.0001 ! size (in q) of region to heat + x_ctrl(5) = 5d9 ! temperature of that region - x_ctrl(4) = 0.0001 ! size (in q) of region to heat - x_ctrl(5) = 5d9 ! temperature of that region + x_ctrl(6) = 0.50 ! mass fraction c12 + x_ctrl(7) = 0.50 ! mass fraction o16 + x_ctrl(8) = 0.00 ! mass fraction ne20 - x_ctrl(6) = 0.50 ! mass fraction c12 - x_ctrl(7) = 0.50 ! mass fraction o16 - x_ctrl(8) = 0.00 ! mass fraction ne20 + ! set up constant pressure/temperature boundary conditions + use_other_surface_PT = .true. - ! set up constant pressure/temperature boundary conditions - use_other_surface_PT = .true. + ! there's no surface here; ignore change in lgL_surf and lgTeff + delta_lgL_limit_L_min = 1d99 + delta_lgTeff_limit = 1d99 - ! there's no surface here; ignore change in lgL_surf and lgTeff - delta_lgL_limit_L_min = 1d99 - delta_lgTeff_limit = 1d99 - - ! don't let convection operate - mlt_option = 'none' + ! don't let convection operate + mlt_option = 'none' - ! meshing/timestep controls - varcontrol_target = 1d-3 - delta_lgT_limit = 0.1d0 - delta_lgT_limit_min_lgT = 8d0 - T_function1_weight = 50 - limit_for_rel_error_in_energy_conservation = 1d-4 - hard_limit_for_rel_error_in_energy_conservation = 1d-3 + ! meshing/timestep controls + varcontrol_target = 1d-3 + delta_lgT_limit = 0.1d0 + delta_lgT_limit_min_lgT = 8d0 + T_function1_weight = 50 + limit_for_rel_error_in_energy_conservation = 1d-4 + hard_limit_for_rel_error_in_energy_conservation = 1d-3 - use_gold2_tolerances = .true. - - ! allow for minuscule timesteps - min_timestep_limit = 1d-20 + use_gold2_tolerances = .true. - ! use the same meshing at high temperature - mesh_delta_coeff = 1.0 - logT_max_for_standard_mesh_delta_coeff = 99d0 - logT_min_for_highT_mesh_delta_coeff = 99d0 + ! allow for minuscule timesteps + min_timestep_limit = 1d-20 - ! we know rates are truncated above 1e10 K, so turn off warnings - warn_rates_for_high_temp = .false. - - ! cannot include L corrections - include_L_in_correction_limits = .false. + ! use the same meshing at high temperature + mesh_delta_coeff = 1.0 + logT_max_for_standard_mesh_delta_coeff = 99d0 + logT_min_for_highT_mesh_delta_coeff = 99d0 - terminal_show_age_units = 'seconds' + ! we know rates are truncated above 1e10 K, so turn off warnings + warn_rates_for_high_temp = .false. - photo_interval = 50 - profile_interval = 100 - history_interval = 10 - terminal_interval = 10 - write_header_frequency = 10 + ! cannot include L corrections + include_L_in_correction_limits = .false. + + terminal_show_age_units = 'seconds' + + photo_interval = 50 + profile_interval = 100 + history_interval = 10 + terminal_interval = 10 + write_header_frequency = 10 / ! end of controls namelist + &pgstar / ! end of pgstar namelist diff --git a/star/test_suite/conductive_flame/inlist_conductive_flame_header b/star/test_suite/conductive_flame/inlist_conductive_flame_header index a42f044dc..e0366c399 100644 --- a/star/test_suite/conductive_flame/inlist_conductive_flame_header +++ b/star/test_suite/conductive_flame/inlist_conductive_flame_header @@ -1,41 +1,39 @@ &star_job - - read_extra_star_job_inlist(2) = .true. - extra_star_job_inlist_name(2) = 'inlist_conductive_flame' + read_extra_star_job_inlist(2) = .true. + extra_star_job_inlist_name(2) = 'inlist_conductive_flame' / ! end of star_job namelist &eos - read_extra_eos_inlist(1) = .true. - extra_eos_inlist_name(1) = 'inlist_conductive_flame' + read_extra_eos_inlist(1) = .true. + extra_eos_inlist_name(1) = 'inlist_conductive_flame' / ! end of eos namelist &kap - read_extra_kap_inlist(1) = .true. - extra_kap_inlist_name(1) = 'inlist_conductive_flame' + read_extra_kap_inlist(1) = .true. + extra_kap_inlist_name(1) = 'inlist_conductive_flame' / ! end of kap namelist - &controls - read_extra_controls_inlist(1) = .true. - extra_controls_inlist_name(1)= 'inlist_conductive_flame' + read_extra_controls_inlist(1) = .true. + extra_controls_inlist_name(1)= 'inlist_conductive_flame' / ! end of controls namelist &pgstar - read_extra_pgstar_inlist(1) = .true. - extra_pgstar_inlist_name(1)= 'inlist_pgstar' + read_extra_pgstar_inlist(1) = .true. + extra_pgstar_inlist_name(1)= 'inlist_pgstar' / ! end of pgstar namelist diff --git a/star/test_suite/conductive_flame/inlist_pgstar b/star/test_suite/conductive_flame/inlist_pgstar index aef9926b6..c390b9375 100644 --- a/star/test_suite/conductive_flame/inlist_pgstar +++ b/star/test_suite/conductive_flame/inlist_pgstar @@ -1,6 +1,5 @@ &pgstar - ! device file_white_on_black_flag = .true. !file_device = 'vcps' ! postscript @@ -8,226 +7,226 @@ file_device = 'png' ! png file_extension = 'png' - pgstar_interval = 1 - pause = .false. - - Grid1_win_flag = .false. - Grid1_title = 'TW92 Flame' - Grid1_win_width = 8 - Grid1_win_aspect_ratio = 0.75 ! aspect_ratio = height/width - - Grid1_xleft = 0.12 ! fraction of full window width for margin on left - Grid1_xright = 0.95 ! fraction of full window width for margin on right - Grid1_ybot = 0.08 ! fraction of full window width for margin on bottom - Grid1_ytop = 0.92 ! fraction of full window width for margin on top - - Grid1_plot_name(:) = '' - Grid1_plot_row(:) = 1 ! number from 1 at top - Grid1_plot_rowspan(:) = 1 ! plot spans this number of rows - Grid1_plot_col(:) = 1 ! number from 1 at left - Grid1_plot_colspan(:) = 1 ! plot spans this number of columns - Grid1_plot_pad_left(:) = 0.0 ! fraction of full window width for padding on left - Grid1_plot_pad_right(:) = 0.0 ! fraction of full window width for padding on right - Grid1_plot_pad_top(:) = 0.0 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(:) = 0.0 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(:) = 0.7 ! multiply txt_scale for subplot by this - - ! set default - Grid1_num_cols = 4 ! divide plotting region into this many equal width cols - Grid1_num_rows = 3 ! divide plotting region into this many equal height rows - Grid1_num_plots = 3 ! <= 10 - - Grid1_plot_name(:) = '' - Grid1_plot_row(:) = 1 ! number from 1 at top - Grid1_plot_rowspan(:) = 1 ! plot spans this number of rows - Grid1_plot_col(:) = 1 ! number from 1 at left - Grid1_plot_colspan(:) = 1 ! plot spans this number of columns - Grid1_plot_pad_left(:) = 0.03 ! fraction of full window width for padding on left - Grid1_plot_pad_right(:) = 0.03 ! fraction of full window width for padding on right - Grid1_plot_pad_top(:) = 0.03 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(:) = 0.03 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(:) = 0.7 ! multiply txt_scale for subplot by this - - - Grid1_plot_name(1) = 'Abundance' - Grid1_plot_row(1) = 1 ! number from 1 at top - Grid1_plot_rowspan(1) = 2 ! plot spans this number of rows - Grid1_plot_col(1) = 1 ! number from 1 at left - Grid1_plot_colspan(1) = 2 ! plot spans this number of columns - Grid1_plot_pad_left(1) = -0.05 ! fraction of full window width for padding on left - Grid1_plot_pad_right(1) = 0.05 ! fraction of full window width for padding on right - Grid1_plot_pad_top(1) = 0.0 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(1) = 0.05 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(1) = 0.6 ! multiply txt_scale for subplot by this - - ! Grid1_plot_name(2) = 'Abundance' - ! Grid1_plot_row(2) = 2 ! number from 1 at top - ! Grid1_plot_rowspan(2) = 1 ! plot spans this number of rows - ! Grid1_plot_col(2) = 1 ! number from 1 at left - ! Grid1_plot_colspan(2) = 2 ! plot spans this number of columns - ! Grid1_plot_pad_left(2) = -0.05 ! fraction of full window width for padding on left - ! Grid1_plot_pad_right(2) = 0.05 ! fraction of full window width for padding on right - ! Grid1_plot_pad_top(2) = 0.025 ! fraction of full window height for padding at top - ! Grid1_plot_pad_bot(2) = 0.025 ! fraction of full window height for padding at bottom - ! Grid1_txt_scale_factor(2) = 0.65 ! multiply txt_scale for subplot by this - - Grid1_plot_name(2) = 'Profile_Panels1' - Grid1_plot_row(2) = 3 ! number from 1 at top - Grid1_plot_rowspan(2) = 1 ! plot spans this number of rows - Grid1_plot_col(2) = 1 ! number from 1 at left - Grid1_plot_colspan(2) = 2 ! plot spans this number of columns - Grid1_plot_pad_left(2) = -0.05 ! fraction of full window width for padding on left - Grid1_plot_pad_right(2) = 0.05 ! fraction of full window width for padding on right - Grid1_plot_pad_top(2) = 0.05 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(2) = 0.0 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(2) = 0.65 ! multiply txt_scale for subplot by this - - Grid1_plot_name(3) = 'History_Panels1' - Grid1_plot_row(3) = 1 ! number from 1 at top - Grid1_plot_rowspan(3) = 3 ! plot spans this number of rows - Grid1_plot_col(3) = 3 ! number from 1 at left - Grid1_plot_colspan(3) = 2 ! plot spans this number of columns - Grid1_plot_pad_left(3) = 0.12 ! fraction of full window width for padding on left - Grid1_plot_pad_right(3) = 0.03 ! fraction of full window width for padding on right - Grid1_plot_pad_top(3) = 0.0 ! fraction of full window height for padding at top - Grid1_plot_pad_bot(3) = 0.0 ! fraction of full window height for padding at bottom - Grid1_txt_scale_factor(3) = 0.65 ! multiply txt_scale for subplot by this - - - ! file output - Grid1_file_flag = .true. - Grid1_file_dir = 'png' - Grid1_file_prefix = 'grid1' - Grid1_file_interval = 10000 ! output when mod(model_number,Grid1_file_interval)==0 - Grid1_file_width = 16 ! negative means use same value as for window - Grid1_file_aspect_ratio = -1 ! negative means use same value as for window - - - Abundance_win_flag = .false. - Abundance_xaxis_name = 'radius_cm' - Abundance_num_isos_to_show = -1 - Abundance_title = '' - - num_abundance_line_labels = 5 - Abundance_line_txt_scale_factor = 0.8 ! relative to other text - - Abundance_legend_max_cnt = -1 - Abundance_legend_txt_scale_factor = 0.8 ! relative to other text - - !### Profile_Panels1 - - Profile_Panels1_win_flag = .false. - - Profile_Panels1_win_width = 6 - Profile_Panels1_win_aspect_ratio = 0.75 ! aspect_ratio = height/width - - Profile_Panels1_xleft = 0.15 - Profile_Panels1_xright = 0.85 - Profile_Panels1_ybot = 0.15 - Profile_Panels1_ytop = 0.85 - Profile_Panels1_txt_scale = 1.0 - Profile_Panels1_title = '' - - Profile_Panels1_xaxis_name = 'radius_cm' - Profile_Panels1_xaxis_reversed = .false. - Profile_Panels1_xmin = 0 ! only used if /= -101d0 - Profile_Panels1_xmax = -101d0 ! only used if /= -101d0 - Profile_Panels1_xmargin = 0d0 - Profile_Panels1_show_mix_regions_on_xaxis = .false. - - Profile_Panels1_yaxis_name(:) = '' - Profile_Panels1_yaxis_reversed(:) = .false. - Profile_Panels1_yaxis_log(:) = .false. ! show log10 of abs value - Profile_Panels1_ymin(:) = -101d0 ! only used if /= -101d0 - Profile_Panels1_ymax(:) = -101d0 ! only used if /= -101d0 - Profile_Panels1_ymargin(:) = 0.1 - Profile_Panels1_dymin(:) = -1 - - Profile_Panels1_other_yaxis_name(:) = '' - Profile_Panels1_other_yaxis_reversed(:) = .false. - Profile_Panels1_other_yaxis_log(:) = .false. ! show log10 of abs value - Profile_Panels1_other_ymin(:) = -101d0 ! only used if /= -101d0 - Profile_Panels1_other_ymax(:) = -101d0 ! only used if /= -101d0 - Profile_Panels1_other_ymargin(:) = 0.1 - Profile_Panels1_other_dymin(:) = -1 - - Profile_Panels1_show_grid = .true. - - ! setup default plot - Profile_Panels1_num_panels = 1 - Profile_Panels1_yaxis_name(1) = 'logT' - Profile_Panels1_other_yaxis_name(1) = 'logRho' - - ! file output - Profile_Panels1_file_flag = .false. - Profile_Panels1_file_dir = 'png' - Profile_Panels1_file_prefix = 'profile_panels1_' - Profile_Panels1_file_interval = 5 ! output when mod(model_number,Profile_Panels1_file_interval)==0 - Profile_Panels1_file_width = -1 ! (inches) negative means use same value as for window - Profile_Panels1_file_aspect_ratio = -1 ! negative means use same value as for window - - - History_Panels1_win_flag = .false. - - History_Panels1_win_width = 6 - History_Panels1_win_aspect_ratio = 0.75 ! aspect_ratio = height/width - - History_Panels1_xleft = 0.15 - History_Panels1_xright = 0.85 - History_Panels1_ybot = 0.15 - History_Panels1_ytop = 0.85 - History_Panels1_txt_scale = 1.0 - History_Panels1_title = '' - - History_Panels1_xaxis_name = 'star_age' - History_Panels1_xmin = -101d0 - History_Panels1_xmax = -101d0 - History_Panels1_max_width = 100 ! only used if > 0. causes xmin to move with xmax. - History_Panels1_dxmin = -1 - History_Panels1_xaxis_reversed = .false. - History_Panels1_xaxis_log = .false. ! show log10 of abs value - - History_Panels1_yaxis_name(:) = '' - History_Panels1_yaxis_reversed(:) = .false. - History_Panels1_yaxis_log(:) = .false. ! show log10 of abs value - History_Panels1_ymin(:) = -101d0 ! only used if /= -101d0 - History_Panels1_ymax(:) = -101d0 ! only used if /= -101d0 - History_Panels1_ymargin(:) = 0.1 - History_Panels1_dymin(:) = -1 - - History_Panels1_other_yaxis_name(:) = '' - History_Panels1_other_yaxis_reversed(:) = .false. - History_Panels1_other_yaxis_log(:) = .false. ! show log10 of abs value - History_Panels1_other_ymin(:) = -101d0 ! only used if /= -101d0 - History_Panels1_other_ymax(:) = -101d0 ! only used if /= -101d0 - History_Panels1_other_ymargin(:) = 0.1 - History_Panels1_other_dymin(:) = -1 - - ! setup default - History_Panels1_num_panels = 2 - - History_Panels1_yaxis_name(1) = 'r_flame' - History_Panels1_yaxis_reversed(1) = .false. - History_Panels1_ymin(1) = 0 ! only used if /= -101d0 - History_Panels1_ymax(1) = 5e-4 ! only used if /= -101d0 - History_Panels1_dymin(1) = -1 - - History_Panels1_other_yaxis_name(1) = '' - History_Panels1_other_yaxis_reversed(1) = .false. - History_Panels1_other_ymin(1) = -101d0 ! only used if /= -101d0 - History_Panels1_other_ymax(1) = -101d0 ! only used if /= -101d0 - History_Panels1_other_dymin(1) = -1 - - History_Panels1_yaxis_name(2) = 'l_flame' - History_Panels1_yaxis_reversed(2) = .false. - History_Panels1_ymin(2) = -101d0 ! only used if /= -101d0 - History_Panels1_ymax(2) = -101d0 ! only used if /= -101d0 - History_Panels1_dymin(2) = -1 - - History_Panels1_other_yaxis_name(2) = '' - History_Panels1_other_yaxis_reversed(2) = .false. - History_Panels1_other_ymin(2) = -101d0 ! only used if /= -101d0 - History_Panels1_other_ymax(2) = -101d0 ! only used if /= -101d0 - History_Panels1_other_dymin(2) = -1 + pgstar_interval = 1 + pause = .false. + + Grid1_win_flag = .false. + Grid1_title = 'TW92 Flame' + Grid1_win_width = 8 + Grid1_win_aspect_ratio = 0.75 ! aspect_ratio = height/width + + Grid1_xleft = 0.12 ! fraction of full window width for margin on left + Grid1_xright = 0.95 ! fraction of full window width for margin on right + Grid1_ybot = 0.08 ! fraction of full window width for margin on bottom + Grid1_ytop = 0.92 ! fraction of full window width for margin on top + + Grid1_plot_name(:) = '' + Grid1_plot_row(:) = 1 ! number from 1 at top + Grid1_plot_rowspan(:) = 1 ! plot spans this number of rows + Grid1_plot_col(:) = 1 ! number from 1 at left + Grid1_plot_colspan(:) = 1 ! plot spans this number of columns + Grid1_plot_pad_left(:) = 0.0 ! fraction of full window width for padding on left + Grid1_plot_pad_right(:) = 0.0 ! fraction of full window width for padding on right + Grid1_plot_pad_top(:) = 0.0 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(:) = 0.0 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(:) = 0.7 ! multiply txt_scale for subplot by this + + ! set default + Grid1_num_cols = 4 ! divide plotting region into this many equal width cols + Grid1_num_rows = 3 ! divide plotting region into this many equal height rows + Grid1_num_plots = 3 ! <= 10 + + Grid1_plot_name(:) = '' + Grid1_plot_row(:) = 1 ! number from 1 at top + Grid1_plot_rowspan(:) = 1 ! plot spans this number of rows + Grid1_plot_col(:) = 1 ! number from 1 at left + Grid1_plot_colspan(:) = 1 ! plot spans this number of columns + Grid1_plot_pad_left(:) = 0.03 ! fraction of full window width for padding on left + Grid1_plot_pad_right(:) = 0.03 ! fraction of full window width for padding on right + Grid1_plot_pad_top(:) = 0.03 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(:) = 0.03 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(:) = 0.7 ! multiply txt_scale for subplot by this + + + Grid1_plot_name(1) = 'Abundance' + Grid1_plot_row(1) = 1 ! number from 1 at top + Grid1_plot_rowspan(1) = 2 ! plot spans this number of rows + Grid1_plot_col(1) = 1 ! number from 1 at left + Grid1_plot_colspan(1) = 2 ! plot spans this number of columns + Grid1_plot_pad_left(1) = -0.05 ! fraction of full window width for padding on left + Grid1_plot_pad_right(1) = 0.05 ! fraction of full window width for padding on right + Grid1_plot_pad_top(1) = 0.0 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(1) = 0.05 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(1) = 0.6 ! multiply txt_scale for subplot by this + + ! Grid1_plot_name(2) = 'Abundance' + ! Grid1_plot_row(2) = 2 ! number from 1 at top + ! Grid1_plot_rowspan(2) = 1 ! plot spans this number of rows + ! Grid1_plot_col(2) = 1 ! number from 1 at left + ! Grid1_plot_colspan(2) = 2 ! plot spans this number of columns + ! Grid1_plot_pad_left(2) = -0.05 ! fraction of full window width for padding on left + ! Grid1_plot_pad_right(2) = 0.05 ! fraction of full window width for padding on right + ! Grid1_plot_pad_top(2) = 0.025 ! fraction of full window height for padding at top + ! Grid1_plot_pad_bot(2) = 0.025 ! fraction of full window height for padding at bottom + ! Grid1_txt_scale_factor(2) = 0.65 ! multiply txt_scale for subplot by this + + Grid1_plot_name(2) = 'Profile_Panels1' + Grid1_plot_row(2) = 3 ! number from 1 at top + Grid1_plot_rowspan(2) = 1 ! plot spans this number of rows + Grid1_plot_col(2) = 1 ! number from 1 at left + Grid1_plot_colspan(2) = 2 ! plot spans this number of columns + Grid1_plot_pad_left(2) = -0.05 ! fraction of full window width for padding on left + Grid1_plot_pad_right(2) = 0.05 ! fraction of full window width for padding on right + Grid1_plot_pad_top(2) = 0.05 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(2) = 0.0 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(2) = 0.65 ! multiply txt_scale for subplot by this + + Grid1_plot_name(3) = 'History_Panels1' + Grid1_plot_row(3) = 1 ! number from 1 at top + Grid1_plot_rowspan(3) = 3 ! plot spans this number of rows + Grid1_plot_col(3) = 3 ! number from 1 at left + Grid1_plot_colspan(3) = 2 ! plot spans this number of columns + Grid1_plot_pad_left(3) = 0.12 ! fraction of full window width for padding on left + Grid1_plot_pad_right(3) = 0.03 ! fraction of full window width for padding on right + Grid1_plot_pad_top(3) = 0.0 ! fraction of full window height for padding at top + Grid1_plot_pad_bot(3) = 0.0 ! fraction of full window height for padding at bottom + Grid1_txt_scale_factor(3) = 0.65 ! multiply txt_scale for subplot by this + + + ! file output + Grid1_file_flag = .true. + Grid1_file_dir = 'png' + Grid1_file_prefix = 'grid1' + Grid1_file_interval = 10000 ! output when mod(model_number,Grid1_file_interval)==0 + Grid1_file_width = 16 ! negative means use same value as for window + Grid1_file_aspect_ratio = -1 ! negative means use same value as for window + + + Abundance_win_flag = .false. + Abundance_xaxis_name = 'radius_cm' + Abundance_num_isos_to_show = -1 + Abundance_title = '' + + num_abundance_line_labels = 5 + Abundance_line_txt_scale_factor = 0.8 ! relative to other text + + Abundance_legend_max_cnt = -1 + Abundance_legend_txt_scale_factor = 0.8 ! relative to other text + + !### Profile_Panels1 + + Profile_Panels1_win_flag = .false. + + Profile_Panels1_win_width = 6 + Profile_Panels1_win_aspect_ratio = 0.75 ! aspect_ratio = height/width + + Profile_Panels1_xleft = 0.15 + Profile_Panels1_xright = 0.85 + Profile_Panels1_ybot = 0.15 + Profile_Panels1_ytop = 0.85 + Profile_Panels1_txt_scale = 1.0 + Profile_Panels1_title = '' + + Profile_Panels1_xaxis_name = 'radius_cm' + Profile_Panels1_xaxis_reversed = .false. + Profile_Panels1_xmin = 0 ! only used if /= -101d0 + Profile_Panels1_xmax = -101d0 ! only used if /= -101d0 + Profile_Panels1_xmargin = 0d0 + Profile_Panels1_show_mix_regions_on_xaxis = .false. + + Profile_Panels1_yaxis_name(:) = '' + Profile_Panels1_yaxis_reversed(:) = .false. + Profile_Panels1_yaxis_log(:) = .false. ! show log10 of abs value + Profile_Panels1_ymin(:) = -101d0 ! only used if /= -101d0 + Profile_Panels1_ymax(:) = -101d0 ! only used if /= -101d0 + Profile_Panels1_ymargin(:) = 0.1 + Profile_Panels1_dymin(:) = -1 + + Profile_Panels1_other_yaxis_name(:) = '' + Profile_Panels1_other_yaxis_reversed(:) = .false. + Profile_Panels1_other_yaxis_log(:) = .false. ! show log10 of abs value + Profile_Panels1_other_ymin(:) = -101d0 ! only used if /= -101d0 + Profile_Panels1_other_ymax(:) = -101d0 ! only used if /= -101d0 + Profile_Panels1_other_ymargin(:) = 0.1 + Profile_Panels1_other_dymin(:) = -1 + + Profile_Panels1_show_grid = .true. + + ! setup default plot + Profile_Panels1_num_panels = 1 + Profile_Panels1_yaxis_name(1) = 'logT' + Profile_Panels1_other_yaxis_name(1) = 'logRho' + + ! file output + Profile_Panels1_file_flag = .false. + Profile_Panels1_file_dir = 'png' + Profile_Panels1_file_prefix = 'profile_panels1_' + Profile_Panels1_file_interval = 5 ! output when mod(model_number,Profile_Panels1_file_interval)==0 + Profile_Panels1_file_width = -1 ! (inches) negative means use same value as for window + Profile_Panels1_file_aspect_ratio = -1 ! negative means use same value as for window + + + History_Panels1_win_flag = .false. + + History_Panels1_win_width = 6 + History_Panels1_win_aspect_ratio = 0.75 ! aspect_ratio = height/width + + History_Panels1_xleft = 0.15 + History_Panels1_xright = 0.85 + History_Panels1_ybot = 0.15 + History_Panels1_ytop = 0.85 + History_Panels1_txt_scale = 1.0 + History_Panels1_title = '' + + History_Panels1_xaxis_name = 'star_age' + History_Panels1_xmin = -101d0 + History_Panels1_xmax = -101d0 + History_Panels1_max_width = 100 ! only used if > 0. causes xmin to move with xmax. + History_Panels1_dxmin = -1 + History_Panels1_xaxis_reversed = .false. + History_Panels1_xaxis_log = .false. ! show log10 of abs value + + History_Panels1_yaxis_name(:) = '' + History_Panels1_yaxis_reversed(:) = .false. + History_Panels1_yaxis_log(:) = .false. ! show log10 of abs value + History_Panels1_ymin(:) = -101d0 ! only used if /= -101d0 + History_Panels1_ymax(:) = -101d0 ! only used if /= -101d0 + History_Panels1_ymargin(:) = 0.1 + History_Panels1_dymin(:) = -1 + + History_Panels1_other_yaxis_name(:) = '' + History_Panels1_other_yaxis_reversed(:) = .false. + History_Panels1_other_yaxis_log(:) = .false. ! show log10 of abs value + History_Panels1_other_ymin(:) = -101d0 ! only used if /= -101d0 + History_Panels1_other_ymax(:) = -101d0 ! only used if /= -101d0 + History_Panels1_other_ymargin(:) = 0.1 + History_Panels1_other_dymin(:) = -1 + + ! setup default + History_Panels1_num_panels = 2 + + History_Panels1_yaxis_name(1) = 'r_flame' + History_Panels1_yaxis_reversed(1) = .false. + History_Panels1_ymin(1) = 0 ! only used if /= -101d0 + History_Panels1_ymax(1) = 5e-4 ! only used if /= -101d0 + History_Panels1_dymin(1) = -1 + + History_Panels1_other_yaxis_name(1) = '' + History_Panels1_other_yaxis_reversed(1) = .false. + History_Panels1_other_ymin(1) = -101d0 ! only used if /= -101d0 + History_Panels1_other_ymax(1) = -101d0 ! only used if /= -101d0 + History_Panels1_other_dymin(1) = -1 + + History_Panels1_yaxis_name(2) = 'l_flame' + History_Panels1_yaxis_reversed(2) = .false. + History_Panels1_ymin(2) = -101d0 ! only used if /= -101d0 + History_Panels1_ymax(2) = -101d0 ! only used if /= -101d0 + History_Panels1_dymin(2) = -1 + + History_Panels1_other_yaxis_name(2) = '' + History_Panels1_other_yaxis_reversed(2) = .false. + History_Panels1_other_ymin(2) = -101d0 ! only used if /= -101d0 + History_Panels1_other_ymax(2) = -101d0 ! only used if /= -101d0 + History_Panels1_other_dymin(2) = -1 / ! end of pgstar namelist From ec05e22a093bc52e9fec31e04729ed5226ac2b07 Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Wed, 7 Aug 2024 16:30:30 -0600 Subject: [PATCH 41/66] [ci skip] updated summer_schools.rst --- docs/source/summer_schools.rst | 60 +++++++++++++++++++++++++++++++--- 1 file changed, 55 insertions(+), 5 deletions(-) diff --git a/docs/source/summer_schools.rst b/docs/source/summer_schools.rst index bb69a3259..9f9b7c5af 100644 --- a/docs/source/summer_schools.rst +++ b/docs/source/summer_schools.rst @@ -8,7 +8,8 @@ MESA Summer School Programs -- this page under construction! History of the MESA Summer School Program ----------------------------------------- -The MESA Summer Schools have traditionally been held in Santa Barbara, California, until 2022. The 2023 MESA Summer School program, branded as MESA@Konkoly, was held in Budapest, Hungary. As of 2023, MESA Summer Schools can be run anywhere in the world. The involvement of the MESA developers is encouraged, and we are happy to help. +The MESA Summer Schools have traditionally been held in Santa Barbara, California, until 2022. The 2023 MESA Summer School program, branded as MESA@Konkoly, was held in Budapest, Hungary. This was follwed by MESA Down Under, hosted in Sydney in June of 2024. +As of 2022, MESA Summer Schools can be run anywhere in the world. The involvement of the MESA developers is encouraged, and we are happy to help. How to run a MESA Summer School @@ -20,12 +21,61 @@ Preparing a good program takes about a year. Historically, the program has taken 1 year + out (September/October) -------------------------------- -- Book a venue -- Choose your organizational team +- Book a venue. The summer schools have traditionally aimed for approximatley 45 students, one TA per 3 students (15 TAs), and 6 lecturers. These numbers are not strict, but they have worked well in the past. Plan for your venue to accommodate roughly 75 people (lecturers, TAs, students, organizers). Be aware that your venue should have reliable, high-speed internet and enough outlets for every student, TA, and lecturer to plug in their laptop simultaneously. + + +- Choose your organizational team. For past programs, it has worked well to have a scientific organization committee that includes MESA developers, a local organizational committee comprising individuals at the host institute and/or in the host country who can help with local logistical matters, and a teaching committee. 9 months out (November) ----------------------- -- Contact lecturers. Try to invite people with a diverse set of research areas and consider focusing on topics that have not been covered in past programs (see previous summer school pages and agendas for this information) -- Contact TAs. +- Contact potential lecturers. Try to invite people with a diverse set of research areas and consider focusing on topics that have not been covered in past programs (see previous summer school pages and agendas for this information). Please be mindful of the fact that academics' schedules fill up quickly, and you may have to ask several candidates before your lecture roster is filled. + +- Contact potential TAs. We recommend that TAs should have attended a Summer School and performed well. TAs should span a range of MESA experience levels but in all cases have a strong baseline level of competence with the code. + +We aim for 50-50 gender representation (50% men, 50% women and gender minorities) among both lecturers and TAs. We have succeeded in having 35% or greater representation among women and gender minorities in past programs. + +9 months to 7 months out (November - January) +----------------------- +- Look for and apply to grant funding schemes. Previous supporters of the MESA Summer Schools include the International Research Network of Nuclear Astrophysics (IReNA; USA), the European ChETEC-INFRA network of research infrastructures, and individual research grants (NSF; Marie Curie scheme, ERC scheme). + +- reserve accommodation. Hotel room blocks can be booked for discounted rates. Some univerisites are willing to provide discounted bulk accommodation through their own facilities (e.g. dorms), as was the case at Santa Barbara. + +- open the application for students. A template for this is available from Meridith Joyce, Earl Bellinger, or Eoin Farrell (MESAdev). A Google form is a good way to provide the application. Be aware that summer schools have been oversubscribed by more than a factor of 2 in recent years, and be prepared to rank applications in a systematic way. We aim for 50-50 gender representation among students and have a track record of achieving 35%-45% participation from women and gender minorities, on average. + +6 months out (February) +----------------------- +- post the Summer School website. Bill Wolf (MESAev) has been the web manager for many Summer Schools + +- assign TAs to lecturers. We recommend assigning one first-time TA, one returning TA, and one very experienced TA per lecturer. This ensures that new TAs receive excellent training while the more experienced TAs can provide leadership on the development of exercises and management of the group. Please be aware that it has not been a requirement historically that the lecturers have any experience with MESA. It is the lecturers' jobs to develop the scientific program and contribute their subject expertise. It is the TAs jobs to turn the lecturers' science into accessible, MESA-based exercises. + + +5 months out (March) +----------------------- +- close applications + +- make selections among applications. An admissions rubric used for the 2022, 2023, and 2024 Summer School programs is available from Meridith Joyce (MESAdev) + +- email the supervisors of potential attendees to confirm that they have their advisor's permission and funding to attend. Be aware that some prospective students may apply without having secured funding and without their advisor's knowledge. + +- send acceptances to students, cc-ing superviors, while maintaining a ranked waitlist. If you do not hear back from an accepted student or their supervisor in, for example, 2 weeks, move on to the waitlist. There are typically several students admitted off the waitlist. + +4 months out (April) +----------------------- +- Begin regular, bi-weekly, all-hands meetings to check in with the organizational team, lecturers, and TAs. Lecturers should begin to schedule separate group meetings with their TAs to design exercises. Bi-weekly meetings serve to check in on the progress of these groups. + +- begin preparing any visa or invitation letters necessary for international students + +1 month out (July) +----------------------- +- Increase the cadence of all-hands meetings to weekly. Lab exercises should be distributed for testing among TAs, leaving at least two weeks before the start of Summer School for final corrections to be implemented. Labs should be tested for coherence, timing, and accessibility of the exercises + + +2 weeks out +----------------------- +- final corrections to labs are underway + +- Lecturers' programs and slides should be near completion. It is helpful if all lecture materials are available before the start of the labs. All lab materials should also be available before the start of the program. + +- send students a schedule or point them to a schedule online. Remind students which version of MESA they will be using and send links to installation instructions. Remind students that having MESA installed and working on their machines must happen before they arrive. \ No newline at end of file From ce5aa65286cb7198ccddd3976cb5dcb53f6fae51 Mon Sep 17 00:00:00 2001 From: Jared Goldberg Date: Thu, 8 Aug 2024 12:01:12 -0400 Subject: [PATCH 42/66] Update summer_schools.rst to include links to MESA Education material site and M@K and MDU sites --- docs/source/summer_schools.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/summer_schools.rst b/docs/source/summer_schools.rst index 9f9b7c5af..93bd18f2f 100644 --- a/docs/source/summer_schools.rst +++ b/docs/source/summer_schools.rst @@ -8,7 +8,7 @@ MESA Summer School Programs -- this page under construction! History of the MESA Summer School Program ----------------------------------------- -The MESA Summer Schools have traditionally been held in Santa Barbara, California, until 2022. The 2023 MESA Summer School program, branded as MESA@Konkoly, was held in Budapest, Hungary. This was follwed by MESA Down Under, hosted in Sydney in June of 2024. +The MESA Summer Schools (material linked `here `_) have traditionally been held in Santa Barbara, California, until 2022. The 2023 MESA Summer School program, branded as `MESA@Konkoly `_, was held in Budapest, Hungary. This was follwed by `MESA Down Under `_, hosted in Sydney in June of 2024. As of 2022, MESA Summer Schools can be run anywhere in the world. The involvement of the MESA developers is encouraged, and we are happy to help. @@ -78,4 +78,4 @@ We aim for 50-50 gender representation (50% men, 50% women and gender minorities - Lecturers' programs and slides should be near completion. It is helpful if all lecture materials are available before the start of the labs. All lab materials should also be available before the start of the program. -- send students a schedule or point them to a schedule online. Remind students which version of MESA they will be using and send links to installation instructions. Remind students that having MESA installed and working on their machines must happen before they arrive. \ No newline at end of file +- send students a schedule or point them to a schedule online. Remind students which version of MESA they will be using and send links to installation instructions. Remind students that having MESA installed and working on their machines must happen before they arrive. From 5d8501efff70ef314644fc33c45efa292a76b83a Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Thu, 8 Aug 2024 13:55:35 -0600 Subject: [PATCH 43/66] [ci skip] make fspot and xspot source controls --- star/defaults/controls.defaults | 9 +++++++++ star/private/ctrls_io.f90 | 11 +++++++++++ star/test_suite/starspots/inlist_starspots | 4 ++-- star/test_suite/starspots/src/run_star_extras.f90 | 4 ++-- star_data/private/star_controls.inc | 5 +++++ 5 files changed, 29 insertions(+), 4 deletions(-) diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index 337c4a31a..808f9a8e5 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -4636,6 +4636,15 @@ use_T_tau_gradr_factor = .false. +! star spot controls +! ================= + + ! reiterate readme docs here + ! describe valid ranges for these parameters + + fspot = 1.0 + xspot = 0.0 + ! mass gain or loss ! ================= diff --git a/star/private/ctrls_io.f90 b/star/private/ctrls_io.f90 index dafa6cced..216092ae8 100644 --- a/star/private/ctrls_io.f90 +++ b/star/private/ctrls_io.f90 @@ -490,6 +490,9 @@ module ctrls_io atm_build_tau_outer, atm_build_dlogtau, atm_build_errtol, & use_T_tau_gradr_factor, & + + ! star spots + fspot, xspot, & ! extra heat near surface to model irradiation irradiation_flux, column_depth_for_irradiation, & @@ -1285,6 +1288,10 @@ subroutine store_controls(s, ierr) s% use_T_tau_gradr_factor = use_T_tau_gradr_factor + ! star spots + s% fspot = fspot + s% xspot = xspot + ! extra heat near surface to model irradiation s% irradiation_flux = irradiation_flux s% column_depth_for_irradiation = column_depth_for_irradiation @@ -2966,6 +2973,10 @@ subroutine set_controls_for_writing(s, ierr) use_T_tau_gradr_factor = s% use_T_tau_gradr_factor + ! star spots + fspot = s% fspot + xspot = s% xspot + ! extra heat near surface to model irradiation irradiation_flux = s% irradiation_flux column_depth_for_irradiation = s% column_depth_for_irradiation diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 53929baa6..2fd5fcfe1 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -65,8 +65,8 @@ use_other_mlt_results = .true. !.true. use_other_surface_PT = .true. !.True. - x_ctrl(1) = 0.34d0 ! fspot - x_ctrl(2) = 0.85d0 ! xspot + fspot = 0.34d0 ! fspot + xspot = 0.85d0 ! xspot atm_option = 'table' atm_table = 'photosphere' diff --git a/star/test_suite/starspots/src/run_star_extras.f90 b/star/test_suite/starspots/src/run_star_extras.f90 index 3aabef591..d448ce3ad 100644 --- a/star/test_suite/starspots/src/run_star_extras.f90 +++ b/star/test_suite/starspots/src/run_star_extras.f90 @@ -57,8 +57,8 @@ subroutine extras_controls(id, ierr) ! otherwise we use a null_ version which does nothing (except warn). - fspot = s% x_ctrl(1) - xspot = s% x_ctrl(2) + fspot = s% fspot + xspot = s% xspot s% extras_startup => extras_startup diff --git a/star_data/private/star_controls.inc b/star_data/private/star_controls.inc index 00cdac22c..cb3381acd 100644 --- a/star_data/private/star_controls.inc +++ b/star_data/private/star_controls.inc @@ -432,6 +432,11 @@ logical :: use_T_tau_gradr_factor + ! star spot controls + + real(dp) :: fspot + real(dp) :: xspot + ! mass gain or loss real(dp) :: mass_change From d0e862aafd0619ede9e136fbcbee1cb1f0cea830 Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Thu, 8 Aug 2024 14:03:32 -0600 Subject: [PATCH 44/66] [ci skip] document fspot,xspot meanings in controls.defaults --- star/defaults/controls.defaults | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index 808f9a8e5..399bd83d1 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -4639,8 +4639,19 @@ ! star spot controls ! ================= - ! reiterate readme docs here - ! describe valid ranges for these parameters + ! The impedence of the surface flux due to magnetic pressure from starspots is parameterized + ! in the style of an atmospheric boundary modification. As first described by + ! Somers et al. (2015; ApJ) https://ui.adsabs.harvard.edu/abs/2015ApJ...807..174S, + ! the degree of "spottiness" on the stellar surface is characterized using two parameters: + + ! * SPOTF (hereafter fspot): a coverage fraction, or "spot filling factor" (in the notation of the YREC documentation); and + + ! * SPOTX (hereafter xspot): the temperature contrast between the spotted and unspotted regions: xspot = T_spot/T_photosphere. + + ! The coverage fraction is set to fspot = 0.34 + ! (for consistency with observations of low-mass stars: + ! Cao et al., 2022 https://ui.adsabs.harvard.edu/abs/2022ApJ...924...84C + ! and the temperature contrast is set to xspot = 0.85 (also from fits to observations). fspot = 1.0 xspot = 0.0 From 3b8599b0b737e9edd4cb41634921253da6243849 Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Thu, 8 Aug 2024 14:27:43 -0600 Subject: [PATCH 45/66] [ci skip] note in changelog --- docs/source/changelog.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 8654dca30..86e8992a1 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -14,6 +14,12 @@ Changes in main New Features ------------ +**Update to starspots ** +star spot parameters + ``fspot`` + ``xspot`` + have been added as general controls and are now accessible outside of ``test_suite/starspots/``. Star spots are off by default + **Replacement of HDF5io by ForUM** The HDF5io module (in the :file:`hdf5io` subdirectory) has been From 8e9a48dbb80f7bc45d69fa019439d1205e208130 Mon Sep 17 00:00:00 2001 From: "M. Joyce" Date: Thu, 8 Aug 2024 14:30:28 -0600 Subject: [PATCH 46/66] add fspot and xspot for starspots as control parameters (#706) * [ci skip] make fspot and xspot source controls * [ci skip] document fspot,xspot meanings in controls.defaults * [ci skip] note in changelog --- docs/source/changelog.rst | 6 ++++++ star/defaults/controls.defaults | 20 +++++++++++++++++++ star/private/ctrls_io.f90 | 11 ++++++++++ star/test_suite/starspots/inlist_starspots | 4 ++-- .../starspots/src/run_star_extras.f90 | 4 ++-- star_data/private/star_controls.inc | 5 +++++ 6 files changed, 46 insertions(+), 4 deletions(-) diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 8654dca30..86e8992a1 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -14,6 +14,12 @@ Changes in main New Features ------------ +**Update to starspots ** +star spot parameters + ``fspot`` + ``xspot`` + have been added as general controls and are now accessible outside of ``test_suite/starspots/``. Star spots are off by default + **Replacement of HDF5io by ForUM** The HDF5io module (in the :file:`hdf5io` subdirectory) has been diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index 337c4a31a..399bd83d1 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -4636,6 +4636,26 @@ use_T_tau_gradr_factor = .false. +! star spot controls +! ================= + + ! The impedence of the surface flux due to magnetic pressure from starspots is parameterized + ! in the style of an atmospheric boundary modification. As first described by + ! Somers et al. (2015; ApJ) https://ui.adsabs.harvard.edu/abs/2015ApJ...807..174S, + ! the degree of "spottiness" on the stellar surface is characterized using two parameters: + + ! * SPOTF (hereafter fspot): a coverage fraction, or "spot filling factor" (in the notation of the YREC documentation); and + + ! * SPOTX (hereafter xspot): the temperature contrast between the spotted and unspotted regions: xspot = T_spot/T_photosphere. + + ! The coverage fraction is set to fspot = 0.34 + ! (for consistency with observations of low-mass stars: + ! Cao et al., 2022 https://ui.adsabs.harvard.edu/abs/2022ApJ...924...84C + ! and the temperature contrast is set to xspot = 0.85 (also from fits to observations). + + fspot = 1.0 + xspot = 0.0 + ! mass gain or loss ! ================= diff --git a/star/private/ctrls_io.f90 b/star/private/ctrls_io.f90 index dafa6cced..216092ae8 100644 --- a/star/private/ctrls_io.f90 +++ b/star/private/ctrls_io.f90 @@ -490,6 +490,9 @@ module ctrls_io atm_build_tau_outer, atm_build_dlogtau, atm_build_errtol, & use_T_tau_gradr_factor, & + + ! star spots + fspot, xspot, & ! extra heat near surface to model irradiation irradiation_flux, column_depth_for_irradiation, & @@ -1285,6 +1288,10 @@ subroutine store_controls(s, ierr) s% use_T_tau_gradr_factor = use_T_tau_gradr_factor + ! star spots + s% fspot = fspot + s% xspot = xspot + ! extra heat near surface to model irradiation s% irradiation_flux = irradiation_flux s% column_depth_for_irradiation = column_depth_for_irradiation @@ -2966,6 +2973,10 @@ subroutine set_controls_for_writing(s, ierr) use_T_tau_gradr_factor = s% use_T_tau_gradr_factor + ! star spots + fspot = s% fspot + xspot = s% xspot + ! extra heat near surface to model irradiation irradiation_flux = s% irradiation_flux column_depth_for_irradiation = s% column_depth_for_irradiation diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 53929baa6..2fd5fcfe1 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -65,8 +65,8 @@ use_other_mlt_results = .true. !.true. use_other_surface_PT = .true. !.True. - x_ctrl(1) = 0.34d0 ! fspot - x_ctrl(2) = 0.85d0 ! xspot + fspot = 0.34d0 ! fspot + xspot = 0.85d0 ! xspot atm_option = 'table' atm_table = 'photosphere' diff --git a/star/test_suite/starspots/src/run_star_extras.f90 b/star/test_suite/starspots/src/run_star_extras.f90 index 3aabef591..d448ce3ad 100644 --- a/star/test_suite/starspots/src/run_star_extras.f90 +++ b/star/test_suite/starspots/src/run_star_extras.f90 @@ -57,8 +57,8 @@ subroutine extras_controls(id, ierr) ! otherwise we use a null_ version which does nothing (except warn). - fspot = s% x_ctrl(1) - xspot = s% x_ctrl(2) + fspot = s% fspot + xspot = s% xspot s% extras_startup => extras_startup diff --git a/star_data/private/star_controls.inc b/star_data/private/star_controls.inc index 00cdac22c..cb3381acd 100644 --- a/star_data/private/star_controls.inc +++ b/star_data/private/star_controls.inc @@ -432,6 +432,11 @@ logical :: use_T_tau_gradr_factor + ! star spot controls + + real(dp) :: fspot + real(dp) :: xspot + ! mass gain or loss real(dp) :: mass_change From 41b6357fd8d8c871196810db163e4573b93819be Mon Sep 17 00:00:00 2001 From: pmocz Date: Thu, 8 Aug 2024 17:46:54 -0400 Subject: [PATCH 47/66] [ci skip] formatting --- star/defaults/controls.defaults | 153 +++++++++--------- star/private/ctrls_io.f90 | 12 +- star/test_suite/starspots/README.rst | 8 +- star/test_suite/starspots/inlist_starspots | 12 +- .../starspots/src/run_star_extras.f90 | 38 ++--- star_data/private/star_controls.inc | 6 +- 6 files changed, 111 insertions(+), 118 deletions(-) diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index 399bd83d1..eb00f74a0 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -542,7 +542,7 @@ ! Format originally defined for the GONG solar model project. A ! definition was given in 2005 for the `CoRoT/ESTA project`_ and ! `GONG itself `_. - ! MESA's implementation largely follows this subsequent + ! MESA's implementation largely follows this subsequent ! `2015 definition `_. ! ``'OSC'`` @@ -673,7 +673,7 @@ ! format_for_OSC_data ! ~~~~~~~~~~~~~~~~~~~ - ! float format for ``'OSC'`` data format + ! float format for ``'OSC'`` data format ! :: @@ -1338,7 +1338,7 @@ ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ! envelope_fraction_left = (star_mass - he_core_mass)/(initial_mass - he_core_mass) - + ! Stop when ``envelope_fraction_left`` < this limit. ! :: @@ -1350,7 +1350,7 @@ ! ~~~~~~~~~~~~~~~~ ! xmstar = mstar - M_center - + ! stop when xmstar in grams is < this. <= 0 means no limit. ! :: @@ -1362,7 +1362,7 @@ ! ~~~~~~~~~~~~~~~~ ! xmstar = mstar - M_center - + ! stop when xmstar in grams is > this. <= 0 means no limit. ! :: @@ -1802,7 +1802,7 @@ ! fe_core_infall_mass ! ~~~~~~~~~~~~~~~~~~~ - ! Amount of mass to check if collapsing, the smaller this is the closer the velocity minima will be to ``fe_core_infall`` but there will be a greater chance of a + ! Amount of mass to check if collapsing, the smaller this is the closer the velocity minima will be to ``fe_core_infall`` but there will be a greater chance of a ! transistent velocity spike causing the model to prematurely exit. In solar masses @@ -1821,7 +1821,7 @@ ! non_fe_core_infall_mass ! ~~~~~~~~~~~~~~~~~~~~~~~ - ! Amount of mass to check if collapsing, the smaller this is the closer the velocity minima will be to ``non_fe_core_infall`` but there will be a greater chance of a + ! Amount of mass to check if collapsing, the smaller this is the closer the velocity minima will be to ``non_fe_core_infall`` but there will be a greater chance of a ! transistent velocity spike causing the model to prematurely exit. In solar masses @@ -1916,8 +1916,8 @@ ! :: stop_near_zams = .false. - - + + ! stop_at_phase_PreMS ! ~~~~~~~~~~~~~~~~~~~ ! stop_at_phase_ZAMS @@ -1952,7 +1952,7 @@ ! :: ! :: - + stop_at_phase_PreMS = .false. stop_at_phase_ZAMS = .false. stop_at_phase_IAMS = .false. @@ -1966,7 +1966,7 @@ stop_at_phase_O_Burn = .false. stop_at_phase_Si_Burn = .false. stop_at_phase_WDCS = .false. - + ! Lnuc_div_L_upper_limit ! ~~~~~~~~~~~~~~~~~~~~~~ @@ -2256,7 +2256,7 @@ ! If false, then stick to the usual definition -- P/(g*rho). ! If true, use min of the usual and sound speed * hydro time scale, sqrt(P/G)/rho. - ! Note that the 'TDC' ``MLT_option`` does not respect the ``alt_scale_height`` option, and continues to use ``h = P / rho g`` + ! Note that the 'TDC' ``MLT_option`` does not respect the ``alt_scale_height`` option, and continues to use ``h = P / rho g`` ! even if that flag is set. ! :: @@ -2372,7 +2372,6 @@ ! :: mlt_make_surface_no_mixing = .false. - ! T_mix_limit @@ -3112,7 +3111,7 @@ RSP_nz_outer = 40 RSP_T_anchor = 11d3 RSP_T_inner = 2d6 - RSP_testing = .false. + RSP_testing = .false. ! :: @@ -3359,7 +3358,7 @@ ! Mixing coefficients are multiplied by this factor. ! The ``mix_factor`` is applied in subroutine ``get_convection_sigmas`` in ``star/private/mix_info.f90`` -- ! the lagrangian diffusion coefficient sigma(k) at cell boundary k is set to - ! ``mix_factor*D*(4*pi*r(k)^2*rho_face(k))^2``. + ! ``mix_factor*D*(4*pi*r(k)^2*rho_face(k))^2``. ! Note that the value of D is not changed -- it is just used as a term in calculating sigma. ! :: @@ -3995,7 +3994,7 @@ ! use_other_j_for_adjust_J_lost option to specify a specific angular momentum ! of removed material different from j_rot_surf - ! In order to prevent the algorithm from digging to deep to adjust J, + ! In order to prevent the algorithm from digging to deep to adjust J, ! there is a timestep limit adjust_J_q_limit ! :: @@ -4060,7 +4059,7 @@ ! When w_div_wc_flag is true, rather than a hard limit on w_div_wcrit ! we use w_div_wcrit_max2infinity, the resulting w_div_wc will match + ! In the limit of j_rot->infinity, the resulting w_div_wc will match ! w_div_wcrit_max, while nothing is done when w_div_wcrit_max`_. ! + ``'ONe'`` : oxygen-neon phase separation using the two-component ! phase diagram of `Blouin & Daligault (2021b) `_. - + ! :: phase_separation_option = 'CO' @@ -7355,7 +7356,7 @@ ! :: phase_separation_mixing_use_brunt = .true. - + ! eos controls ! ============ @@ -7510,7 +7511,7 @@ ! or use the faster method by allowing for a small tolerance on the mixture used for the computations of these variables (``'mombarg'``). ! :: - + op_mono_method = 'hu' ! emesh_data_for_op_mono_path @@ -7526,7 +7527,7 @@ ! and then unpack it in place with ``unxz -v OP_mono_master_grid_MESA_emesh.txt.xz`` ! :: - + emesh_data_for_op_mono_path = '' ! '' defaults to $MESA_OP_MONO_MASTER_GRID @@ -7733,14 +7734,10 @@ min_magnitude_brunt_B = -1d99 - - - ! structure equations ! =================== - ! energy_eqn_option ! ~~~~~~~~~~~~~~~~~ ! Available options are ``'dedt'`` or ``'eps_grav'``. @@ -7908,7 +7905,7 @@ ! :: velocity_q_upper_bound = 1d99 - + ! velocity_tau_lower_bound ! ~~~~~~~~~~~~~~~~~~~~~~~~ @@ -8221,9 +8218,9 @@ ! :: use_dPrad_dm_form_of_T_gradient_eqn = .false. - use_gradT_actual_vs_gradT_MLT_for_T_gradient_eqn = .false. - - + use_gradT_actual_vs_gradT_MLT_for_T_gradient_eqn = .false. + + ! drag_coefficient ! ~~~~~~~~~~~~~~~~ ! min_q_for_drag @@ -8236,7 +8233,7 @@ ! burning in massive stars and AGB stars. ! Under certain circumstances we will not have drag in the surface k=1 zone - ! To force the drag term to be on in the outer zone you must enable one of the + ! To force the drag term to be on in the outer zone you must enable one of the ! following surface boundary conditions: ! ``use_momentum_outer_BC``, ``use_zero_Pgas_outer_BC``, or ``use_fixed_Psurf_outer_BC`` @@ -8254,7 +8251,7 @@ use_drag_energy = .true. drag_coefficient = 0d0 min_q_for_drag = 0d0 - + ! for hydro comparison tests (e.g., Sedov) @@ -8324,7 +8321,7 @@ RTI_m_full_boost = 4d0 RTI_m_no_boost = 5d0 - + ! retry_for_v_above_clight ! ~~~~~~~~~~~~~~~~~~~~~~~~ @@ -8335,7 +8332,7 @@ ! :: retry_for_v_above_clight = .true. - + ! solver controls ! =============== @@ -8542,7 +8539,6 @@ include_w_in_correction_limits = .true. - ! max_X_for_conv_timescale ! ~~~~~~~~~~~~~~~~~~~~~~~~ ! min_X_for_conv_timescale @@ -8557,7 +8553,7 @@ ! ~~~~~~~~~~~~~~~~~~~~~~~~ ! :: - + max_X_for_conv_timescale = 1d0 min_X_for_conv_timescale = 0d0 max_q_for_conv_timescale = 1d0 @@ -8706,7 +8702,7 @@ ! do_normalize_dqs_as_part_of_set_qs ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - + ! normalize_dqs destroys bit-for-bit read as inverse of write for models. ! ok for create pre ms etc., but not for read model ! create_pre_ms calls normalize_dqs even if this flag is false. @@ -8714,12 +8710,12 @@ ! :: do_normalize_dqs_as_part_of_set_qs = .false. - + ! use_DGESVX_in_bcyclic ! use_equilibration_in_DGESVX ! report_min_rcond_from_DGESXV - + ! FOR DEBUGGING ONLY. NOT FOR GENERAL USE. ! :: @@ -9207,7 +9203,7 @@ ! 'Lnuc_cat' delta_lgL_nuc_cat_limit ! 'Lnuc_H' delta_lgL_H_limit ! 'Lnuc_He' delta_lgL_He_limit - ! 'lgL_power_phot' delta_lgL_power_photo_limit + ! 'lgL_power_phot' delta_lgL_power_photo_limit ! 'Lnuc_z' delta_lgL_z_limit ! 'bad_X_sum' (solver found bad mass sum) ! 'dL/L' dL_div_L_limit @@ -9269,12 +9265,12 @@ ! time_delta_coeff - smaller forces smaller timesteps giving better time resolution. ! multiplier for all real number timestep limits and hard limits. ! does not apply to integer valued limits such as - + ! + solver_iters_timestep_limit ! + burn_steps_limit ! + diffusion_steps_limit ! + diffusion_iters_limit - + ! does not apply to varcontrol_target. ! analogous to mesh_delta_coeff for better spatial resolution. @@ -10345,7 +10341,7 @@ min_lgT_for_lgL_power_photo_limit = 9d0 lgL_power_photo_burn_min = 10d0 lgL_power_photo_drop_factor = 10 - + ! limits based on changes at photosphere @@ -10442,7 +10438,7 @@ ! ``abs_du_div_cs`` > ``min_abs_du_div_cs_for_dt_div_min_dr_div_cs_limit`` and ! and ! ``abs_u_div_cs`` > ``min_abs_u_div_cs_for_dt_div_min_dr_div_cs_limit`` - ! + ! ! allow focus on regions near shock face. ! :: @@ -10879,7 +10875,6 @@ delta_lg_XSi_cntr_hard_limit = -1 - ! delta_XH_cntr_limit ! ~~~~~~~~~~~~~~~~~~~ @@ -11038,9 +11033,9 @@ ! ~~~~~~~~~~~~~~~~~~ ! delta_XSi_drop_only ! ~~~~~~~~~~~~~~~~~~~ - - ! If true, then only limit drops in abundance. + + ! If true, then only limit drops in abundance. ! :: @@ -11121,7 +11116,7 @@ ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ! hard_limit_for_rel_error_in_energy_conservation ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - + ! :: ! rel_error_in_energy_conservation = abs(error_in_energy_conservation/total_energy) @@ -11252,7 +11247,7 @@ solver_test_partials_write_eos_call_info = .false. solver_epsder_struct = 1d-5 solver_epsder_chem = 1d-5 - + energy_conservation_dump_model_number = -1 @@ -11489,7 +11484,7 @@ use_other_set_pgstar_controls = .false. use_other_accreting_state = .false. use_other_eval_i_rot = .false. - + ! :: use_other_export_pulse_data = .false. diff --git a/star/private/ctrls_io.f90 b/star/private/ctrls_io.f90 index 216092ae8..251379874 100644 --- a/star/private/ctrls_io.f90 +++ b/star/private/ctrls_io.f90 @@ -175,7 +175,7 @@ module ctrls_io RSP_relax_initial_model, RSP_trace_RSP_build_model, & RSP_GREKM_avg_abs_limit, RSP_GREKM_avg_abs_frac_new, RSP_kap_density_factor, RSP_map_columns_filename, & RSP_relax_alfap_before_alfat, RSP_max_outer_dm_tries, RSP_max_inner_scale_tries, RSP_T_anchor_tolerance, & - ! mass gain or loss + ! mass gain or loss mass_change, mass_change_full_on_dt, mass_change_full_off_dt, trace_dt_control_mass_change, & min_wind, max_wind, use_accreted_material_j, accreted_material_j, D_omega_mixing_rate, & D_omega_mixing_across_convection_boundary, max_q_for_D_omega_zero_in_convection_region, nu_omega_mixing_rate, & @@ -451,7 +451,7 @@ module ctrls_io delta_dX_div_X_cntr_min, delta_dX_div_X_cntr_max, delta_dX_div_X_cntr_limit, delta_dX_div_X_cntr_hard_limit, & delta_dX_div_X_drop_only, delta_lg_XH_drop_only, & delta_lg_XHe_drop_only, delta_lg_XC_drop_only, delta_lg_XNe_drop_only, delta_lg_XO_drop_only, delta_lg_XSi_drop_only, & - delta_XH_drop_only, delta_XHe_drop_only, delta_XC_drop_only, delta_XNe_drop_only, delta_XO_drop_only, delta_XSi_drop_only, & + delta_XH_drop_only, delta_XHe_drop_only, delta_XC_drop_only, delta_XNe_drop_only, delta_XO_drop_only, delta_XSi_drop_only, & delta_lg_XH_cntr_min, delta_lg_XH_cntr_max, delta_lg_XH_cntr_limit, delta_lg_XH_cntr_hard_limit, & delta_lg_XHe_cntr_min, delta_lg_XHe_cntr_max, delta_lg_XHe_cntr_limit, delta_lg_XHe_cntr_hard_limit, & delta_lg_XC_cntr_min, delta_lg_XC_cntr_max, delta_lg_XC_cntr_limit, delta_lg_XC_cntr_hard_limit, & @@ -491,7 +491,7 @@ module ctrls_io use_T_tau_gradr_factor, & - ! star spots + ! starspots fspot, xspot, & ! extra heat near surface to model irradiation @@ -1288,7 +1288,7 @@ subroutine store_controls(s, ierr) s% use_T_tau_gradr_factor = use_T_tau_gradr_factor - ! star spots + ! starspots s% fspot = fspot s% xspot = xspot @@ -2973,7 +2973,7 @@ subroutine set_controls_for_writing(s, ierr) use_T_tau_gradr_factor = s% use_T_tau_gradr_factor - ! star spots + ! starspots fspot = s% fspot xspot = s% xspot @@ -4151,7 +4151,7 @@ subroutine get_control(s, name, val, ierr) exit end if if(is_iostat_end(iostat)) exit - end do + end do if(len_trim(val) == 0 .and. ind==0 ) ierr = -1 diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index 990c0f06a..f7b60e9c1 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -16,14 +16,14 @@ in the style of an atmospheric boundary modification. As first described by `Somers et al. (2015; ApJ) `__, the degree of "spottiness" on the stellar surface is characterized using two parameters: -* SPOTF (hereafter fspot): a coverage fraction, or "spot filling factor" (in the notation of the YREC documentation); and +* SPOTF (hereafter ``fspot``): a coverage fraction, or "spot filling factor" (in the notation of the YREC documentation); and -* SPOTX (hereafter xspot): the temperature contrast between the spotted and unspotted regions: xspot = T_spot/T_photosphere. +* SPOTX (hereafter ``xspot``): the temperature contrast between the spotted and unspotted regions: xspot = T_spot/T_photosphere. -The coverage fraction is set to fspot = 0.34 +The coverage fraction is set to ``fspot = 0.34`` (for consistency with observations of low-mass stars: `Cao et al., 2022 `__) -and the temperature contrast is set to xspot = 0.85 (also from fits to observations). +and the temperature contrast is set to ``xspot = 0.85`` (also from fits to observations). Detailed discussion of this functionality can be found in `MESA Instrument Paper VI: Starspots `__. diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 2fd5fcfe1..ef54ff85d 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -62,11 +62,11 @@ max_age = 24.63d9 !26d9 !0.8d9 - use_other_mlt_results = .true. !.true. - use_other_surface_PT = .true. !.True. + use_other_mlt_results = .true. + use_other_surface_PT = .true. - fspot = 0.34d0 ! fspot - xspot = 0.85d0 ! xspot + fspot = 0.34d0 + xspot = 0.85d0 atm_option = 'table' atm_table = 'photosphere' @@ -83,7 +83,7 @@ photo_interval = 100 ! starting specifications - initial_mass = 0.9 !1.0 ! in Msun units + initial_mass = 0.9 ! in Msun units min_timestep_limit=0 max_model_number = -1 !1500 @@ -94,7 +94,7 @@ Blocker_scaling_factor = 0.2 max_wind = 1d-3 - mixing_length_alpha = 1.9500 !1.95 + mixing_length_alpha = 1.9500 MLT_option = 'Henyey' do_element_diffusion = .false. diff --git a/star/test_suite/starspots/src/run_star_extras.f90 b/star/test_suite/starspots/src/run_star_extras.f90 index d448ce3ad..9145d2541 100644 --- a/star/test_suite/starspots/src/run_star_extras.f90 +++ b/star/test_suite/starspots/src/run_star_extras.f90 @@ -27,7 +27,7 @@ module run_star_extras use const_def use math_lib use chem_def !! maybe taking up uncessary space but whatever - + implicit none real(dp) :: fspot, xspot, PB_i, Teff_local @@ -37,10 +37,10 @@ module run_star_extras contains include "test_suite_extras.inc" - + ! these routines are called by the standard run_star check_model - + subroutine extras_controls(id, ierr) integer, intent(in) :: id integer, intent(out) :: ierr @@ -48,7 +48,7 @@ subroutine extras_controls(id, ierr) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - + ! this is the place to set any procedure pointers you want to change ! e.g., other_wind, other_mixing, other_energy (see star_data.inc) @@ -69,7 +69,7 @@ subroutine extras_controls(id, ierr) s% how_many_extra_history_columns => how_many_extra_history_columns s% data_for_extra_history_columns => data_for_extra_history_columns s% how_many_extra_profile_columns => how_many_extra_profile_columns - s% data_for_extra_profile_columns => data_for_extra_profile_columns + s% data_for_extra_profile_columns => data_for_extra_profile_columns s% how_many_extra_history_header_items => how_many_extra_history_header_items s% data_for_extra_history_header_items => data_for_extra_history_header_items @@ -92,7 +92,7 @@ subroutine extras_startup(id, restart, ierr) if (ierr /= 0) return call test_suite_startup(s, restart, ierr) end subroutine extras_startup - + integer function extras_start_step(id) integer, intent(in) :: id @@ -115,9 +115,9 @@ integer function extras_start_step(id) ! set PB_i here and then other_mlt will know about it, because ! quantities set here are carried over the course of a timestep, ! AKA all newton iterations - + mu_ideal_gas = s% mu(1) !1.00794d0 ! for hydrogen, 1 gram per mole - !write(*,*) 'MESA def, my def: ', s% mu(1), mu_ideal_gas + !write(*,*) 'MESA def, my def: ', s% mu(1), mu_ideal_gas R2 = pow2(s%R(1)) Teff_local = pow(s%L(1)/(pi4*boltz_sigma*R2), 0.25d0) @@ -162,7 +162,7 @@ subroutine YREC_spots_other_mlt_results(id, k, MLT_option, & ! NOTE: k=0 is a v ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - + !------------------------------ !if (s% star_age >= 10d0) then if (.not. s% doing_relax .and. .not. s% doing_first_model_of_run) then @@ -190,7 +190,7 @@ subroutine starspot_tweak_PT(id, skip_partials, & logical, intent(in) :: skip_partials logical :: need_atm_Psurf, need_atm_Tsurf - + real(dp), intent(out) :: & lnT_surf, dlnT_dL, dlnT_dlnR, dlnT_dlnM, dlnT_dlnkap, & lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap @@ -211,7 +211,7 @@ subroutine starspot_tweak_PT(id, skip_partials, & need_atm_Psurf = .true. need_atm_Tsurf = .true. - + alp = 1d0 - fspot + fspot*pow4(xspot) ! This is the surface-average value for luminosity @@ -248,7 +248,7 @@ integer function extras_check_model(id) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - extras_check_model = keep_going + extras_check_model = keep_going if (.false. .and. s% star_mass_h1 < 0.35d0) then ! stop when star hydrogen mass drops to specified level @@ -272,7 +272,7 @@ integer function how_many_extra_history_columns(id) how_many_extra_history_columns = 0 end function how_many_extra_history_columns - + subroutine data_for_extra_history_columns(id, n, names, vals, ierr) integer, intent(in) :: id, n @@ -283,14 +283,14 @@ subroutine data_for_extra_history_columns(id, n, names, vals, ierr) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - + ! note: do NOT add the extras names to history_columns.list ! the history_columns.list is only for the built-in history column options. ! it must not include the new column names you are adding here. end subroutine data_for_extra_history_columns - + integer function how_many_extra_profile_columns(id) integer, intent(in) :: id integer :: ierr @@ -300,8 +300,8 @@ integer function how_many_extra_profile_columns(id) if (ierr /= 0) return how_many_extra_profile_columns = 0 end function how_many_extra_profile_columns - - + + subroutine data_for_extra_profile_columns(id, n, nz, names, vals, ierr) integer, intent(in) :: id, n, nz character (len=maxlen_profile_column_name) :: names(n) @@ -381,8 +381,8 @@ integer function extras_finish_step(id) ! by default, indicate where (in the code) MESA terminated if (extras_finish_step == terminate) s% termination_code = t_extras_finish_step end function extras_finish_step - - + + subroutine extras_after_evolve(id, ierr) integer, intent(in) :: id integer, intent(out) :: ierr diff --git a/star_data/private/star_controls.inc b/star_data/private/star_controls.inc index cb3381acd..64233afca 100644 --- a/star_data/private/star_controls.inc +++ b/star_data/private/star_controls.inc @@ -432,10 +432,8 @@ logical :: use_T_tau_gradr_factor - ! star spot controls - - real(dp) :: fspot - real(dp) :: xspot + ! starspots + real(dp) :: fspot, xspot ! mass gain or loss From 668d23fbe26c2b40657b45efd3287512828f7d43 Mon Sep 17 00:00:00 2001 From: pmocz Date: Thu, 8 Aug 2024 17:46:54 -0400 Subject: [PATCH 48/66] [ci skip] formatting --- star/defaults/controls.defaults | 153 +++++++++--------- star/private/ctrls_io.f90 | 12 +- star/test_suite/starspots/README.rst | 8 +- star/test_suite/starspots/inlist_starspots | 12 +- .../starspots/src/run_star_extras.f90 | 38 ++--- star_data/private/star_controls.inc | 6 +- 6 files changed, 111 insertions(+), 118 deletions(-) diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index 399bd83d1..eb00f74a0 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -542,7 +542,7 @@ ! Format originally defined for the GONG solar model project. A ! definition was given in 2005 for the `CoRoT/ESTA project`_ and ! `GONG itself `_. - ! MESA's implementation largely follows this subsequent + ! MESA's implementation largely follows this subsequent ! `2015 definition `_. ! ``'OSC'`` @@ -673,7 +673,7 @@ ! format_for_OSC_data ! ~~~~~~~~~~~~~~~~~~~ - ! float format for ``'OSC'`` data format + ! float format for ``'OSC'`` data format ! :: @@ -1338,7 +1338,7 @@ ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ! envelope_fraction_left = (star_mass - he_core_mass)/(initial_mass - he_core_mass) - + ! Stop when ``envelope_fraction_left`` < this limit. ! :: @@ -1350,7 +1350,7 @@ ! ~~~~~~~~~~~~~~~~ ! xmstar = mstar - M_center - + ! stop when xmstar in grams is < this. <= 0 means no limit. ! :: @@ -1362,7 +1362,7 @@ ! ~~~~~~~~~~~~~~~~ ! xmstar = mstar - M_center - + ! stop when xmstar in grams is > this. <= 0 means no limit. ! :: @@ -1802,7 +1802,7 @@ ! fe_core_infall_mass ! ~~~~~~~~~~~~~~~~~~~ - ! Amount of mass to check if collapsing, the smaller this is the closer the velocity minima will be to ``fe_core_infall`` but there will be a greater chance of a + ! Amount of mass to check if collapsing, the smaller this is the closer the velocity minima will be to ``fe_core_infall`` but there will be a greater chance of a ! transistent velocity spike causing the model to prematurely exit. In solar masses @@ -1821,7 +1821,7 @@ ! non_fe_core_infall_mass ! ~~~~~~~~~~~~~~~~~~~~~~~ - ! Amount of mass to check if collapsing, the smaller this is the closer the velocity minima will be to ``non_fe_core_infall`` but there will be a greater chance of a + ! Amount of mass to check if collapsing, the smaller this is the closer the velocity minima will be to ``non_fe_core_infall`` but there will be a greater chance of a ! transistent velocity spike causing the model to prematurely exit. In solar masses @@ -1916,8 +1916,8 @@ ! :: stop_near_zams = .false. - - + + ! stop_at_phase_PreMS ! ~~~~~~~~~~~~~~~~~~~ ! stop_at_phase_ZAMS @@ -1952,7 +1952,7 @@ ! :: ! :: - + stop_at_phase_PreMS = .false. stop_at_phase_ZAMS = .false. stop_at_phase_IAMS = .false. @@ -1966,7 +1966,7 @@ stop_at_phase_O_Burn = .false. stop_at_phase_Si_Burn = .false. stop_at_phase_WDCS = .false. - + ! Lnuc_div_L_upper_limit ! ~~~~~~~~~~~~~~~~~~~~~~ @@ -2256,7 +2256,7 @@ ! If false, then stick to the usual definition -- P/(g*rho). ! If true, use min of the usual and sound speed * hydro time scale, sqrt(P/G)/rho. - ! Note that the 'TDC' ``MLT_option`` does not respect the ``alt_scale_height`` option, and continues to use ``h = P / rho g`` + ! Note that the 'TDC' ``MLT_option`` does not respect the ``alt_scale_height`` option, and continues to use ``h = P / rho g`` ! even if that flag is set. ! :: @@ -2372,7 +2372,6 @@ ! :: mlt_make_surface_no_mixing = .false. - ! T_mix_limit @@ -3112,7 +3111,7 @@ RSP_nz_outer = 40 RSP_T_anchor = 11d3 RSP_T_inner = 2d6 - RSP_testing = .false. + RSP_testing = .false. ! :: @@ -3359,7 +3358,7 @@ ! Mixing coefficients are multiplied by this factor. ! The ``mix_factor`` is applied in subroutine ``get_convection_sigmas`` in ``star/private/mix_info.f90`` -- ! the lagrangian diffusion coefficient sigma(k) at cell boundary k is set to - ! ``mix_factor*D*(4*pi*r(k)^2*rho_face(k))^2``. + ! ``mix_factor*D*(4*pi*r(k)^2*rho_face(k))^2``. ! Note that the value of D is not changed -- it is just used as a term in calculating sigma. ! :: @@ -3995,7 +3994,7 @@ ! use_other_j_for_adjust_J_lost option to specify a specific angular momentum ! of removed material different from j_rot_surf - ! In order to prevent the algorithm from digging to deep to adjust J, + ! In order to prevent the algorithm from digging to deep to adjust J, ! there is a timestep limit adjust_J_q_limit ! :: @@ -4060,7 +4059,7 @@ ! When w_div_wc_flag is true, rather than a hard limit on w_div_wcrit ! we use w_div_wcrit_max2infinity, the resulting w_div_wc will match + ! In the limit of j_rot->infinity, the resulting w_div_wc will match ! w_div_wcrit_max, while nothing is done when w_div_wcrit_max`_. ! + ``'ONe'`` : oxygen-neon phase separation using the two-component ! phase diagram of `Blouin & Daligault (2021b) `_. - + ! :: phase_separation_option = 'CO' @@ -7355,7 +7356,7 @@ ! :: phase_separation_mixing_use_brunt = .true. - + ! eos controls ! ============ @@ -7510,7 +7511,7 @@ ! or use the faster method by allowing for a small tolerance on the mixture used for the computations of these variables (``'mombarg'``). ! :: - + op_mono_method = 'hu' ! emesh_data_for_op_mono_path @@ -7526,7 +7527,7 @@ ! and then unpack it in place with ``unxz -v OP_mono_master_grid_MESA_emesh.txt.xz`` ! :: - + emesh_data_for_op_mono_path = '' ! '' defaults to $MESA_OP_MONO_MASTER_GRID @@ -7733,14 +7734,10 @@ min_magnitude_brunt_B = -1d99 - - - ! structure equations ! =================== - ! energy_eqn_option ! ~~~~~~~~~~~~~~~~~ ! Available options are ``'dedt'`` or ``'eps_grav'``. @@ -7908,7 +7905,7 @@ ! :: velocity_q_upper_bound = 1d99 - + ! velocity_tau_lower_bound ! ~~~~~~~~~~~~~~~~~~~~~~~~ @@ -8221,9 +8218,9 @@ ! :: use_dPrad_dm_form_of_T_gradient_eqn = .false. - use_gradT_actual_vs_gradT_MLT_for_T_gradient_eqn = .false. - - + use_gradT_actual_vs_gradT_MLT_for_T_gradient_eqn = .false. + + ! drag_coefficient ! ~~~~~~~~~~~~~~~~ ! min_q_for_drag @@ -8236,7 +8233,7 @@ ! burning in massive stars and AGB stars. ! Under certain circumstances we will not have drag in the surface k=1 zone - ! To force the drag term to be on in the outer zone you must enable one of the + ! To force the drag term to be on in the outer zone you must enable one of the ! following surface boundary conditions: ! ``use_momentum_outer_BC``, ``use_zero_Pgas_outer_BC``, or ``use_fixed_Psurf_outer_BC`` @@ -8254,7 +8251,7 @@ use_drag_energy = .true. drag_coefficient = 0d0 min_q_for_drag = 0d0 - + ! for hydro comparison tests (e.g., Sedov) @@ -8324,7 +8321,7 @@ RTI_m_full_boost = 4d0 RTI_m_no_boost = 5d0 - + ! retry_for_v_above_clight ! ~~~~~~~~~~~~~~~~~~~~~~~~ @@ -8335,7 +8332,7 @@ ! :: retry_for_v_above_clight = .true. - + ! solver controls ! =============== @@ -8542,7 +8539,6 @@ include_w_in_correction_limits = .true. - ! max_X_for_conv_timescale ! ~~~~~~~~~~~~~~~~~~~~~~~~ ! min_X_for_conv_timescale @@ -8557,7 +8553,7 @@ ! ~~~~~~~~~~~~~~~~~~~~~~~~ ! :: - + max_X_for_conv_timescale = 1d0 min_X_for_conv_timescale = 0d0 max_q_for_conv_timescale = 1d0 @@ -8706,7 +8702,7 @@ ! do_normalize_dqs_as_part_of_set_qs ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - + ! normalize_dqs destroys bit-for-bit read as inverse of write for models. ! ok for create pre ms etc., but not for read model ! create_pre_ms calls normalize_dqs even if this flag is false. @@ -8714,12 +8710,12 @@ ! :: do_normalize_dqs_as_part_of_set_qs = .false. - + ! use_DGESVX_in_bcyclic ! use_equilibration_in_DGESVX ! report_min_rcond_from_DGESXV - + ! FOR DEBUGGING ONLY. NOT FOR GENERAL USE. ! :: @@ -9207,7 +9203,7 @@ ! 'Lnuc_cat' delta_lgL_nuc_cat_limit ! 'Lnuc_H' delta_lgL_H_limit ! 'Lnuc_He' delta_lgL_He_limit - ! 'lgL_power_phot' delta_lgL_power_photo_limit + ! 'lgL_power_phot' delta_lgL_power_photo_limit ! 'Lnuc_z' delta_lgL_z_limit ! 'bad_X_sum' (solver found bad mass sum) ! 'dL/L' dL_div_L_limit @@ -9269,12 +9265,12 @@ ! time_delta_coeff - smaller forces smaller timesteps giving better time resolution. ! multiplier for all real number timestep limits and hard limits. ! does not apply to integer valued limits such as - + ! + solver_iters_timestep_limit ! + burn_steps_limit ! + diffusion_steps_limit ! + diffusion_iters_limit - + ! does not apply to varcontrol_target. ! analogous to mesh_delta_coeff for better spatial resolution. @@ -10345,7 +10341,7 @@ min_lgT_for_lgL_power_photo_limit = 9d0 lgL_power_photo_burn_min = 10d0 lgL_power_photo_drop_factor = 10 - + ! limits based on changes at photosphere @@ -10442,7 +10438,7 @@ ! ``abs_du_div_cs`` > ``min_abs_du_div_cs_for_dt_div_min_dr_div_cs_limit`` and ! and ! ``abs_u_div_cs`` > ``min_abs_u_div_cs_for_dt_div_min_dr_div_cs_limit`` - ! + ! ! allow focus on regions near shock face. ! :: @@ -10879,7 +10875,6 @@ delta_lg_XSi_cntr_hard_limit = -1 - ! delta_XH_cntr_limit ! ~~~~~~~~~~~~~~~~~~~ @@ -11038,9 +11033,9 @@ ! ~~~~~~~~~~~~~~~~~~ ! delta_XSi_drop_only ! ~~~~~~~~~~~~~~~~~~~ - - ! If true, then only limit drops in abundance. + + ! If true, then only limit drops in abundance. ! :: @@ -11121,7 +11116,7 @@ ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ! hard_limit_for_rel_error_in_energy_conservation ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - + ! :: ! rel_error_in_energy_conservation = abs(error_in_energy_conservation/total_energy) @@ -11252,7 +11247,7 @@ solver_test_partials_write_eos_call_info = .false. solver_epsder_struct = 1d-5 solver_epsder_chem = 1d-5 - + energy_conservation_dump_model_number = -1 @@ -11489,7 +11484,7 @@ use_other_set_pgstar_controls = .false. use_other_accreting_state = .false. use_other_eval_i_rot = .false. - + ! :: use_other_export_pulse_data = .false. diff --git a/star/private/ctrls_io.f90 b/star/private/ctrls_io.f90 index 216092ae8..251379874 100644 --- a/star/private/ctrls_io.f90 +++ b/star/private/ctrls_io.f90 @@ -175,7 +175,7 @@ module ctrls_io RSP_relax_initial_model, RSP_trace_RSP_build_model, & RSP_GREKM_avg_abs_limit, RSP_GREKM_avg_abs_frac_new, RSP_kap_density_factor, RSP_map_columns_filename, & RSP_relax_alfap_before_alfat, RSP_max_outer_dm_tries, RSP_max_inner_scale_tries, RSP_T_anchor_tolerance, & - ! mass gain or loss + ! mass gain or loss mass_change, mass_change_full_on_dt, mass_change_full_off_dt, trace_dt_control_mass_change, & min_wind, max_wind, use_accreted_material_j, accreted_material_j, D_omega_mixing_rate, & D_omega_mixing_across_convection_boundary, max_q_for_D_omega_zero_in_convection_region, nu_omega_mixing_rate, & @@ -451,7 +451,7 @@ module ctrls_io delta_dX_div_X_cntr_min, delta_dX_div_X_cntr_max, delta_dX_div_X_cntr_limit, delta_dX_div_X_cntr_hard_limit, & delta_dX_div_X_drop_only, delta_lg_XH_drop_only, & delta_lg_XHe_drop_only, delta_lg_XC_drop_only, delta_lg_XNe_drop_only, delta_lg_XO_drop_only, delta_lg_XSi_drop_only, & - delta_XH_drop_only, delta_XHe_drop_only, delta_XC_drop_only, delta_XNe_drop_only, delta_XO_drop_only, delta_XSi_drop_only, & + delta_XH_drop_only, delta_XHe_drop_only, delta_XC_drop_only, delta_XNe_drop_only, delta_XO_drop_only, delta_XSi_drop_only, & delta_lg_XH_cntr_min, delta_lg_XH_cntr_max, delta_lg_XH_cntr_limit, delta_lg_XH_cntr_hard_limit, & delta_lg_XHe_cntr_min, delta_lg_XHe_cntr_max, delta_lg_XHe_cntr_limit, delta_lg_XHe_cntr_hard_limit, & delta_lg_XC_cntr_min, delta_lg_XC_cntr_max, delta_lg_XC_cntr_limit, delta_lg_XC_cntr_hard_limit, & @@ -491,7 +491,7 @@ module ctrls_io use_T_tau_gradr_factor, & - ! star spots + ! starspots fspot, xspot, & ! extra heat near surface to model irradiation @@ -1288,7 +1288,7 @@ subroutine store_controls(s, ierr) s% use_T_tau_gradr_factor = use_T_tau_gradr_factor - ! star spots + ! starspots s% fspot = fspot s% xspot = xspot @@ -2973,7 +2973,7 @@ subroutine set_controls_for_writing(s, ierr) use_T_tau_gradr_factor = s% use_T_tau_gradr_factor - ! star spots + ! starspots fspot = s% fspot xspot = s% xspot @@ -4151,7 +4151,7 @@ subroutine get_control(s, name, val, ierr) exit end if if(is_iostat_end(iostat)) exit - end do + end do if(len_trim(val) == 0 .and. ind==0 ) ierr = -1 diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index 990c0f06a..f7b60e9c1 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -16,14 +16,14 @@ in the style of an atmospheric boundary modification. As first described by `Somers et al. (2015; ApJ) `__, the degree of "spottiness" on the stellar surface is characterized using two parameters: -* SPOTF (hereafter fspot): a coverage fraction, or "spot filling factor" (in the notation of the YREC documentation); and +* SPOTF (hereafter ``fspot``): a coverage fraction, or "spot filling factor" (in the notation of the YREC documentation); and -* SPOTX (hereafter xspot): the temperature contrast between the spotted and unspotted regions: xspot = T_spot/T_photosphere. +* SPOTX (hereafter ``xspot``): the temperature contrast between the spotted and unspotted regions: xspot = T_spot/T_photosphere. -The coverage fraction is set to fspot = 0.34 +The coverage fraction is set to ``fspot = 0.34`` (for consistency with observations of low-mass stars: `Cao et al., 2022 `__) -and the temperature contrast is set to xspot = 0.85 (also from fits to observations). +and the temperature contrast is set to ``xspot = 0.85`` (also from fits to observations). Detailed discussion of this functionality can be found in `MESA Instrument Paper VI: Starspots `__. diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index 2fd5fcfe1..ef54ff85d 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -62,11 +62,11 @@ max_age = 24.63d9 !26d9 !0.8d9 - use_other_mlt_results = .true. !.true. - use_other_surface_PT = .true. !.True. + use_other_mlt_results = .true. + use_other_surface_PT = .true. - fspot = 0.34d0 ! fspot - xspot = 0.85d0 ! xspot + fspot = 0.34d0 + xspot = 0.85d0 atm_option = 'table' atm_table = 'photosphere' @@ -83,7 +83,7 @@ photo_interval = 100 ! starting specifications - initial_mass = 0.9 !1.0 ! in Msun units + initial_mass = 0.9 ! in Msun units min_timestep_limit=0 max_model_number = -1 !1500 @@ -94,7 +94,7 @@ Blocker_scaling_factor = 0.2 max_wind = 1d-3 - mixing_length_alpha = 1.9500 !1.95 + mixing_length_alpha = 1.9500 MLT_option = 'Henyey' do_element_diffusion = .false. diff --git a/star/test_suite/starspots/src/run_star_extras.f90 b/star/test_suite/starspots/src/run_star_extras.f90 index d448ce3ad..9145d2541 100644 --- a/star/test_suite/starspots/src/run_star_extras.f90 +++ b/star/test_suite/starspots/src/run_star_extras.f90 @@ -27,7 +27,7 @@ module run_star_extras use const_def use math_lib use chem_def !! maybe taking up uncessary space but whatever - + implicit none real(dp) :: fspot, xspot, PB_i, Teff_local @@ -37,10 +37,10 @@ module run_star_extras contains include "test_suite_extras.inc" - + ! these routines are called by the standard run_star check_model - + subroutine extras_controls(id, ierr) integer, intent(in) :: id integer, intent(out) :: ierr @@ -48,7 +48,7 @@ subroutine extras_controls(id, ierr) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - + ! this is the place to set any procedure pointers you want to change ! e.g., other_wind, other_mixing, other_energy (see star_data.inc) @@ -69,7 +69,7 @@ subroutine extras_controls(id, ierr) s% how_many_extra_history_columns => how_many_extra_history_columns s% data_for_extra_history_columns => data_for_extra_history_columns s% how_many_extra_profile_columns => how_many_extra_profile_columns - s% data_for_extra_profile_columns => data_for_extra_profile_columns + s% data_for_extra_profile_columns => data_for_extra_profile_columns s% how_many_extra_history_header_items => how_many_extra_history_header_items s% data_for_extra_history_header_items => data_for_extra_history_header_items @@ -92,7 +92,7 @@ subroutine extras_startup(id, restart, ierr) if (ierr /= 0) return call test_suite_startup(s, restart, ierr) end subroutine extras_startup - + integer function extras_start_step(id) integer, intent(in) :: id @@ -115,9 +115,9 @@ integer function extras_start_step(id) ! set PB_i here and then other_mlt will know about it, because ! quantities set here are carried over the course of a timestep, ! AKA all newton iterations - + mu_ideal_gas = s% mu(1) !1.00794d0 ! for hydrogen, 1 gram per mole - !write(*,*) 'MESA def, my def: ', s% mu(1), mu_ideal_gas + !write(*,*) 'MESA def, my def: ', s% mu(1), mu_ideal_gas R2 = pow2(s%R(1)) Teff_local = pow(s%L(1)/(pi4*boltz_sigma*R2), 0.25d0) @@ -162,7 +162,7 @@ subroutine YREC_spots_other_mlt_results(id, k, MLT_option, & ! NOTE: k=0 is a v ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - + !------------------------------ !if (s% star_age >= 10d0) then if (.not. s% doing_relax .and. .not. s% doing_first_model_of_run) then @@ -190,7 +190,7 @@ subroutine starspot_tweak_PT(id, skip_partials, & logical, intent(in) :: skip_partials logical :: need_atm_Psurf, need_atm_Tsurf - + real(dp), intent(out) :: & lnT_surf, dlnT_dL, dlnT_dlnR, dlnT_dlnM, dlnT_dlnkap, & lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap @@ -211,7 +211,7 @@ subroutine starspot_tweak_PT(id, skip_partials, & need_atm_Psurf = .true. need_atm_Tsurf = .true. - + alp = 1d0 - fspot + fspot*pow4(xspot) ! This is the surface-average value for luminosity @@ -248,7 +248,7 @@ integer function extras_check_model(id) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - extras_check_model = keep_going + extras_check_model = keep_going if (.false. .and. s% star_mass_h1 < 0.35d0) then ! stop when star hydrogen mass drops to specified level @@ -272,7 +272,7 @@ integer function how_many_extra_history_columns(id) how_many_extra_history_columns = 0 end function how_many_extra_history_columns - + subroutine data_for_extra_history_columns(id, n, names, vals, ierr) integer, intent(in) :: id, n @@ -283,14 +283,14 @@ subroutine data_for_extra_history_columns(id, n, names, vals, ierr) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - + ! note: do NOT add the extras names to history_columns.list ! the history_columns.list is only for the built-in history column options. ! it must not include the new column names you are adding here. end subroutine data_for_extra_history_columns - + integer function how_many_extra_profile_columns(id) integer, intent(in) :: id integer :: ierr @@ -300,8 +300,8 @@ integer function how_many_extra_profile_columns(id) if (ierr /= 0) return how_many_extra_profile_columns = 0 end function how_many_extra_profile_columns - - + + subroutine data_for_extra_profile_columns(id, n, nz, names, vals, ierr) integer, intent(in) :: id, n, nz character (len=maxlen_profile_column_name) :: names(n) @@ -381,8 +381,8 @@ integer function extras_finish_step(id) ! by default, indicate where (in the code) MESA terminated if (extras_finish_step == terminate) s% termination_code = t_extras_finish_step end function extras_finish_step - - + + subroutine extras_after_evolve(id, ierr) integer, intent(in) :: id integer, intent(out) :: ierr diff --git a/star_data/private/star_controls.inc b/star_data/private/star_controls.inc index cb3381acd..64233afca 100644 --- a/star_data/private/star_controls.inc +++ b/star_data/private/star_controls.inc @@ -432,10 +432,8 @@ logical :: use_T_tau_gradr_factor - ! star spot controls - - real(dp) :: fspot - real(dp) :: xspot + ! starspots + real(dp) :: fspot, xspot ! mass gain or loss From ae4228d12a00750f435f6d3a310db6a1de0a6558 Mon Sep 17 00:00:00 2001 From: Philip Mocz Date: Fri, 9 Aug 2024 18:54:23 -0400 Subject: [PATCH 49/66] starspots Part 2 (#713) * [ci skip] adding some stuff, not yet done * [ci skip] updates to starspots * [ci skip] run_stars_extras * [ci skip] fix controls formatting * [ci skip] remove redundant library * [ci skip] modify turb_support * [ci skip] switch run_stars_extra to plain again * [ci skip] move need_atm_Psurf to right place * [ci skip] mv starspot stuff in hydro_vars.f90 * oh I think I found it --------- Co-authored-by: Meridith Joyce --- star/defaults/controls.defaults | 26 +- star/make/makefile_base | 1 + star/private/ctrls_io.f90 | 4 +- star/private/hydro_vars.f90 | 20 +- star/private/starspots.f90 | 111 +++++++ star/private/turb_support.f90 | 17 +- star/test_suite/starspots/README.rst | 2 +- star/test_suite/starspots/inlist_starspots | 6 +- .../starspots/src/run_star_extras.f90 | 299 ++---------------- star_data/private/star_controls.inc | 1 + 10 files changed, 199 insertions(+), 288 deletions(-) create mode 100644 star/private/starspots.f90 diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index eb00f74a0..68077fa56 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -4640,20 +4640,34 @@ ! ========= - ! fspot - ! ~~~~~~~~~~~ + ! do_starspots + ! ~~~~~~~~~~~~ + + ! If ``.true.``, switch on impedence of the surface flux due to magnetic pressure from starspots, + ! parameterized in the style of an atmospheric boundary modification. First described by + ! `Somers et al. (2015; ApJ) `__. + ! Detailed discussion of this functionality can be found in |MESA VI|. + + ! :: - ! Filling Factor of starspots (in [0,1]) + do_starspots = .false. + + ! fspot + ! ~~~~~ + + ! Filling Factor of starspots. Valid values between 0.0 and 1.0 (no spots to 100% coverage) ! :: fspot = 0d0 ! xspot - ! ~~~~~~~~~~~ + ! ~~~~~ - ! Temperature contrast between the spotted and unspotted regions (in [0,1]) + ! Temperature contrast between the spotted and unspotted regions. + ! Valid values are between 1.0 (no contribution from magnetic pressure) and 0.5 + ! (half of the total pressure is due to magnetic pressure) ! :: @@ -8291,7 +8305,7 @@ ! Note that these parameters are not exactly the same ! as used by Paul Duffell. - ! His calibrated D is 2, where mesa has default D = 3 (see mesaIV paper). + ! His calibrated D is 2, where mesa has default D = 3 (see |MESA IV|). ! Users should try various values since the choice is not clear cut. ! :: diff --git a/star/make/makefile_base b/star/make/makefile_base index 9568ed966..4afdafa85 100644 --- a/star/make/makefile_base +++ b/star/make/makefile_base @@ -205,6 +205,7 @@ SRCS = \ star_solver.f90 \ struct_burn_mix.f90 \ winds.f90 \ + starspots.f90 \ gravity_darkening.f90 \ mass_utils.f90 \ eps_mdot.f90 \ diff --git a/star/private/ctrls_io.f90 b/star/private/ctrls_io.f90 index 251379874..6a277c844 100644 --- a/star/private/ctrls_io.f90 +++ b/star/private/ctrls_io.f90 @@ -492,7 +492,7 @@ module ctrls_io use_T_tau_gradr_factor, & ! starspots - fspot, xspot, & + do_starspots, fspot, xspot, & ! extra heat near surface to model irradiation irradiation_flux, column_depth_for_irradiation, & @@ -1289,6 +1289,7 @@ subroutine store_controls(s, ierr) s% use_T_tau_gradr_factor = use_T_tau_gradr_factor ! starspots + s% do_starspots = do_starspots s% fspot = fspot s% xspot = xspot @@ -2974,6 +2975,7 @@ subroutine set_controls_for_writing(s, ierr) use_T_tau_gradr_factor = s% use_T_tau_gradr_factor ! starspots + do_starspots = s% do_starspots fspot = s% fspot xspot = s% xspot diff --git a/star/private/hydro_vars.f90 b/star/private/hydro_vars.f90 index bb1a2fab7..e190885cb 100644 --- a/star/private/hydro_vars.f90 +++ b/star/private/hydro_vars.f90 @@ -387,22 +387,27 @@ end subroutine set_Teff subroutine set_Teff_info_for_eqns(s, skip_partials, & - need_atm_Psurf, need_atm_Tsurf, r_surf, L_surf, Teff, & + need_atm_Psurf_in, need_atm_Tsurf_in, r_surf, L_surf, Teff, & lnT_surf, dlnT_dL, dlnT_dlnR, dlnT_dlnM, dlnT_dlnkap, & lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap, & ierr) use star_utils, only: set_phot_info use atm_lib, only: atm_Teff + use starspots, only: starspot_tweak_PT, starspot_restore_PT type (star_info), pointer :: s logical, intent(in) :: skip_partials, & - need_atm_Psurf, need_atm_Tsurf + need_atm_Psurf_in, need_atm_Tsurf_in real(dp), intent(out) :: r_surf, L_surf, Teff, & lnT_surf, dlnT_dL, dlnT_dlnR, dlnT_dlnM, dlnT_dlnkap, & lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap integer, intent(out) :: ierr + logical :: need_atm_Psurf, need_atm_Tsurf include 'formats' + need_atm_Psurf = need_atm_Psurf_in + need_atm_Tsurf = need_atm_Tsurf_in + ierr = 0 r_surf = s% r(1) @@ -435,11 +440,21 @@ subroutine set_Teff_info_for_eqns(s, skip_partials, & lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap, & ierr) else + ! starspot YREC routine + if (s% do_starspots) then + need_atm_Psurf = .true. + need_atm_Tsurf = .true. + call starspot_tweak_PT(s) + end if call get_surf_PT( & s, skip_partials, need_atm_Psurf, need_atm_Tsurf, & lnT_surf, dlnT_dL, dlnT_dlnR, dlnT_dlnM, dlnT_dlnkap, & lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap, & ierr) + ! starspot YREC routine + if (s% do_starspots) then + call starspot_restore_PT(s) + end if end if if (ierr /= 0) then if (s% report_ierr) then @@ -785,7 +800,6 @@ subroutine get_surf_PT( & real(dp) :: kap_surf real(dp) :: M_surf - include 'formats' ! Set up stellar surface parameters diff --git a/star/private/starspots.f90 b/star/private/starspots.f90 new file mode 100644 index 000000000..da13b27b9 --- /dev/null +++ b/star/private/starspots.f90 @@ -0,0 +1,111 @@ +! *********************************************************************** +! +! Copyright (C) 2010-2019 Meridith Joyce & The MESA Team +! +! MESA is free software; you can use it and/or modify +! it under the combined terms and restrictions of the MESA MANIFESTO +! and the GNU General Library Public License as published +! by the Free Software Foundation; either version 2 of the License, +! or (at your option) any later version. +! +! You should have received a copy of the MESA MANIFESTO along with +! this software; if not, it is available at the mesa website: +! http://mesa.sourceforge.net/ +! +! MESA is distributed in the hope that it will be useful, +! but WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +! See the GNU Library General Public License for more details. +! +! You should have received a copy of the GNU Library General Public License +! along with this software; if not, write to the Free Software +! Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +! +! *********************************************************************** + +module starspots + + use star_private_def + use const_def + use utils_lib + + implicit none + + private + + public :: starspot_tweak_gradr + public :: starspot_tweak_PT + public :: starspot_restore_PT + + real(dp) :: L_init + +contains + +! ------------- +! parameterized YREC routines +! MESA models a pressure contrast rather than temperature contrast +! ------------- + + subroutine starspot_tweak_gradr(s, P, gradr, gradr_spot) + ! adjusts the gradient of the radius to account for starspots. + ! This subroutine is called at the beginning of Get_results() + ! in turb_support.f90 + ! ------------------------------------------------------------ + use auto_diff_support + type(star_info), pointer :: s + type(auto_diff_real_star_order1), intent(in) :: P + type(auto_diff_real_star_order1), intent(in) :: gradr + type(auto_diff_real_star_order1), intent(out) :: gradr_spot + + real(dp) :: mu_ideal_gas, R2, Teff_local, PB_i + type(auto_diff_real_star_order1) :: xspot_of_r ! xspot4 + + if (.not. s%doing_relax .and. .not. s%doing_first_model_of_run) then + mu_ideal_gas = s%mu(1) !1.00794d0 ! for hydrogen, 1 gram per mole + R2 = pow2(s%R(1)) + Teff_local = pow(s%L(1)/(pi4*boltz_sigma*R2), 0.25d0) + PB_i = (cgas*s%rho(1)/mu_ideal_gas)*(1.0 - s%xspot)*Teff_local + xspot_of_r = (P - PB_i)/P + gradr_spot = gradr/(s%fspot*pow4(xspot_of_r) + 1d0 - s%fspot) + else + gradr_spot = gradr + end if + end subroutine starspot_tweak_gradr + + subroutine starspot_tweak_PT(s) + ! saves the surface luminosity and adjusts it and the effective + ! temperature to account for starspots. + ! This subroutine is called at the beginning of get_surf_PT() + ! in hydro_vars.f90 + ! ------------------------------------------------------------ + + type(star_info), pointer :: s + + real(dp) :: alp + + alp = 1d0 - s%fspot + s%fspot*pow4(s%xspot) + + ! This is the surface-average value for luminosity + L_init = s%L(1) + + ! Set the surface L to the unspotted, ambient L + s%L(1) = s%L(1)/alp + + ! Now, set the Teff. Used in atm table lookup to set boundary conditions + s%Teff = pow(s%L(1)/(pi4*pow2(s%r(1))*boltz_sigma), 0.25_dp) + + end subroutine starspot_tweak_PT + + subroutine starspot_restore_PT(s) + ! restores the surface luminosity effective temeperature. + ! Called at the end of get_surf_PT() + ! ------------------------------------------------------------ + + type(star_info), pointer :: s + + s%Teff = pow(L_init/(pi4*pow2(s%r(1))*boltz_sigma), 0.25_dp) + s%L(1) = L_init + + end subroutine starspot_restore_PT + +end module starspots diff --git a/star/private/turb_support.f90 b/star/private/turb_support.f90 index 08ec63107..6fa8326d8 100644 --- a/star/private/turb_support.f90 +++ b/star/private/turb_support.f90 @@ -105,13 +105,14 @@ end subroutine get_gradT subroutine do1_mlt_eval( & s, k, MLT_option, gradL_composition_term, & - gradr, grada, scale_height, mixing_length_alpha, & + gradr_in, grada, scale_height, mixing_length_alpha, & mixing_type, gradT, Y_face, mlt_vc, D, Gamma, ierr) use chem_def, only: ih1 + use starspots, only: starspot_tweak_gradr type (star_info), pointer :: s integer, intent(in) :: k character (len=*), intent(in) :: MLT_option - type(auto_diff_real_star_order1), intent(in) :: gradr, grada, scale_height + type(auto_diff_real_star_order1), intent(in) :: gradr_in, grada, scale_height real(dp), intent(in) :: gradL_composition_term, mixing_length_alpha integer, intent(out) :: mixing_type type(auto_diff_real_star_order1), intent(out) :: & @@ -120,9 +121,11 @@ subroutine do1_mlt_eval( & real(dp) :: cgrav, m, XH1, gradL_old, grada_face_old integer :: iso, old_mix_type - type(auto_diff_real_star_order1) :: r, L, T, P, opacity, rho, dV, chiRho, chiT, Cp + type(auto_diff_real_star_order1) :: gradr, r, L, T, P, opacity, rho, dV, chiRho, chiT, Cp include 'formats' ierr = 0 + + gradr = gradr_in cgrav = s% cgrav(k) m = s% m_grav(k) @@ -145,7 +148,12 @@ subroutine do1_mlt_eval( & iso, XH1, cgrav, m, gradL_composition_term, mixing_length_alpha, & s% alpha_semiconvection, s% thermohaline_coeff, & mixing_type, gradT, Y_face, mlt_vc, D, Gamma, ierr) - else + else + ! starspot YREC routine + if (s% do_starspots) then + dV = 0d0 ! dV = 1/rho - 1/rho_start and we assume rho = rho_start. + call starspot_tweak_gradr(s, P, gradr_in, gradr) + end if call Get_results(s, k, MLT_option, & r, L, T, P, opacity, rho, dV, chiRho, chiT, Cp, gradr, grada, scale_height, & iso, XH1, cgrav, m, gradL_composition_term, mixing_length_alpha, & @@ -228,7 +236,6 @@ subroutine Get_results(s, k, MLT_option, & ! NOTE: k=0 is a valid arg end if - ! check if this particular k can be done with TDC using_TDC = .false. if (s% MLT_option == 'TDC') using_TDC = .true. diff --git a/star/test_suite/starspots/README.rst b/star/test_suite/starspots/README.rst index f7b60e9c1..f80abafd3 100644 --- a/star/test_suite/starspots/README.rst +++ b/star/test_suite/starspots/README.rst @@ -34,6 +34,6 @@ A plot of the HR diagram for the problem is included below: :width: 100% -Last-Updated: 06Aug2024 by Meridith Joyce +Last-Updated: 09Aug2024 by Meridith Joyce Last-Run: 06Aug2024 (MESA 7890d305) by pmocz on C916PXT6XW in 629 seconds using 8 threads. diff --git a/star/test_suite/starspots/inlist_starspots b/star/test_suite/starspots/inlist_starspots index ef54ff85d..df1f3213b 100644 --- a/star/test_suite/starspots/inlist_starspots +++ b/star/test_suite/starspots/inlist_starspots @@ -61,10 +61,8 @@ star_history_name = 'history.data' max_age = 24.63d9 !26d9 !0.8d9 - - use_other_mlt_results = .true. - use_other_surface_PT = .true. - + + do_starspots = .true. fspot = 0.34d0 xspot = 0.85d0 diff --git a/star/test_suite/starspots/src/run_star_extras.f90 b/star/test_suite/starspots/src/run_star_extras.f90 index 9145d2541..89743ce76 100644 --- a/star/test_suite/starspots/src/run_star_extras.f90 +++ b/star/test_suite/starspots/src/run_star_extras.f90 @@ -1,6 +1,6 @@ ! *********************************************************************** ! -! Copyright (C) 2010-2019 Bill Paxton & The MESA Team +! Copyright (C) 2011 The MESA Team ! ! this file is part of mesa. ! @@ -26,21 +26,18 @@ module run_star_extras use star_def use const_def use math_lib - use chem_def !! maybe taking up uncessary space but whatever - - + use auto_diff + implicit none - real(dp) :: fspot, xspot, PB_i, Teff_local include "test_suite_extras_def.inc" - + + ! these routines are called by the standard run_star check_model contains include "test_suite_extras.inc" - - - ! these routines are called by the standard run_star check_model - + + subroutine extras_controls(id, ierr) integer, intent(in) :: id integer, intent(out) :: ierr @@ -48,40 +45,17 @@ subroutine extras_controls(id, ierr) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - - ! this is the place to set any procedure pointers you want to change - ! e.g., other_wind, other_mixing, other_energy (see star_data.inc) - - ! the extras functions in this file will not be called - ! unless you set their function pointers as done below. - ! otherwise we use a null_ version which does nothing (except warn). - - - fspot = s% fspot - xspot = s% xspot - - s% extras_startup => extras_startup - s% extras_start_step => extras_start_step s% extras_check_model => extras_check_model s% extras_finish_step => extras_finish_step s% extras_after_evolve => extras_after_evolve s% how_many_extra_history_columns => how_many_extra_history_columns s% data_for_extra_history_columns => data_for_extra_history_columns s% how_many_extra_profile_columns => how_many_extra_profile_columns - s% data_for_extra_profile_columns => data_for_extra_profile_columns - - s% how_many_extra_history_header_items => how_many_extra_history_header_items - s% data_for_extra_history_header_items => data_for_extra_history_header_items - s% how_many_extra_profile_header_items => how_many_extra_profile_header_items - s% data_for_extra_profile_header_items => data_for_extra_profile_header_items - - s% other_surface_PT => starspot_tweak_PT - s% other_mlt_results => YREC_spots_other_mlt_results - + s% data_for_extra_profile_columns => data_for_extra_profile_columns end subroutine extras_controls - - + + subroutine extras_startup(id, restart, ierr) integer, intent(in) :: id logical, intent(in) :: restart @@ -92,153 +66,19 @@ subroutine extras_startup(id, restart, ierr) if (ierr /= 0) return call test_suite_startup(s, restart, ierr) end subroutine extras_startup - - - integer function extras_start_step(id) + + + subroutine extras_after_evolve(id, ierr) integer, intent(in) :: id - integer :: ierr - real(dp) :: mu_ideal_gas, R2 + integer, intent(out) :: ierr type (star_info), pointer :: s - real(dp) :: power_he_burn, power_c_burn, power_neutrinos, & - center_h1, center_he4, ocz_top_mass, ocz_bot_mass, & - ocz_top_radius, ocz_bot_radius!, mass_difference_prev !! no!! - integer :: nz, j, i, k, k_ocz_top, k_ocz_bot, n_conv_bdy -! include 'formats' + real(dp) :: dt ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - extras_start_step = 0 - - !! to use constants as defined in MESA, import const_def and call - !! variables by their names there - - ! set PB_i here and then other_mlt will know about it, because - ! quantities set here are carried over the course of a timestep, - ! AKA all newton iterations - - mu_ideal_gas = s% mu(1) !1.00794d0 ! for hydrogen, 1 gram per mole - !write(*,*) 'MESA def, my def: ', s% mu(1), mu_ideal_gas - - R2 = pow2(s%R(1)) - Teff_local = pow(s%L(1)/(pi4*boltz_sigma*R2), 0.25d0) - PB_i = (cgas* s%rho(1)/mu_ideal_gas) * (1.0 - xspot) * Teff_local - - end function extras_start_step - - -!----------------------------------------------------------------------------------------- -! -! YREC routines -! -!---------------------------------------------------------------------------------------- - subroutine YREC_spots_other_mlt_results(id, k, MLT_option, & ! NOTE: k=0 is a valid arg - r, L, T, P, opacity, rho, chiRho, chiT, Cp, gradr, grada, scale_height, & - iso, XH1, cgrav, m, gradL_composition_term, mixing_length_alpha, & - alpha_semiconvection, thermohaline_coeff, & - mixing_type, gradT, Y_face, conv_vel, D, Gamma, ierr) - use const_def, only: dp - use auto_diff - integer, intent(in) :: id - integer, intent(in) :: k - ! integer, intent(out) :: ierr - ! type (star_info), pointer :: s - ! integer :: nz, j - character (len=*), intent(in) :: MLT_option - type(auto_diff_real_star_order1), intent(in) :: & - r, L, T, P, opacity, rho, chiRho, chiT, Cp, gradr, grada, scale_height - integer, intent(in) :: iso - real(dp), intent(in) :: & - XH1, cgrav, m, gradL_composition_term, & - mixing_length_alpha, alpha_semiconvection, thermohaline_coeff - integer, intent(out) :: mixing_type - type(auto_diff_real_star_order1), intent(out) :: & - gradT, Y_face, conv_vel, D, Gamma - integer, intent(out) :: ierr - type(auto_diff_real_star_order1) :: xspot_of_r !, xspot4 - type(auto_diff_real_star_order1) :: gradr_spot - !ierr = 0 - ! ------------------------------ 10/26/21 - type (star_info), pointer :: s - ierr = 0 - call star_ptr(id, s, ierr) - if (ierr /= 0) return - - !------------------------------ - !if (s% star_age >= 10d0) then - if (.not. s% doing_relax .and. .not. s% doing_first_model_of_run) then - xspot_of_r = (P - PB_i)/P - gradr_spot = gradr/( fspot*pow4(xspot_of_r) + 1d0 - fspot) - else - gradr_spot = gradr - end if - - call star_mlt_results(id, k, MLT_option, & - r, L, T, P, opacity, rho, chiRho, chiT, Cp, gradr_spot, grada, scale_height, & - iso, XH1, cgrav, m, gradL_composition_term, mixing_length_alpha, & - alpha_semiconvection, thermohaline_coeff, & - mixing_type, gradT, Y_face, conv_vel, D, Gamma, ierr) - end subroutine YREC_spots_other_mlt_results - - - subroutine starspot_tweak_PT(id, skip_partials, & - lnT_surf, dlnT_dL, dlnT_dlnR, dlnT_dlnM, dlnT_dlnkap, & - lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap, ierr) - - use const_def, only: dp - - integer, intent(in) :: id - logical, intent(in) :: skip_partials - - logical :: need_atm_Psurf, need_atm_Tsurf - - real(dp), intent(out) :: & - lnT_surf, dlnT_dL, dlnT_dlnR, dlnT_dlnM, dlnT_dlnkap, & - lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap - integer, intent(out) :: ierr - - ! For my tweaks - real(dp) :: alp - - ! Call the stock get_surf_PT - type (star_info), pointer :: s - real(dp) :: L_init - - include 'formats' - - ierr = 0 - call star_ptr(id, s, ierr) - if (ierr /= 0) return - - need_atm_Psurf = .true. - need_atm_Tsurf = .true. - - alp = 1d0 - fspot + fspot*pow4(xspot) - - ! This is the surface-average value for luminosity - L_init = s% L(1) - - ! Set the surface L to the unspotted, ambient L - s% L(1) = s% L(1) / alp - - ! Now, set the Teff. Used in atm table lookup to set boundary conditions - s% Teff = pow(s% L(1)/(pi4*pow2(s% r(1))*boltz_sigma), 0.25_dp) - - ! Set everything with Lamb. - call star_get_surf_PT(id, skip_partials, need_atm_Psurf, need_atm_Tsurf, & - lnT_surf, dlnT_dL, dlnT_dlnR, dlnT_dlnM, dlnT_dlnkap, & - lnP_surf, dlnP_dL, dlnP_dlnR, dlnP_dlnM, dlnP_dlnkap, & - ierr) - - s% Teff = pow(L_init/(pi4*pow2(s% r(1))*boltz_sigma), 0.25_dp) - s% L(1) = L_init - - end subroutine starspot_tweak_PT - -!------------------------------------------------------------------------------ -! -! end YREC routines -! -!------------------------------------------------------------------------------ + call test_suite_after_evolve(s, ierr) + end subroutine extras_after_evolve + ! returns either keep_going, retry, or terminate. integer function extras_check_model(id) @@ -248,17 +88,7 @@ integer function extras_check_model(id) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - extras_check_model = keep_going - - if (.false. .and. s% star_mass_h1 < 0.35d0) then - ! stop when star hydrogen mass drops to specified level - extras_check_model = terminate - write(*, *) 'have reached desired hydrogen mass' - return - end if - - ! by default, indicate where (in the code) MESA terminated - if (extras_check_model == terminate) s% termination_code = t_extras_check_model + extras_check_model = keep_going end function extras_check_model @@ -269,11 +99,10 @@ integer function how_many_extra_history_columns(id) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - how_many_extra_history_columns = 0 end function how_many_extra_history_columns - - + + subroutine data_for_extra_history_columns(id, n, names, vals, ierr) integer, intent(in) :: id, n character (len=maxlen_history_column_name) :: names(n) @@ -283,15 +112,11 @@ subroutine data_for_extra_history_columns(id, n, names, vals, ierr) ierr = 0 call star_ptr(id, s, ierr) if (ierr /= 0) return - - ! note: do NOT add the extras names to history_columns.list - ! the history_columns.list is only for the built-in history column options. - ! it must not include the new column names you are adding here. - end subroutine data_for_extra_history_columns - + integer function how_many_extra_profile_columns(id) + use star_def, only: star_info integer, intent(in) :: id integer :: ierr type (star_info), pointer :: s @@ -300,9 +125,11 @@ integer function how_many_extra_profile_columns(id) if (ierr /= 0) return how_many_extra_profile_columns = 0 end function how_many_extra_profile_columns - - + + subroutine data_for_extra_profile_columns(id, n, nz, names, vals, ierr) + use star_def, only: star_info, maxlen_profile_column_name + use const_def, only: dp integer, intent(in) :: id, n, nz character (len=maxlen_profile_column_name) :: names(n) real(dp) :: vals(nz,n) @@ -313,56 +140,9 @@ subroutine data_for_extra_profile_columns(id, n, nz, names, vals, ierr) call star_ptr(id, s, ierr) if (ierr /= 0) return end subroutine data_for_extra_profile_columns - - - integer function how_many_extra_history_header_items(id) - integer, intent(in) :: id - integer :: ierr - type (star_info), pointer :: s - ierr = 0 - call star_ptr(id, s, ierr) - if (ierr /= 0) return - how_many_extra_history_header_items = 0 - end function how_many_extra_history_header_items - - - subroutine data_for_extra_history_header_items(id, n, names, vals, ierr) - integer, intent(in) :: id, n - character (len=maxlen_history_column_name) :: names(n) - real(dp) :: vals(n) - type(star_info), pointer :: s - integer, intent(out) :: ierr - ierr = 0 - call star_ptr(id,s,ierr) - if(ierr/=0) return - end subroutine data_for_extra_history_header_items - - - integer function how_many_extra_profile_header_items(id) - integer, intent(in) :: id - integer :: ierr - type (star_info), pointer :: s - ierr = 0 - call star_ptr(id, s, ierr) - if (ierr /= 0) return - how_many_extra_profile_header_items = 0 - end function how_many_extra_profile_header_items - - - subroutine data_for_extra_profile_header_items(id, n, names, vals, ierr) - integer, intent(in) :: id, n - character (len=maxlen_profile_column_name) :: names(n) - real(dp) :: vals(n) - type(star_info), pointer :: s - integer, intent(out) :: ierr - ierr = 0 - call star_ptr(id,s,ierr) - if(ierr/=0) return - end subroutine data_for_extra_profile_header_items - + ! returns either keep_going or terminate. - ! note: cannot request retry; extras_check_model can do that. integer function extras_finish_step(id) integer, intent(in) :: id integer :: ierr @@ -371,26 +151,9 @@ integer function extras_finish_step(id) call star_ptr(id, s, ierr) if (ierr /= 0) return extras_finish_step = keep_going - - ! to save a profile, - ! s% need_to_save_profiles_now = .true. - ! to update the star log, - ! s% need_to_update_history_now = .true. - - ! see extras_check_model for information about custom termination codes - ! by default, indicate where (in the code) MESA terminated - if (extras_finish_step == terminate) s% termination_code = t_extras_finish_step end function extras_finish_step - - - subroutine extras_after_evolve(id, ierr) - integer, intent(in) :: id - integer, intent(out) :: ierr - type (star_info), pointer :: s - ierr = 0 - call star_ptr(id, s, ierr) - if (ierr /= 0) return - call test_suite_after_evolve(s, ierr) - end subroutine extras_after_evolve + + end module run_star_extras + diff --git a/star_data/private/star_controls.inc b/star_data/private/star_controls.inc index 64233afca..855cc6a5f 100644 --- a/star_data/private/star_controls.inc +++ b/star_data/private/star_controls.inc @@ -433,6 +433,7 @@ logical :: use_T_tau_gradr_factor ! starspots + logical :: do_starspots real(dp) :: fspot, xspot ! mass gain or loss From 98a236d5aa18892734a5abc405d5d46d1ae87f71 Mon Sep 17 00:00:00 2001 From: pmocz Date: Mon, 12 Aug 2024 10:54:34 -0400 Subject: [PATCH 50/66] trying out predictive mix search loop exit criterion fix --- star/defaults/controls.defaults | 3 --- star/private/predictive_mix.f90 | 22 +++++++++++----------- 2 files changed, 11 insertions(+), 14 deletions(-) diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index c8c5b9c04..8cc84bed2 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -2781,9 +2781,6 @@ ! ~~~~~~~~~~~~~~ ! Set to .true. to enable this set of parameters - - ! ``predictive_mix`` is incompattible with ``convective premixing`` - ! and mlt_option = ``TDC``, due to conflicting assumptions. ! :: diff --git a/star/private/predictive_mix.f90 b/star/private/predictive_mix.f90 index 5aa634f55..fedc9e7aa 100644 --- a/star/private/predictive_mix.f90 +++ b/star/private/predictive_mix.f90 @@ -175,10 +175,10 @@ subroutine add_predictive_mixing (s, ierr) stop end if - if (s% MLT_option == 'TDC') then - call mesa_error(__FILE__,__LINE__,'Predictive mixing and TDC cannot be enabled at the same time') - stop - end if + !if (s% MLT_option == 'TDC') then + ! call mesa_error(__FILE__,__LINE__,'Predictive mixing and TDC cannot be enabled at the same time') + ! stop + !end if call do_predictive_mixing(s, i, j, ierr, mix_mask) if (ierr /= 0) return @@ -375,6 +375,13 @@ subroutine do_predictive_mixing (s, i, j, ierr, mix_mask) k_bot_mz = k_bot_mz + 1 endif + ! See if the mixed region has reached went out of bounds [1, s%nz-1] + + if (( outward .AND. k_top_mz < 1) .OR. & + (.NOT. outward .AND. k_bot_mz > s%nz-1)) then + exit search_loop + endif + ! Evaluate average abundance in the mixed zone call eval_abundances(s, k_bot_mz, k_top_mz, xa_mz, xa_mz_burn) @@ -490,13 +497,6 @@ subroutine do_predictive_mixing (s, i, j, ierr, mix_mask) exit search_loop endif - ! See if the mixed region has reached the center or surface - - if (( outward .AND. k_top_mz == 1) .OR. & - (.NOT. outward .AND. k_bot_mz == s%nz-1)) then - exit search_loop - endif - end do search_loop ! If necessary, dump out the mixing prediction for this boundary From 5631c5e9ccf468f7aceb14de071e6f8a1b62ae5f Mon Sep 17 00:00:00 2001 From: pmocz Date: Mon, 12 Aug 2024 11:00:40 -0400 Subject: [PATCH 51/66] [ci skip typo] --- star/private/predictive_mix.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/star/private/predictive_mix.f90 b/star/private/predictive_mix.f90 index fedc9e7aa..9cac95b64 100644 --- a/star/private/predictive_mix.f90 +++ b/star/private/predictive_mix.f90 @@ -375,7 +375,7 @@ subroutine do_predictive_mixing (s, i, j, ierr, mix_mask) k_bot_mz = k_bot_mz + 1 endif - ! See if the mixed region has reached went out of bounds [1, s%nz-1] + ! See if the mixed region has gone out of bounds [1, s%nz-1] if (( outward .AND. k_top_mz < 1) .OR. & (.NOT. outward .AND. k_bot_mz > s%nz-1)) then From d8521cc8c9a17298b28263a4a9ee2e31021af331 Mon Sep 17 00:00:00 2001 From: pmocz Date: Mon, 12 Aug 2024 16:10:17 -0400 Subject: [PATCH 52/66] [ci skip] spaces --- star/defaults/controls.defaults | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/star/defaults/controls.defaults b/star/defaults/controls.defaults index 8cc84bed2..145eb0a3f 100644 --- a/star/defaults/controls.defaults +++ b/star/defaults/controls.defaults @@ -2781,7 +2781,7 @@ ! ~~~~~~~~~~~~~~ ! Set to .true. to enable this set of parameters - + ! :: predictive_mix(1) = .false. From 3676acbdf0a1a41d765a1c10a2e07cd05a4f0a7b Mon Sep 17 00:00:00 2001 From: pmocz Date: Tue, 13 Aug 2024 07:48:21 -0400 Subject: [PATCH 53/66] bugfix nn_in --- astero/private/adipls_support.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/astero/private/adipls_support.f90 b/astero/private/adipls_support.f90 index 68545137c..6fcffa082 100644 --- a/astero/private/adipls_support.f90 +++ b/astero/private/adipls_support.f90 @@ -683,7 +683,7 @@ subroutine read_and_store(iriche, iturpr, cgrav) call mesa_error(__FILE__,__LINE__) end if call fgong_amdl( & - cgrav, nn, iconst, ivar, ivers, glob, var, data, aa, nn, ierr) + cgrav, nn_in, iconst, ivar, ivers, glob, var, data, aa, nn, ierr) if (ierr /= 0) then write(*,*) 'read_and_store failed in fgong_amdl' call mesa_error(__FILE__,__LINE__) From cb4af98cf41dc1d2463f47fea0c0430cc32cbf1a Mon Sep 17 00:00:00 2001 From: Meridith Joyce Date: Tue, 13 Aug 2024 11:24:29 -0400 Subject: [PATCH 54/66] [ci skip] turn off force dV=0 in starspots turb_support --- star/private/turb_support.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/star/private/turb_support.f90 b/star/private/turb_support.f90 index 6fa8326d8..cc5756730 100644 --- a/star/private/turb_support.f90 +++ b/star/private/turb_support.f90 @@ -151,7 +151,7 @@ subroutine do1_mlt_eval( & else ! starspot YREC routine if (s% do_starspots) then - dV = 0d0 ! dV = 1/rho - 1/rho_start and we assume rho = rho_start. + !dV = 0d0 ! dV = 1/rho - 1/rho_start and we assume rho = rho_start. call starspot_tweak_gradr(s, P, gradr_in, gradr) end if call Get_results(s, k, MLT_option, & From a5cc65c2bf3c1e73dcdd41d7cb6379216e1d1bd6 Mon Sep 17 00:00:00 2001 From: pmocz Date: Wed, 14 Aug 2024 07:34:47 -0400 Subject: [PATCH 55/66] [ci skip] update release script to work with new PEP440 TAG SYSTEM --- docs/source/developing/release.rst | 24 ++++++++++++++---------- release | 9 ++++++--- 2 files changed, 20 insertions(+), 13 deletions(-) diff --git a/docs/source/developing/release.rst b/docs/source/developing/release.rst index fd812de13..0ec6c9121 100644 --- a/docs/source/developing/release.rst +++ b/docs/source/developing/release.rst @@ -40,7 +40,7 @@ Documentation Testing ------- -- TestHub should report all tests pass for both Linux and macOS on multiple machines and with different OS versions +- TestHub should report all tests pass for both Linux and macOS on multiple machines and with different OS versions. - The previous SDK version should be tested. .. note:: @@ -81,7 +81,7 @@ Making a release ---------------- Run the release script in ``MESA_DIR``. This requires ``$MESA_DIR`` to be set and takes one argument the release version (you should add the ``r`` prefix as well). -For version ``r12345`` this script will make a branch ``release/r12345`` and then it: +For version ``rXX.YY.Z`` this script will make a branch ``release/rXX.YY.Z`` and then it: - Updates :file:`data/version_number` @@ -91,7 +91,7 @@ For version ``r12345`` this script will make a branch ``release/r12345`` and the - Updates :file:`docs/source/conf.py` - Updates :file:`Doxyfile` -To the new version ``r12345``. +To the new version ``rXX.YY.Z``. This script will also make zip archive, which can be used for local testing to make sure the release builds. @@ -99,7 +99,7 @@ This script will also make zip archive, which can be used for local testing to m This zip folder is not what we release. The actual zip folder is generated by Github, so that should be tested as well once it has been made. .. note:: - Once the script has generated the new release branch, update the changelog headings from "Changes in main" to "Changes in r12345" etc, + Once the script has generated the new release branch, update the changelog headings from "Changes in main" to "Changes in rXX.YY.Z" etc, and delete the note near the top of the changelog about changes in ``main`` relative to the most recent release. The release script does not push any changes to Github. Once you are ready to push the release branch, this must be done manually with a ``git push``. (This is a separate step from pushing the tag in the next step.) @@ -110,16 +110,19 @@ Release steps To make an actual release (once testing is complete), first push the git tag made by the release script: -- ``git push origin r12345`` +- ``git push origin XX.YY.Z`` This is the key bit, as the Github release will be anchored to this tag. +.. note:: + The tag follows PEP440 standards -- there is no ``r`` or ``-`` (hyphen) in the tag (unlike the branch name) -- so readthedocs can automatically determine the stable version and add version warning banners. + Go to https://github.com/MESAHub/mesa/releases and craft a new release following the guidelines `here `_. .. note:: If this is a RC release, then make sure to click ``This is a pre-release``. -Add an appropriate title and description. The title should be kept simple, like ``Release: r12345``. +Add an appropriate title and description. The title should be kept simple, like ``Release: rXX.YY.Z``. Once created, this zip folder should be downloaded and checked that it installs and runs a test case. @@ -129,7 +132,7 @@ Zenodo Once the zip folder has been created, it should be uploaded to Zenodo prior to sending a release announcement. This helps avoid swamping our GitHub bandwidth with user downloads. -- For a pre-release, do not upload to the main MESA zenodo repository. +- For a pre-release, do not upload to the main MESA Zenodo repository. Instead upload to its own Zenodo entry. This can be done on a personal account. - Official releases need to be uploaded to `this MESA Zenodo page `_. @@ -174,12 +177,13 @@ needs fixes to simply push a new release, and flag the current release as not wo New readthedocs version ----------------------- -First gain access to the readthedocs account (that is currently accessible by Rich, Evan, Joey, and Earl). Then: +First gain access to the readthedocs account (that is currently accessible by Rich, Evan, Joey, Earl, Meridith, and Philip). Then: - Go to the ``Versions`` page -- Find the release branch (not the tag) and ``Activate`` it -- We want the branch, not the tag, so that we can update the docs post release. +- Find the release tag (not the branch) and ``Activate`` it +- We want the tag (following PEP440 standards), so readthedocs can automatically deduce the stable version and create a version banner warning. - Wait for it to build, and check that it works - Go to the ``Admin`` page and then the ``Advanced settings`` tab - Switch the default version to the release - Click ``save`` at the bottom of the page +- To update docs post release, we will need to use git to change the tag to point to the new commit (SHA). diff --git a/release b/release index a69bf3098..f7b6bf19d 100755 --- a/release +++ b/release @@ -3,10 +3,13 @@ VERSION="$1" if [[ ! -n ${VERSION}} ]]; then - echo 'Please specify version number' + echo 'Please specify version number, e.g. r2X.YY.Z ot r2X.YY.Z-rcA' exit 1 fi +# strip the r and hypen from version number to create a PEP440 standard tag +TAG=${${VERSION:1}//-} + cd ${MESA_DIR} || exit 1 # Do the work in a sperate branch @@ -27,7 +30,7 @@ sed -i 's/version\ =.*/version\ =\ '"'${VERSION}'"'/' docs/source/conf.py git add docs/source/conf.py git commit -a -m "Release: ${VERSION}" -git tag ${VERSION} +git tag ${TAG} # Make the archive git archive --prefix=mesa-${VERSION}/ --format=zip ${VERSION} > mesa-${VERSION}.zip @@ -38,5 +41,5 @@ exit 0 # Cleanup when testing git checkout main -git tag -d ${VERSION} +git tag -d ${TAG} git branch -D release/${VERSION} From 74271490ea1efb75fe63a2db96fac2652ab771c7 Mon Sep 17 00:00:00 2001 From: Philip Mocz Date: Wed, 14 Aug 2024 08:06:15 -0400 Subject: [PATCH 56/66] [ci skip] add checks in release --- release | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/release b/release index f7b6bf19d..d608bca30 100755 --- a/release +++ b/release @@ -1,14 +1,22 @@ #!/bin/bash VERSION="$1" +echo ${VERSION} -if [[ ! -n ${VERSION}} ]]; then - echo 'Please specify version number, e.g. r2X.YY.Z ot r2X.YY.Z-rcA' +if [[ ! -n ${VERSION} ]]; then + echo "Please specify version number. E.g. r2X.YY.Z or r2X.YY.Z-rcA" + exit 1 +fi + +if [[ ! ${VERSION} == r* ]]; then + echo "Version number must start with 'r'. E.g. r2X.YY.Z or r2X.YY.Z-rcA" exit 1 fi # strip the r and hypen from version number to create a PEP440 standard tag -TAG=${${VERSION:1}//-} +TAG=${VERSION:1} +TAG=${TAG//-} +echo "The associated (PEP440) tag version ${VERSION} is: ${TAG}" cd ${MESA_DIR} || exit 1 From 02f751ede3acf00fc822018fadb6b8856d547b27 Mon Sep 17 00:00:00 2001 From: Philip Mocz Date: Wed, 14 Aug 2024 08:55:47 -0400 Subject: [PATCH 57/66] [ci skip] git archive arg fix in release script --- release | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/release b/release index d608bca30..1ee62f8bc 100755 --- a/release +++ b/release @@ -41,7 +41,7 @@ git commit -a -m "Release: ${VERSION}" git tag ${TAG} # Make the archive -git archive --prefix=mesa-${VERSION}/ --format=zip ${VERSION} > mesa-${VERSION}.zip +git archive --prefix=mesa-${VERSION}/ --format=zip ${TAG} > mesa-${VERSION}.zip echo "Now check the archive builds before pushing the changes" From a85106fc22dd624f92b6940a64ed9accd9f28e1c Mon Sep 17 00:00:00 2001 From: Philip Mocz Date: Wed, 14 Aug 2024 09:57:36 -0400 Subject: [PATCH 58/66] [ci skip] fix doc warnings in summer_schools.rst --- docs/source/summer_schools.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/summer_schools.rst b/docs/source/summer_schools.rst index 93bd18f2f..b5a089ed1 100644 --- a/docs/source/summer_schools.rst +++ b/docs/source/summer_schools.rst @@ -37,7 +37,7 @@ Preparing a good program takes about a year. Historically, the program has taken We aim for 50-50 gender representation (50% men, 50% women and gender minorities) among both lecturers and TAs. We have succeeded in having 35% or greater representation among women and gender minorities in past programs. 9 months to 7 months out (November - January) ------------------------ +--------------------------------------------- - Look for and apply to grant funding schemes. Previous supporters of the MESA Summer Schools include the International Research Network of Nuclear Astrophysics (IReNA; USA), the European ChETEC-INFRA network of research infrastructures, and individual research grants (NSF; Marie Curie scheme, ERC scheme). - reserve accommodation. Hotel room blocks can be booked for discounted rates. Some univerisites are willing to provide discounted bulk accommodation through their own facilities (e.g. dorms), as was the case at Santa Barbara. @@ -52,7 +52,7 @@ We aim for 50-50 gender representation (50% men, 50% women and gender minorities 5 months out (March) ------------------------ +-------------------- - close applications - make selections among applications. An admissions rubric used for the 2022, 2023, and 2024 Summer School programs is available from Meridith Joyce (MESAdev) @@ -62,18 +62,18 @@ We aim for 50-50 gender representation (50% men, 50% women and gender minorities - send acceptances to students, cc-ing superviors, while maintaining a ranked waitlist. If you do not hear back from an accepted student or their supervisor in, for example, 2 weeks, move on to the waitlist. There are typically several students admitted off the waitlist. 4 months out (April) ------------------------ +-------------------- - Begin regular, bi-weekly, all-hands meetings to check in with the organizational team, lecturers, and TAs. Lecturers should begin to schedule separate group meetings with their TAs to design exercises. Bi-weekly meetings serve to check in on the progress of these groups. - begin preparing any visa or invitation letters necessary for international students 1 month out (July) ------------------------ +------------------ - Increase the cadence of all-hands meetings to weekly. Lab exercises should be distributed for testing among TAs, leaving at least two weeks before the start of Summer School for final corrections to be implemented. Labs should be tested for coherence, timing, and accessibility of the exercises 2 weeks out ------------------------ +----------- - final corrections to labs are underway - Lecturers' programs and slides should be near completion. It is helpful if all lecture materials are available before the start of the labs. All lab materials should also be available before the start of the program. From a07658e14df72dc564b8364f71974bcb3a13eb07 Mon Sep 17 00:00:00 2001 From: Philip Mocz Date: Wed, 14 Aug 2024 10:02:22 -0400 Subject: [PATCH 59/66] [ci skip] adding Mesa IV reference to docs --- docs/source/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index 6bf00ef9f..953652a93 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -136,6 +136,7 @@ .. |MESA III| replace:: `MESA III `__ .. |MESA IV| replace:: `MESA IV `__ .. |MESA V| replace:: `MESA V `__ +.. |MESA VI| replace:: `MESA V `__ .. |Msun| replace:: :math:`{\rm M}_\odot` .. |Lsun| replace:: :math:`{\rm L}_\odot` .. |Rsun| replace:: :math:`{\rm R}_\odot` From c6735d66dc1c38d11311e1725992f06db9dd74d7 Mon Sep 17 00:00:00 2001 From: Philip Mocz Date: Wed, 14 Aug 2024 10:02:53 -0400 Subject: [PATCH 60/66] [ci skip] rst formatting --- docs/source/summer_schools.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/summer_schools.rst b/docs/source/summer_schools.rst index b5a089ed1..65aaacb82 100644 --- a/docs/source/summer_schools.rst +++ b/docs/source/summer_schools.rst @@ -1,9 +1,9 @@ MESA Summer Schools =================== -*** +************************************************************ MESA Summer School Programs -- this page under construction! -*** +************************************************************ History of the MESA Summer School Program ----------------------------------------- From 38c1e12e51b36436ad9d85343550a71b605a16f6 Mon Sep 17 00:00:00 2001 From: Philip Mocz Date: Wed, 14 Aug 2024 10:35:46 -0400 Subject: [PATCH 61/66] [ci skip] update orcidid's in .zenodo.json --- .zenodo.json | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 53d01ed68..0286d4a5c 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -11,18 +11,21 @@ }, { "affiliation": "Center for Computational Astrophysics", - "name": "Bauer, Evan" + "name": "Bauer, Evan", + "orcid": "0000-0002-4791-6724" }, { - "affiliation": "Max Planck Institute for Astrophysics", - "name": "Bellinger, Earl" + "affiliation": "Yale University", + "name": "Bellinger, Earl", + "orcid": "0000-0003-4456-4863" }, { "affiliation": "Kavli Institute for Theoretical Physics", - "name": "Bildsten, Lars" + "name": "Bildsten, Lars", + "orcid": "0000-0001-8038-6836" }, { - "affiliation": "Center for Computational Astrophysics", + "affiliation": "Flatiron Institute", "name": "Cantiello, Matteo", "orcid": "0000-0002-8171-8596" }, @@ -47,8 +50,8 @@ "orcid": "0000-0001-5048-9973" }, { - "affiliation": "Space Telescope Science Institute", - "name": "Meridith, Joyce", + "affiliation": "University of Wyoming", + "name": "Joyce, Meridith", "orcid": "0000-0002-8717-127X" }, { @@ -56,6 +59,11 @@ "name": "Marchant, Pablo", "orcid": "0000-0002-0338-8181" }, + { + "affiliation": "Flatiron Institute", + "name": "Mocz, Philip", + "orcid": "0000-0001-6631-2566" + }, { "name": "Schwab, Josiah", "orcid": "0000-0002-4870-8855" From 4ef2850cda2a393895fed96325cf3ab69b8d480c Mon Sep 17 00:00:00 2001 From: pmocz Date: Thu, 15 Aug 2024 09:21:37 -0400 Subject: [PATCH 62/66] test new TDC exit search criteria --- star/private/predictive_mix.f90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/star/private/predictive_mix.f90 b/star/private/predictive_mix.f90 index 9cac95b64..08e0ef06e 100644 --- a/star/private/predictive_mix.f90 +++ b/star/private/predictive_mix.f90 @@ -375,10 +375,10 @@ subroutine do_predictive_mixing (s, i, j, ierr, mix_mask) k_bot_mz = k_bot_mz + 1 endif - ! See if the mixed region has gone out of bounds [1, s%nz-1] + ! Exit search if the mixed region has gone out of bounds if (( outward .AND. k_top_mz < 1) .OR. & - (.NOT. outward .AND. k_bot_mz > s%nz-1)) then + (.NOT. outward .AND. k_bot_mz > s%nz)) then exit search_loop endif From 8bc821197e678d85405f35e7cb3a59e086dcb83f Mon Sep 17 00:00:00 2001 From: EbF Date: Thu, 15 Aug 2024 20:15:56 -0400 Subject: [PATCH 63/66] [ci optional] update ZAMS models and changelog --- data/star_data/zams_models/zams_z2m2_y28.data | 2 +- docs/source/changelog.rst | 44 +++++++++---------- 2 files changed, 21 insertions(+), 25 deletions(-) diff --git a/data/star_data/zams_models/zams_z2m2_y28.data b/data/star_data/zams_models/zams_z2m2_y28.data index cd51c7313..477b2e382 100644 --- a/data/star_data/zams_models/zams_z2m2_y28.data +++ b/data/star_data/zams_models/zams_z2m2_y28.data @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:799ab61d136a41f4a7c18297c3400c182414887f6d096fb5e393ac815a5f8fa0 +oid sha256:84651346e4313c7160c7b6f2b8d15629da71fc50a9ffa7eb019dcd24413fddbb size 31825816 diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 86e8992a1..a03e7b781 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -7,18 +7,30 @@ Changelog Changes in main =============== -.. note:: This describes changes present in the development version of MESA (``main`` branch) relative to the most recent release. - .. _New Features main: New Features ------------ -**Update to starspots ** -star spot parameters - ``fspot`` - ``xspot`` - have been added as general controls and are now accessible outside of ``test_suite/starspots/``. Star spots are off by default +.. _Bug Fixes main: + +Bug Fixes +--------- + +Changes in r24.08.1 +=================== + +.. _New Features r24.08.1: + +New Features +------------ + +``max_allowed_nz`` is now ignored if the value is less than or equal to zero. + +**Update to starspots** + +Star spot parameters ``fspot``, and ``xspot`` have been added as general controls +and are now accessible outside of ``test_suite/starspots/``. Star spots are off by default. **Replacement of HDF5io by ForUM** @@ -54,22 +66,6 @@ against :file:`libgyre_mea.a`. These changes will likely only affect those users that make calls to GYRE from inside :file:`run_star_extras.f90`. -.. _Bug Fixes main: - -Bug Fixes ---------- - - -Changes in r24.06.1-rc1 -======================= - -.. _New Features r24.06.1-rc1: - -New Features ------------- - -``max_allowed_nz`` is now ignored if the value is less than or equal to zero. - Kap ~~~ @@ -177,7 +173,7 @@ Chem New initial metal mass fractions ``initial_zfracs`` taken from photospheric estimates of the solar heavy element abundances in (AAG21, Asplund et al. 2021) and (MB22, Magg et al. 2022) are now available. See :ref:`reference/star_job:initial_zfracs` for more details. -.. _Bug Fixes r24.06.1-rc1: +.. _Bug Fixes r24.08.1: Bug Fixes --------- From 6cb10c738f803a5e4f6e13a2a72e698095dc60bb Mon Sep 17 00:00:00 2001 From: Ebraheem Farag <63124736+Debraheem@users.noreply.github.com> Date: Thu, 15 Aug 2024 20:19:59 -0400 Subject: [PATCH 64/66] [ci skip] Update changelog.rst --- docs/source/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index a03e7b781..0073b1c19 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -4,6 +4,8 @@ Changelog .. warning:: As of r24.08.1, building MESA now requires Python (3.5 or newer) be installed. +.. note:: This describes changes present in the development version of MESA (``main`` branch) relative to the most recent release. + Changes in main =============== From b3611de48830939b8fe9d2c62f78698ff4af6e9c Mon Sep 17 00:00:00 2001 From: pmocz Date: Mon, 19 Aug 2024 10:47:28 -0400 Subject: [PATCH 65/66] [ci skip] note in changlog a bit more descriptive --- docs/source/changelog.rst | 4 +++- docs/source/changelog_template.rst | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 0073b1c19..a565d59cd 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -4,7 +4,7 @@ Changelog .. warning:: As of r24.08.1, building MESA now requires Python (3.5 or newer) be installed. -.. note:: This describes changes present in the development version of MESA (``main`` branch) relative to the most recent release. +.. note:: This section describes changes present in the development version of MESA (``main`` branch) relative to the most recent release. Changes in main =============== @@ -19,6 +19,8 @@ New Features Bug Fixes --------- +.. note:: Before releasing a new version of MESA, move `Changes in main` to a new section below with the version number as the title, and add a new `Changes in main` section at the top of the file (see ```changelog_template.rst```). + Changes in r24.08.1 =================== diff --git a/docs/source/changelog_template.rst b/docs/source/changelog_template.rst index e31b3e2c9..25e41c5c1 100644 --- a/docs/source/changelog_template.rst +++ b/docs/source/changelog_template.rst @@ -1,7 +1,8 @@ +.. note:: This section describes changes present in the development version of MESA (``main`` branch) relative to the most recent release. + Changes in main =============== -.. note:: This describes changes present in the development version of MESA (``main`` branch) relative to the most recent release. .. _Backwards-incompatible changes main: @@ -21,3 +22,4 @@ Bug Fixes --------- +.. note:: Before releasing a new version of MESA, move `Changes in main` to a new section below with the version number as the title, and add a new `Changes in main` section at the top of the file (see ```changelog_template.rst```). From 4badedee3405c422cbec2058aa0c2896ca507d3b Mon Sep 17 00:00:00 2001 From: pmocz Date: Mon, 19 Aug 2024 11:19:36 -0400 Subject: [PATCH 66/66] [ci skip] adding check in release script that changelog has been updated --- release | 30 ++++++++++++++++++++++++------ 1 file changed, 24 insertions(+), 6 deletions(-) diff --git a/release b/release index 1ee62f8bc..ac58efbaf 100755 --- a/release +++ b/release @@ -1,15 +1,21 @@ #!/bin/bash VERSION="$1" -echo ${VERSION} +echo "Preparing to release MESA version ${VERSION}" if [[ ! -n ${VERSION} ]]; then - echo "Please specify version number. E.g. r2X.YY.Z or r2X.YY.Z-rcA" + echo "Error: Please specify version number. E.g. r2X.YY.Z or r2X.YY.Z-rcA" exit 1 fi if [[ ! ${VERSION} == r* ]]; then - echo "Version number must start with 'r'. E.g. r2X.YY.Z or r2X.YY.Z-rcA" + echo "Error: Version number must start with 'r'. E.g. r2X.YY.Z or r2X.YY.Z-rcA" + exit 1 +fi + +# check that the changelog has been updated +if ! grep -q "Changes in ${VERSION}" docs/source/changelog.rst; then + echo "Error: Please update the changelog by moving 'Changes in main' to a new section called 'Changes in ${VERSION}' and add a new 'Changes in main' section at the top of the file following 'changelog_template.rst'. Make sure this change is commited in the 'main' development branch of MESA." exit 1 fi @@ -20,7 +26,7 @@ echo "The associated (PEP440) tag version ${VERSION} is: ${TAG}" cd ${MESA_DIR} || exit 1 -# Do the work in a sperate branch +# Do the work in a seperate branch git checkout -b release/${VERSION} # Add version_number file @@ -32,11 +38,23 @@ sed -i "s/PROJECT_NUMBER\ \ \ .*/PROJECT_NUMBER\ \ \ \ \ \ \ \ \ =\ ${VERSION}/" git add Doxyfile # Update docs/source/conf.py -sed -i 's/release\ =.*/release\ =\ '"'${VERSION}'"'/' docs/source/conf.py -sed -i 's/version\ =.*/version\ =\ '"'${VERSION}'"'/' docs/source/conf.py +sed -i 's/release\ =.*/release\ =\ '"'${TAG}'"'/' docs/source/conf.py +sed -i 's/version\ =.*/version\ =\ '"'${TAG}'"'/' docs/source/conf.py git add docs/source/conf.py +# Update docs/source/changelog.rst +PATTERN1="This section describes changes present in the development" +PATTERN2="Before releasing a new version of MESA" +if grep -q "$PATTERN1" docs/source/changelog.rst; then + if grep -q "$PATTERN2" docs/source/changelog.rst; then + sed -i "/$PATTERN1/,/$PATTERN2/d" docs/source/changelog.rst + fi +fi + +git add docs/source/changelog.rst + +# Commit and tag the changes git commit -a -m "Release: ${VERSION}" git tag ${TAG}