Changelog
Changes in r23.05.1
Backwards-incompatible changes
Extra inlist controls are now arrays
Almost all MESA inlists have the option of reading other inlists,
which is a feature canonically used in the main inlist file.
e.g. the inlist in the standard star/work directory has
read_extra_controls_inlist1 = .true.
extra_controls_inlist1_name = 'inlist_project'
where the inlist number could range from 1 to 5.
These and all similar controls have been replaced with arrays like
read_extra_controls_inlist(1) = .true.
extra_controls_inlist_name(1) = 'inlist_project'
That is, the number should be moved to the end of the control name and placed in round brackets.
This allows a lot of duplicate code to be refactored but will break
almost all existing MESA inlists. To update an old inlist to this new
style, you can use the following sed terminal command:
sed -E '/inlist[1-5]/s/([1-5])([_a-z]*) =/\2\(\1\) =/' -i inlist_name
where inlist_name is the inlist (or inlists) that you’d like to update.
This will replace the file inlist_name. Omit the -i flag if you’d
like to see the changes without modifying the file.
sed is a standard tool that is included with macOS and most Linux distributions.
For convenience, we have also included a bash script that will call a version of
this sed command (along with sed commands for the next changlog entry as well)
to update all inlist files (inlist*), which you can run in any work directory
where you want to update every inlist by invoking
$MESA_DIR/scripts/update_inlists
This script will save the previous versions of your inlists to a directory named
backup_inlists.
Renamed controls for upper limits
The following controls in &controls for upper limits on
when to stop have
been renamed:
Old |
New |
|---|---|
|
|
You can substitute the new names for the old ones using the command
line tool sed with, e.g.
$ sed 's/log_center_density_limit/log_center_density_upper_limit/' -i <inlist_filename>
Abundance-based timestep controls are now arrays
The previous controls
dH_limit_min_H = 1d99
dH_limit = 1d99
dH_hard_limit = 1d99
dH_decreases_only = .true.
dH_div_H_limit_min_H = 1d-3
dH_div_H_limit = 0.9d0
dH_div_H_hard_limit = 1d99
and similar controls for He and He3 have been replaced with
arrays. This simplifies the code and allows the controls to be
applied to any species in the net. A new control
dX_limit_species(...) specifies which elements will be checked.
The previous behaviour for H, for example, has been replaced with
dX_limit_species(1) = 'h1'
dX_limit_min_X(1) = 1d99
dX_limit(1) = 1d99
dX_hard_limit(1) = 1d99
dX_decreases_only(1) = .true.
dX_div_X_limit_min_X(1) = 1d-3
dX_div_X_limit(1) = 0.9d0
dX_div_X_hard_limit(1) = 1d99
The old H, He and He3 controls correspond to species
h1, he4 and he3, respectively. You can also set the
species to X, Y or Z, in which case the checks are applied
individually to all isotopes of hydrogen, helium or metals,
respectively.
Colors
The colors module now returns -1d99 when asking for a value that is
off table.
New Features
White Dwarf C/O Phase Separation
An option to include carbon-oxygen phase separation for crystallizing C/O white dwarfs is now available,
using the phase diagram of Blouin et al. (2021).
The MESA implementation is described in Bauer (2023).
More documentation and associated controls can be found at do_phase_separation.
This option is off by default, but it is on in the wd_cool_0.6M test case.
Module enhancement: pgbinary
When running ./binary models it is useful to have graphical
output to ‘see’ what’s going on.
Previously, this was only possible on the pgstar level, meaning you would
need to setup two pgstar windows if you are evolving two stars in the
binary.
Here we introduce pgbinary, which acts much like pgstar. You enable it
with the &binary_job inlist with pgbinary_flag = .true.. Then you
select windows and/or files to be plotted in the &pgbinary inlist.
Currently the following plot types can be created:
History_Track[1-9],
Summary_History,
History_Panels[1-9],
Text_Summary[1-9],
Grid[1-9],
analogous to their pgstar equivalents, and two pgbinary-only plots:
Star[1-2], to plot a star window through
&pgstarcontrols, withinpgbinary.Orbit, a visual representation of the stars’ sizes to their separation
Main use case is to have a single window containing both stars’ pgstar info,
through using Grid at the pgbinary level, populating it with Star1
and Star2, and have each plot profile info, Kipp diagrams etc…
Resolution control convective_bdy_weight has been reintroduced
The option to add extra resolution at convective boundaries
with the control convective_bdy_weight was removed after
version 12115, but has now been reintroduced in a simplified form.
This control no longer applies to newly nonconvective zones, but
does add resolution at the location of convective boundaries.
This was found to be important for smooth convective boundary
evolution with convective premixing.
Hooks
A new other_close_gaps hook has been added. Provided by Simon Guichandut
Bug Fixes
Rates
There has been a bug present in the rate r_c12_to_he4_he4_he4 in r22.05.1 and r22.11.1.
This causes an excessive amount of C12 to be burnt during core helium burning.
We strongly recommend that users update to the latest MESA.
See gh-526
RTI
A bug has existed since shortly after r15140 where RTI
mixing will be effectively zero in a model even with the
RTI_flag=.true. set.
This has now been fixed. Users of RTI mixing are recommended to upgrade to the newest MESA version.
See gh-503
Changes in r22.11.1
Backwards-incompatible changes
Note
A large amount of internal clean up has occurred since the last release. This lists some of the most important changes, but the list is not exhaustive.
Module-level changes
astero
The main controls for the selection of parameters and non-seismic constraints (which were dubbed “variables”) has changed. The defaults files document the new interface but the most important changes are repeated here.
Each non-seismic constraint is now given a name, target value,
uncertainty and flag for whether to include it in the \(\chi^2\)
calculation. The default work folder will either try for one of
the custom options included for backward compatibility (e.g. Rcz)
or fall back to computing the matching history column (e.g. for
log_g). So whereas an effective temperature constraint would
previously be included using, say
include_Teff_in_chi2_spectro = .true.
Teff_target = 6000
Teff_sigma = 100
you would now use
constraint_name(1) = 'Teff'
include_constraint_in_chi2_spectro(1) = .true.
constraint_target(1) = 6000
constraint_sigma(1) = 100
The maximum number of such constraints is currently 100 but can
trivially be increased at compile time by modifying
max_constraints in astero/public/astero_def.f90.
Similarly, each parameter now has a name, initial value, minimum, maximum and grid-spacing. So whereas the mixing-length parameter was previously controlled with something like
vary_alpha = .true.
first_alpha = 1.7
min_alpha = 1.5
max_alpha = 1.9
delta_alpha = 0.1
you would now use
param_name(1) = 'alpha'
vary_param(1) = .true.
first_param(1) = 1.7
min_param(1) = 1.5
max_param(1) = 1.9
delta_param(1) = 0.1
Again, the maximum number of parameters is 100 and can be increased at
compile time by modifying max_parameters in
astero/public/astero_def.f90.
The default run_star_extras.f90 defines the hooks
set_constraint_value and set_param so that the old options
remain available, though with a new syntax. Users can also use those
routines to define their own parameters and constraints.
The output files contain information for constraints or parameters
with names that are not ''. Thus, the column order now varies but
the same information is present and now follows the same structure as
histories and profiles.
star
For wind mass loss, schemes that scale with metallicity now employ
Zbase rather than Z (as long as Zbase is set to a non-negative value,
otherwise we fall back to Z). This reflects the fact that wind recipes primarily
account for the opacity of iron-group elements, which have surface abundances that
are unlikely to change during evolution. This change therefore avoids
unphysical influence on winds by, e.g., evolution of surface CNO abundances.
test_suite
All test cases have now had the inlist option, makefile variable, and shell script variable, MESA_DIR removed.
This means that you no longer need to do anything to make a MESA test case work outside of the test suite.
Test cases now infer their MESA_DIR variable entirely by the environment variable $MESA_DIR.
The history output option tri_alfa (and other quantities that relate to the triple-alpha nuclear reaction) have been renamed to tri_alpha for better consistency with other _alpha reactions.
net
The derived type net_info (conventional given the symbol n) is no longer a pointer. If you declare a local copy of the variable, you should also ensure to do n% g => g to make sure that net_info knows
about the net_general_info derived type. g can be had from a call to get_net_ptr(handle, g, ierr).
The pointer array net_work and its size net_lwork have been removed from the net interface, thus these variables should be removed form any other_net_get and other_split_burn hooks.
The following routines have also been removed as they are no longer needed net_work_size, get_net_rate_ptrs, net_1_zone_burn_work_size, get_burn_work_array_pointers, net_1_zone_burn_const_density_work_size, and get_burn_const_density_work_array_pointers
Previously you could pass arg_not_provided for either the temperature (density) or log(temperature) (log(density)). Now you must pass both explicity.
ADIPLS
ADIPLS now has a USE_ADIPLS flag in utils/makefile_header to enable is build to be disabled.
Changes in r22.05.1
Backwards-incompatible changes
Note
A large amount of internal clean up has occurred since the last release. This lists some of the most important changes, but the list is not exhaustive.
Module-level changes
astero
&astero_search_controls now has an option astero_results_directory to specify a folder into which all of
astero’s results are saved (like log_directory in star). The default is outputs, so if you
can’t seem to find your astero output, have a look there.
&astero_search_controls also now has options
astero_results_dbl_format = '(1pes26.16)'
astero_results_int_format = '(i26)'
astero_results_txt_format = '(a26)'
by which the user can set the formats of floats, integers and strings in the astero results file,
much like star_history_*_format does for history files.
The format of the astero results file has changed to match histories and profiles.
The contents of the file are unchanged.
rates
The 7Be(e-,nu)7Li has been switched from REACLIB rate to that of Simonucci et al 2013. This is due to the fact that the REACLIB rate does not take into account the neutral ion rate below 10^7 K.
The ability to set the rates preferences has been removed. This added alot of complexity to the rates code handling NACRE and REACLIB and made it difficult to reason about where a rate actually came from. From now on we excusivily use NACRE for any rate that cares about temperatures below 10^7K (for all temperatures), REACLIB for almost all other rates, and a small number of rates from CF88 (if they aren’t in REACLIB or NACRE).
Of note is that the default C12(a,g)O16 rate has thus changed from NACRE to that of REACLIB.
The options set_rates_preferences, new_rates_preference, and set_rate_c1212 have been removed without replacements.
The options set_rate_c12ag, set_rate_n14pg, and set_rate_3a have been removed. However, those rates can now be access thorugh a new
rate selection mechanism. In $MESA_DIR/data/rates_data/rate_tables we now ship a number of MESA provided rate tables. These can be loaded,
either by the normal mechanism of adding the filename to a rates_list file, or by using the new option filename_of_special_rate.
This option sets the filename to load the rate from for the rate specified by reaction_for_special_factor.
Thus the options:
num_special_rate_factors = 1
reaction_for_special_factor(1) = 'r_c12_ag_o16'
special_rate_factor(1) = 1
filename_of_special_rate(1) = 'r_c12_ag_o16_kunz.txt'
replaces the previous:
set_rate_c12ag = 'Kunz'
option.
As part of this new scheme we now ship a set of rates from NACREII Xu et al 2013. These rates do not, by default,
override the default NACRE rates. You must explicitly ask for them with filename_of_special_rate.
There is now a new hook other_rate_get to provide a simple way to change an existing rate in a run_star_extras.f90. Note this hook
only works on rates that are NOT currently in your rates_cache. It is recommended when using this option to set a custom rates_cache_dir otherwise the cache files in
MESA_DIR will be over written.
The previous option:
use_rate_3a = 'Fl87'
has been replaced with:
use_3a_fl87 = .true.
net
There is a new hook other_net_derivs that allows for modifying the dydt term MESA computes for each zone inside net/.
This allows adding changes in composition due to nuclear reactions that MESA could otherwise not handle or does not know about.
This hook only works with soft networks (thus no approx nets). This hook requires many derivatives to be set,
thus users should look at net_derivs.f90 for reference to what needs setting.
There is now a hook other_split_burn for replacing MESA’s split burn routine.
star
Diffusion coefficients for white dwarf interiors are now included based on Caplan et al. (2022). By default, these coefficients are used for strong plasma coupling \(\Gamma > 10\), but there is an inlist option to turn them off and revert to the previous default Stanton & Murillo (2016) coefficients if desired.
Fixed a combination of bugs whereby the atmosphere data written to pulsation file formats (e.g. FGONG)
was incorrect or wouldn’t work if tau_factor or atm_T_tau_opacity differed from their defaults
(1.0 and 'fixed', respectively).
pgstar
Due to re-organization of the star_type derived type, all pgstar controls have been moved into a separate pgstar derived type.
If you access a pgstar option XX in your run_star_extras.f90 then you need to replace s% XX with s% pg% XX.
RSP
In r21.12.1 an experimental RSP solver feature was turned on by default, leading to convergence issues in nonlinear model integration. This is now turned off by default. Users that continue to use RSP in r.21.12.1 should include RSP_do_check_omega = .true. in the &controls section of their inlists to get rid of this issue.
Changes in r21.12.1
Backwards-incompatible changes
Note
A large amount of internal clean up has occurred since the last release. This lists some of the most important changes, but the list is not exhaustive.
Simplification of energy equation options
The desired form of the MESA energy equation is now selected via the control energy_eqn_option. The available options are
'dedt' (default) and 'eps_grav'. See the documentation at energy_eqn_option for more information about these forms.
The controls use_dedt_form_of_energy_eqn, always_use_dedt_form_of_energy_eqn, and use_eps_grav_form_of_energy_eqn were removed and replaced by the functionality of energy_eqn_option.
Simplifications to the energy equation code mean that this selection applies globally (i.e., to all cells in the model and at all timesteps).
The per-cell energy equation controls
max_eta_for_dedt_form_of_energy_eqnandmax_gamma_for_dedt_form_of_energy_eqnwere removed.The form-switching control
steps_before_always_use_dedt_form_of_energy_eqnwas removed.
Name changes
The
star_joboptionsaved_model_namehas been replaced withload_model_filenameeverywhere.The
controlsoptionspower_c_burn_{lower,upper}_limitwere replaced with the more genericpower_z_burn_{lower,upper}_limit.The
controlsoptiondelta_lgL_phot_limitwas renamed todelta_lgL_power_photo_limit(“phot” was easily confused with photosphere instead of photodisintegration).The
controlsoptionssurf_w_div_w_crit_limitandsurf_w_div_w_crit_tolwere renamed tosurf_omega_div_omega_crit_limitandsurf_omega_div_omega_crit_tolThe core/layer mass values
c_core_*,c_rich_layer, ando_core_*have been renamed toco_core_*,co_rich_layer_*, andone_core_*. This better reflects the typical carbon/oxygen and oxygen/neon compositions of these regions. This affects the names of both the relevant controls and history columns.The
controlsoptionuse_d_eos_dxawas renamed tofix_d_eos_dxa_partials. This control originally had a broader function during the implementation of eos composition derivatives, but is now restricted to selecting whether we do a finite-difference-based fix up when on a component EOS that doesn’t provide composition derivatives.The history and profile columns
burn_*where replace with*_alpha.History, profile, and binary history column files are now case insensitive.
Removed options
The time-smoothing scheme for mixing diffusion coefficients was removed. All associated options (e.g.,
new_D_smooth_flagandD_smooth_replacement_fraction) were removed.Removed option
semiconvection_upper_limit_center_h1. This can be implemented by settings% alpha_semiconvectioninrun_star_extras.f90/extras_start_step.Removed the option
use_brunt_gradmuX_form. Alternative forms of the Brunt can be calculated using theother_brunthook.
Removed history and profile columns
A major clean up of the history and profile columns was undertaken. Some of the removed values include:
Removed profile columns
total_energyandtotal_energy_integral.
Relocation of eos hooks
The other_eos hooks have been removed from star. See the eos section for information about their replacements.
Hook interface changes
The
Teffargument has been removed from theother_surface_PThook. (Teffis instead available in thestar_infopointer.)other_mesh_delta_coeff_factorno longer takeseps_h,eps_heoreps_zas arguments.
Auto diff
We now make more extensive use of the new autodiff module for automatically differentiating variables. If you are using a hook
in your run_star_extras.f90 then you will need to add use auto_diff to the top of your run_star_extras.f90 file.
If you see errors such as:
Error: Cannot convert REAL(8) to TYPE(auto_diff_real_star_order1) at (1)
Then this means you are missing the use auto_diff statement.
An example of using autodiff in a hook can be found at Example of auto_diff in run_star_extras
Module-level changes
astero
Many of the one-dimensional arrays of mode data (e.g. l0_obs) have
been consolidated into two-dimensional arrays (e.g. freq_target)
in which the first index is the angular degree l. The following
controls in &astero_search_controls have changed:
Old |
New |
|---|---|
|
|
|
|
|
|
|
|
The call signatures to the surface correction subroutines have also changed, generally from
subroutine get_some_freq_corr(...,
nl0, l0_obs, l0_sigma, l0_freq, l0_freq_corr, l0_inertia,
nl1, l1_obs, l1_sigma, l1_freq, l1_freq_corr, l1_inertia,
nl2, l2_obs, l2_sigma, l2_freq, l2_freq_corr, l2_inertia,
nl3, l3_obs, l3_sigma, l3_freq, l3_freq_corr, l3_inertia)
to
subroutine get_some_freq_corr(...,
nl, obs, sigma, freq, freq_corr, inertia)
binary
There are new hooks other_binary_photo_read and
other_binary_photo_write. These allow the user to save/restore
values in run_binary_extras.
eos
There are new module-level eos hooks (see eos/other) that replace
the star-level eos hooks (previously in star/other). Usage of
these hooks is similar to hooks in star. However, the relevant
procedure pointer is part of the EOS_General_Info structure and
not the star_info structure. Therefore, in extras_controls,
the procedure pointer statement should look like s% eos_rq %
other_eos_results => my_other_eos_results. The boolean option
use_other_eos_results controlling whether to use the hook is part
of the eos namelist rather than controls. For the first
required argument handle, pass s% eos_handle. This ensures
that the routine uses the same configuration options as other calls
from star to the eos module.
The hook other_eos_component allows the user to replace all or
part of the MESA EOS by providing a new component EOS and to control
the location of the blends between this and the other component EOSes.
It is controlled by the option use_other_eos_component. The
user-provided routine must return a complete set of EOS results. This
EOS component has the highest priority in the blend. This hook
should be used along with the hook other_eos_frac, which defines
the region over to use other_eos_component.
The hook other_eos_results allows the user to modify the results
returned by the EOS. The user-provided routine receives the results
from the EOS right before they are returned, after all components have
been evaluated. This allows the user make minor modifications to the
results from the existing EOS without having to provide a full replacement.
Two alternative eos module entry points (eosDT_HELMEOS_get and
eosDT_ideal_gas_get) and the star options that replaced the
standard eosDT calls to be with these routines
(use_eosDT_ideal_gas and use_eosDT_HELMEOS). This enables
significant simplifications of eos_support. Restriction to a single
component EOS can be achieved through the eos namelist options and
replacement of the EOS should be performed through the other hook.
The HELM table was updated to a new, larger 100 points per decade version.
The HELM-related controls logT_ion_HELM, logT_neutral_HELM, and
max_logRho_neutral_HELM were removed. These were used in an
now-unsupported variant of HELM that blended the normal, fully-ionized
HELM and a neutral version (which dropped the electron-positron terms).
The HELM-related controls always_skip_elec_pos and
always_include_elec_pos were combined in the
simplified control include_elec_pos which defaults to .true..
There is a new backstop EOS (ideal) which analytically models an ideal ion gas with radiation pressure.
The purpose of this EOS is to provide coverage over the whole density-temperature plane for times when MESA needs
to run to extreme densities or temperatures.
No electrons are included in this EOS.
kap
The call signatures of kap_get and the hook other_kap_get have
changed. The set of arguments is now conceptually equivalent between
the two subroutines. The inputs include the density, temperature, and
full composition vector. The free electron/positron number and the
electron degeneracy parameter (and their derivatives) are also
required. The outputs include the opacity and its derivatives as well
as information about the fractions of various opacity sources used in
the blended opacity.
subroutine kap_get( &
handle, species, chem_id, net_iso, xa, &
logRho, logT, &
lnfree_e, d_lnfree_e_dlnRho, d_lnfree_e_dlnT, &
eta, d_eta_dlnRho, d_eta_dlnT , &
kap_fracs, kap, dlnkap_dlnRho, dlnkap_dlnT, dlnkap_dxa, ierr)
! INPUT
integer, intent(in) :: handle ! from alloc_kap_handle; in star, pass s% kap_handle
integer, intent(in) :: species
integer, pointer :: chem_id(:) ! maps species to chem id
integer, pointer :: net_iso(:) ! maps chem id to species number
real(dp), intent(in) :: xa(:) ! mass fractions
real(dp), intent(in) :: logRho ! density
real(dp), intent(in) :: logT ! temperature
real(dp), intent(in) :: lnfree_e, d_lnfree_e_dlnRho, d_lnfree_e_dlnT
! free_e := total combined number per nucleon of free electrons and positrons
real(dp), intent(in) :: eta, d_eta_dlnRho, d_eta_dlnT
! eta := electron degeneracy parameter from eos
! OUTPUT
real(dp), intent(out) :: kap_fracs(num_kap_fracs)
real(dp), intent(out) :: kap ! opacity
real(dp), intent(out) :: dlnkap_dlnRho ! partial derivative at constant T
real(dp), intent(out) :: dlnkap_dlnT ! partial derivative at constant Rho
real(dp), intent(out) :: dlnkap_dxa(:) ! partial derivative w.r.t. species
integer, intent(out) :: ierr ! 0 means AOK.
The Compton scattering opacity routine has been updated to use the prescription of Poutanen (2017).
The conductive opacity routine has been updated to include the corrections from
Blouin et al. (2020)
for H and He in the regime of moderate coupling and moderate degeneracy.
These are on by default, controlled by the kap option use_blouin_conductive_opacities.
There are new module-level kap hooks (see kap/other) that allow
individual components of the opacity module to be replaced with a
user-specified routine given in run_star_extras. Usage of these hooks
is similar to hooks in star. However, the relevant procedure pointer
is part of the Kap_General_Info structure and not the
star_info structure. Therefore, in extras_controls, the
procedure pointer statement should look like s% kap_rq %
other_elect_cond_opacity => my_routine. The boolean option
use_other_elect_cond_opacity controlling whether to use the hook
is part of the kap namelist rather than controls. For the
first required argument handle, pass s% kap_handle. This
ensures that the routine uses the same configuration options as other
calls from star to the kap module.
neu
The call signature of other_neu has changed. You no longer need to pass in z2bar
The value of the Weinberg angle was updated to be be consistent with CODATA 2018.
net
The screening mode classic_screening has been removed. Anyone using other_net_get needs
to remove theta_e_for_graboske_et_al from its argument list.
The options reuse_rate_raw and reuse_rate_screened have been removed from other_net_get (and eval_net)
rates
The format for custom weak rate tables (see e.g., data/rates_data/rate_tables/weak_rate_list.txt and test suite case custom_rates) no longer supports the (previously optional) Coulomb correction datasets delta_Q and Vs.
When this capability was first added, the energetics associated with
the change in the composition were calculated in rates and
included in eps_nuc. This meant the rates module needed to
have access to information about the Coulomb-induced shifts in the
electron and ion chemical potentials.
After the changes in the definition of eps_nuc and the energy
equation described in MESA V, the energetics associated with the
changing composition are self-consistently accounted for in the energy
equation using information provided by the MESA EOS. Therefore, the
ability to provide these unneeded and unused quantities has been
removed.
Other changes
Analogous to
kap_frac_Type2, information about the fractional contribution of the lowT tables, highT tables, and Compton opacities to the final result from the opacity module are now included in star_info arrays and profile columns with the nameskap_frac_lowT,kap_frac_highT,kap_frac_Compton.The control
format_for_FGONG_datahas been replaced by the integerfgong_ivers, which can be either 300 or 1300. This enforces adherence to the FGONG standard. In addition, users can now set the four-line plain-text header of FGONG output using the new controlsfgong_header(1:4).mixing_typenow reports the mixing process that generates the largest D_mix, rather than prioritizing convection and thermohaline mixing over all others.Added profile panel and history panel controls in pgstar to specify same yaxis range for both left and right axes (e.g., Profile_Panels1_same_yaxis_range(1) = .true.)
Experimental options have been moved into
*_dev.defaultsfiles and experimental test cases are now prefixed withdev_. These options and test cases are not ready for general use.The
ionizationmodule has been removed. Theeval_typical_chargeroutine has been moved intomod_typical_charge.f90within thestarmodule. Theeval_ionizationroutine is no longer supported, as it was untested, undocumented, and unused.A new module
hdf5iofor working with HDF5 files has been added.The controls
diffusion_gamma_full_{on,off}are no longer used by default. The EOS now returns phase information and by default that EOS phase will automatically turn off diffusion for crystallized material.The issue with the value of free_e when using FreeEOS has been corrected. Thanks to Jason Wright for the report.
An
other_screeninghook was added.All parts of test suite cases are now run by default. To skip running the optional inlists, set the environment variable
MESA_SKIP_OPTIONAL(to any value). Previously, optional parts were skipped by default, and running all parts required settingMESA_RUN_OPTIONAL.The headers for history and profile data now contain the value of Msun (grams), Rsun (cm), and Lsun (erg/s) used.
A bug has been identified and fixed in the
Brown_Garaud_Stellmach_13thermohaline mixing routine. The routine was meant to use Newton-Raphson relaxation to converge to a solution for the Nusselt number based on an initial guess from the asymptotic analysis in Appendix B of Brown, Garaud, & Stellmach (2013). However, a bug previously caused the routine to immediately return the asymptotic guess and skip the NR relaxation step. The asymptotic guess is usually fairly accurate, so this usually still produced a thermohaline result that was fairly close to the right answer, but the bug has been fixed now so that the NR relaxation is applied as well.
Changes in r15140
Backwards-incompatible changes
Addition of eos and kap namelists
The options associated with the eos and kap modules have been
moved into their own namelists. (That is, there now exist &eos
and &kap at the same level as &star_job and &controls.)
User inlists will need to be updated. See Module-level changes
for more specific information.
If you previously accessed the values of eos/kap related options from
star_job or controls via run_star_extras, you will need to
adjust your code to access the option values using the pointers to the
EoS_General_Info and Kap_General_Info structures. These are
exposed in star as s% eos_rq and s% kap_rq, respectively. So
for example, the inlist value of Zbase is now accessible via s% kap_rq% Zbase
(instead of s% Zbase).
Some file suffixes changed to .f90
Many source file names have been changed to have an .f90 suffix. For users, the most important changes are to the star and binary work directories.
In an existing star work directory (i.e., a copy of star/work or
star test suite case), rename the files
src/run.f→src/run.f90src/run_star_extras.f→src/run_star_extras.f90
In an existing binary work directory (i.e., a copy of
binary/work or binary test suite case), rename the files
src/binary_run.f→src/binary_run.f90src/run_star_extras.f→src/run_star_extras.f90src/run_binary_extras.f→src/run_binary_extras.f90
Changes to local makefiles that are not part of MESA might also need to be updated to reflect these changes.
Removal of backups
MESA no longer has the concept of a “backup”. (In a backup, after the failure of a retry, MESA would return to the previous model and evolve it with a smaller timestep.)
Models that previously relied on the use of backups in order to complete should instead use appropriate timestep controls such that retries alone are sufficient to enable the model to run.
All backup-related options and output quantities have been removed.
Users migrating inlists or history_column.list files from previous
MESA versions will need to remove these options, all of which contain
the string “backup”.
Changes to solver reporting
MESA can report information about the progress of the iterative Newton–Raphson solution process that forms a key part of taking a timestep. The names of numerous options related to the solver have changed. These changes follow two main patterns.
First, the word “newton” was replaced with the word “solver”. For
example, the history column that records the number of iterations
changed from num_newton_iterations to num_solver_iterations.
The controls option that defines a number iterations above which to
reduce the timestep changed from newton_iterations_limit to
solver_iters_timestep_limit and the terminal output correspondingly
shows the message solver iters instead of newton iters. (The
control newton_iterations_hard_limit was removed and not renamed.)
Second, the word “hydro” was removed or replaced with the word
“solver” in the controls related to monitoring the solver internals.
For example, the control report_hydro_solver_progress is now
report_solver_progress and report_hydro_dt_info is now
report_solver_dt_info. The use of these and other related
controls is described in the developer documentation.
Changes to eps_grav and eps_mdot
A new method for handling the energetics associated with mass changes
in MESA models was presented in MESA V, Section 3.2. The approach
discussed therein, incorporated in a term named eps_mdot, has now
become standard. As such, the option use_eps_mdot has been
removed (because it is now effectively always true).
This eps_mdot approach supersedes the approach described in
MESA III, Section 7, and so that implementation has been removed. This
resulted in the removal of the &controls options
eps_grav_time_deriv_separationzero_eps_grav_in_just_added_materialmin_dxm_Eulerian_div_dxm_removedmin_dxm_Eulerian_div_dxm_addedmin_cells_for_Eulerian_to_Lagrangian_transitionfix_eps_grav_transition_to_grid
the history columns
k_below_Eulerian_eps_gravq_below_Eulerian_eps_gravlogxq_below_Eulerian_eps_gravk_Lagrangian_eps_gravq_Lagrangian_eps_gravlogxq_Lagrangian_eps_grav
and the profile columns
eps_grav_h_effectiveeps_mdot_sub_eps_grav_h_effectiveeps_mdot_rel_diff_eps_grav_h_effectiveeps_grav_heps_mdot_sub_eps_grav_heps_mdot_rel_diff_eps_grav_h
Removal of lnPgas_flag
The option to use gas pressure instead of density as a structure variable has been removed. Users migrating inlists from previous MESA versions will need to remove these options, all of which contain the string “lnPgas_flag”.
Removal of logQ limits
As a consequence of the changes to eos, star no longer
enforces limits on the quantity logQ (logQ = logRho - 2*logT + 12 in cgs).
Therefore the controls options
logQ_limitlogQ_min_limit
and the pgstar option
show_TRho_Profile_logQ_limit
have been removed.
The removal of these controls does not indicate that the EOS is reliable at all values of logQ. Users should consult the description of the component EOSes and the regions in which they are applied to understand if MESA provides a suitable EOS for the conditions of interest.
Removal of GR factors
The control use_gr_factors and corresponding code has been
removed. (This provided only a simple correction to the momentum
equation and not a full GR treatment of the stellar structure
equations.) Users wishing to include GR corrections to MESA’s
Newtonian equations can achieve the same effect by using the
other_cgrav or other_momentum hooks. For an example, see the
neutron star test cases (ns_h, ns_he, and ns_c).
Change in STELLA file output
The options to create output files suitable for input to STELLA have
been removed from MESA/star and the star_job namelist. These
capabilities are now included as part of the ccsn_IIp test case
(see inlist_stella and run_star_extras.f90). Users desiring
STELLA-format output should re-use the code from that example.
This affects the options
save_stella_data_for_model_numbersave_stella_data_when_terminatesave_stella_data_filenamestella_num_pointsstella_nz_extrastella_min_surf_logRhostella_min_velocitystella_skip_inner_dmstella_skip_inner_v_limitstella_mdot_years_for_windstella_mdot_for_windstella_v_windstella_show_headers
Removal of mesh adjustment parameters around convective boundaries
Controls matching the following patterns, which adjust the mesh resolution around convective boundaries, have been removed:
xtra_coef_czb_full_{on,off}xtra_coef_{a,b}_{l,u}_{n,h,he,z}b_czbxtra_dist_{a,b}_{l,u}_{n,h,he,z}b_czbxtra_coef_scz_above_{n,h,he,z}b_cz
Convective boundaries can be resolved using a custom mesh-spacing
function or mesh_delta coefficient. The
simplex_solar_calibration test case has an example custom
mesh-spacing function.
Change to mixing_type codes
The mixing_type codes (defined in const/public/const_def.f90)
have changed. User code and/or analysis routines (e.g., scripts
interpreting the mixing_type profile column) may need to be
revised. We recommend that users use the mixing_type variables
rather than the corresponding integers in their own code. e.g. rather
than writing
if (mixing_type == 1) then
use
if (mixing_type == convective_mixing) then
assuming use const_def appears somewhere, as in the default
run_star_extras.f90.
Limitations on use of varcontrol_target
A new variable min_allowed_varcontrol_target (default 1d-4) has
been introduced to discourage the use of small values of
varcontrol_target. MESA will exit with an error if the value is
below this threshold.
The value of varcontrol is an unweighted average over all cells of the
relative changes in the structure variables. For situations that need
tighter timestep limits, there are many specific timestep controls
that should be used instead of reducing the general target. The use
of controls that specifically apply to the problem being studied will
typically provide more effective and efficient timestep limiters. In
addition, small values of varcontrol_target can lead to poor
performance when it forces the size of the step-to-step corrections to
become too small.
The option varcontrol_target is NOT the recommended way to push
time resolution to convergence levels. To perform temporal convergence
studies, use the new control time_delta_coeff, which acts as a
multiplier for timestep limits (analogous to mesh_delta_coeff for
spatial resolution).
One strategy for choosing effective timestep limits is to first set
varcontrol_target = 1d-3. Then add some additional specific
timestep limits relevant to the problem. Do a run, watching the
reason for the timestep limits and the number of retries. Summary
information about the conditions that limited the timestep can be
printed at the end of run using the star_job option
show_timestep_limit_counts_when_terminate. Repeat the runs,
adding/removing or adjusting timestep limits until there are few
retries and few places where the timestep is limited by varcontrol.
Finally, repeat the calculation with a smaller value of
time_delta_coeff (e.g., 0.5) and compare the results to gain
confidence that they are numerically converged.
Module-level changes
astero
Material previously present in star/astero and test cases using
these capabilities have been promoted into their own module.
The csound_rms observational constraint has been removed.
The options for executing an arbitrary shell script
(shell_script_num_string_char and
shell_script_for_each_sample) have been removed. The usual use
for these options—renaming output files at the end of each sample—can
be replicated using the system tools available through
utils_lib. For example, the following extras_after_evolve
in run_star_extras.f90 moves the best profile and FGONG file
to outputs/sample_#.{profile,fgong}.
subroutine extras_after_evolve(id, ierr)
use astero_def
use utils_lib, only: mv
integer, intent(in) :: id
integer, intent(out) :: ierr
character (len=256) :: format_string, num_string, basename
ierr = 0
write(format_string,'( "(i",i2.2,".",i2.2,")" )') num_digits, num_digits
write(num_string,format_string) sample_number+1 ! sample number hasn't been incremented yet
basename = trim(sample_results_prefix) // trim(num_string)
call mv(best_model_fgong_filename, trim(basename) // trim('.fgong'), skip_errors=.true.)
call mv(best_model_profile_filename, trim(basename) // trim('.profile'), skip_errors=.true.)
end subroutine extras_after_evolve
turb
This new module implements local theories of turbulence, including
MLT, TDC, semiconvection, and thermohaline turbulence. These used to be
a part of star. TDC (which stands for time-dependent convection) is
now the recommended method for situations where the time dependence of
convection must be taken into account. Other methods for time dependent
convection present in the code have been removed, including the options
min_T_for_acceleration_limited_conv_velocity and set_conv_vel_flag.
TDC can be turned on with the option MLT_option = "TDC" in the
controls section of an inlist.
Users will not generally
need to interact with this module, but it can be used within
run_star_extras by writing use turb.
auto_diff
This new module provides Fortran types that support algorithmic
differentiation via operator overloading. Users will not generally
need to interact with this module, but it can be used within
run_star_extras to make derivatives easier to calculate (e.g. in the
implicit hooks like other_surface).
Usage is by writing use auto_diff. This imports types such as
auto_diff_real_4var_order1, which supports first-order derivatives
with respect to up to four independent variables.
A variable of this type could be declared via:
type(auto_diff_real_4var_order1) :: x
This variable then holds five fields: x%val stores the value of x.
x%d1val1 stores the derivative of x with respect to the first independent
variable. x%d1val2 is the same for the second independent variable, and so on.
All d1val_ fields are initialized to zero when the variable is first set.
Once an auto_diff variable it initialized, all mathematical operations can be performed
as they would be on a real(dp) variable. auto_diff variables also interoperate with
real(dp) and integer types.
So for instance in the following f%d1val1 stores df/dx and f%d1val2 stores df/dy.
x = 3d0
x%d1val1 = 1d0
y = 2d0
y%d1val2 = 1d0
f = exp(x) * y + x + 4
Similar types are included supporting higher-order and mixed-partial
derivatives. These derivatives are accessed via e.g. d2val1
(d²f/dx²), d1val1_d2val2 (d³f/dx dy²).
const
The const module has been updated to account for the revision of
the SI and now uses CODATA 2018 values of the physical constants.
For astronomical constants, MESA follows IAU recommendations. MESA adopts nominal solar and planetary quantities from IAU 2015 Resolution B3 and now follows the recommended procedure of deriving nominal solar and planetary masses from the mass parameters \((GM)\) and the adopted value of \(G\).
As a result of these changes, most constants now have slightly different values than in previous MESA versions. For example, \({\rm M}_\odot\) changed from 1.9892e33 g to 1.9884e33 g.
eos
EOS-related options have been moved into their own eos namelist.
The module controls and their default
values are contained in the file eos/defaults/eos.defaults.
The PTEH EOS has been removed. Tables from the FreeEOS project now provide coverage of similar conditions.
The region covered by the PC EOS has been increased. The boundaries of the region where PC is used no longer consider composition and so now include H/He-dominated material. The upper limit of the region where PC is used is now determined using the electron Coulomb coupling parameter and generally corresponds to higher temperatures than the previous approach.
For more information about the component EOSes and the regions in which they are applied, see the new overview of the EOS module.
gyre
GYRE has been upgraded to version 6.0. See the GYRE Documentation for information about this release.
kap
Opacity-related options have been moved into their own kap namelist.
The module controls and their default
values are contained in the file kap/defaults/kap.defaults.
The OPAL Type 2 opacity tables are now on by default
(use_Type2_opacities = .true.). These tables separately account
for carbon and oxygen enhancements. Since this is especially
important during core helium burning, the default transition from the
OPAL Type 1 tables to the Type 2 tables occurs when material becomes
nearly hydrogen free. As a result of this change, by default, users
are required to specify the base metallicity of material using the
kap namelist control Zbase. Usually, this physically
corresponds to the initial metallicity of the star.
For more information about the opacity tables and how they are combined, see the new overview of the kap module.
rates & net
A number of rates have had their defaults switched to using JINA’s REACLIB.
When using a custom user rate (i.e from a rate table) the reverse rate is now computed in detailed balance from the user rate. Previously the reverse rate was computed using the default rate choice.
A bug with burning li7 at low temperatures rate has been fixed. Users stuck using previous versions of MESA and a soft network (something that is not an approx net) should add these lines to their nuclear network as a fix until they can update to a newer MESA:
remove_reaction(r_h1_li7_to_he4_he4)
add_reaction(r_li7_pa_he4)
With thanks to Ian Foley for the bug report.
We now define the forward reaction to always be the exothermic reaction, not the reaction as defined by REACLIB. This fixes an issue with exothermic photo-disintegrations which would generate wrong values when computed in detailed balance.
A lot of work has been done getting operator split burning (op_split_burn = .true.) to work. This option can provide a large speed up during advanced nuclear burning stages. See the various split_burn test cases for examples.
Other changes
Saved model files now contain a
version_numberfield in their header. This indicates the version of MESA that was used to generate the model.binary now automatically writes photo (restart) files at the end of the run.
If not provided with an argument, the binary
./rescript will now restart from the most recent photo (determined by filesystem modification time). The star./rescript also has this behavior as of r12778.The test case for building C/O white dwarf models has been overhauled to be more robust. See documentation for the new version in make_co_wd.
The builder for NS envelopes (test case
neutron_star_envelope) has been replaced with a more general envelope builder (test casemake_env). The test casesns_{h,he,c}have been overhauled to start from these new models.Added
other_remove_surface. This routine is called at the start of a step and returns an integer k. All cells with j < k will be removed from the model at the start of the step, making cell k the new surface.Installations are now blocked from using sudo. This is generally not what you want to use to fix installation issues. If you want to install MESA in a root location then you will need to edit out the check in the install file.
The install script now blocks attempts to use a
MESA_DIRwhich contains spaces in it. This has never really worked as makefiles can not handle the spaces. To work round this either moveMESA_DIRto a folder location with no spaces in its path or symlink yourMESA_DIRto another location with no spaces in its path and setMESA_DIRto point at the symlink.The option to create a pre main sequence model now relaxes the model until a radiative core forms. This is activated with the
star_joboptionpre_ms_relax_to_start_radiative_core, which can be set to .false. to restore the old behavior.
Acknowledgments
Thanks to all who reported problems and asked or answered questions on mesa-users. Special thanks to Siemen Burssens, Mathias Michielsen, Joey Mombarg, Mathieu Renzo, and Samantha Wu for their assistance in testing pre-release versions.
Changes in r12778
This section describes changes that occurred since r12115.
SDK changes (Version 20.3.1 or later required)
To use the this MESA release, you must upgrade your SDK to 20.3.1.
In previous releases of MESA, we have included the CR-LIBM library to provide versions of standard math functions (exp, log, sin, etc) that guarantee correct rounding of floating-point numbers. In this new release, we made the decision to move CR-LIBM into the software development kit (SDK), where it properly belongs and can be maintained as one of the pre-requisites of MESA.
This means that to use this release (and subsequent releases) of MESA, you’ll need to upgrade to version 20.3.1 of the SDK or later. MESA checks the SDK version during compilation, and will stop with an error message if the SDK is too old.
Backwards-incompatible changes
Replacement of crlibm_lib with math_lib
MESA now talks to CR-LIBM via an intermediate module called
math_lib. To make sure any code you add can properly access the
CR-LIBM math routines, you’ll need to make sure that a use
math_lib statement appears in the preamble of the file. At the same
time, you should remove any use crlibm_lib statements, as they will no
longer work (and are not needed). With math_lib, the names of the
correctly rounded math functions are the same as the Fortran
intrinsics (i.e., they no longer have a _cr suffix).
Existing run_star_extras, run_binary_extras, or other
user-written code will need to be updated. To migrate, you should
replace use crlibm_lib with use math_lib and remove the _cr
suffix from any math functions (e.g., exp_cr → exp).
Removal of DT2 and ELM EOS options
The ELM and DT2 EOS options have been removed. (These options were underpinned by HELM and OPAL/SCVH data, but used bicubic spline interpolation in tables of lnPgas, lnS, and lnE as a way to get numerically accurate 1st and 2nd partial derivatives with respect to lnRho and lnT. A more detailed description can be found in previous release notes and Appendix A.1 of MESA V.) These options were introduced in r10398 and were turned on by default in r11532.
The numerical issues that ELM/DT2 were designed to address have been dealt with via another approach. MESA now separately treats quantities that appear in the equations (and happen to be partials) and the places where these theoretically equivalent, but numerically different quantities appear in the Jacobian (as partials of other quantities that appear in the equations). This is an implementation detail that should be transparent to users.
This change has two pleasant side effects. One, it lowers the memory demands of many MESA models, which should aid users of virtualized, containerized, or otherwise memory-constrained systems. Two, it removes small, interpolation-related wiggles that were present in partial derivative quantities such as \(\Gamma_1\).
These changes may require inlists that made use of DT2/ELM related options to be updated.
The following controls options have been deleted:
use_eosDT2
max_logT_for_max_logQ_eosDT2
max_logQ_for_use_eosDT2
use_eosELM
logT_max_for_ELM
logQ_min_for_ELM
check_elm_abar_zbar
check_elm_helm_agreement
The following star_job options have been renamed:
eosDT2PTEH_use_linear_interp_for_XtoeosPTEH_use_linear_interp_for_X
The following controls options have been renamed/removed, as well
as moved to star_job (see next entry):
logRho_max_for_all_PTEH_or_DT2tologRho_max_for_all_PTEH
logRho_max_for_any_PTEH_or_DT2tologRho_max_for_any_PTEH
logQ_max_for_low_Z_PTEH_or_DT2(removed)
logQ_max_for_high_Z_PTEH_or_DT2tologQ_max_for_PTEH
Change in location of PTEH EOS options
Options that modify the parameters associated with the PTEH EOS have
be moved from controls to star_job. This brings PTEH in line
with the behavior of the other component EOSes.
If you explicitly set any of following options in your inlist, you
will need to move them from controls to star_job. Their
meaning and default values remain unchanged.
use_eosPTEH_for_low_density
use_eosPTEH_for_high_Z
Z_for_all_PTEH
Z_for_any_PTEH
logRho_min_for_all_OPAL
logRho_min_for_any_OPAL
logRho_max_for_all_PTEH
logRho_max_for_any_PTEH
In addition, you must add the new option set_eosPTEH_parameters =
.true. to star_job to indicate that these values should override
the eos module-level defaults.
The removal of DT2 (see previous entry) has also resulted in the
change that the controls option logQ_max_for_low_Z_PTEH_or_DT2 has
been removed (as it applied primarily to DT2) and
logQ_max_for_high_Z_PTEH_or_DT2 (which applied primarily to PTEH)
has been renamed to logQ_max_for_PTEH and moved from controls
to star_job.
New overshooting controls
The new controls for overshooting, briefly described in the release notes of version 12115, are now the default in MESA (and the old controls have been removed). All test_suite cases now use these new controls.
There are two schemes implemented in MESA to treat overshooting: a step overshoot scheme and an exponential scheme that follows Herwig (2000).
The old “double exponential overshoot scheme” is no longer accessible through simple controls. An example of how to implement such a scheme via the other_overshooting_scheme hook is contained in the other_physics_hooks test suite case.
The new overshooting controls are based on convection-zone and convection-boundary matching criteria.
In the new set of controls, for each convective boundary it is possible
to define an overshoot_zone_type, overshoot_zone_loc and an
overshoot_bdy_loc, as well as values for the overshooting parameters.
The permitted values are the following:
overshoot_scheme = exponential, step
overshoot_zone_type = burn_H, burn_He, burn_Z, nonburn, any
overshoot_zone_loc = core, shell, any
overshoot_bdy_loc = bottom, top, any
The following controls assign values for the diffusive or step overshooting parameters:
overshoot_f
overshoot_f0
overshoot_D0
overshoot_Delta0
overshoot_f0 is defined so that the switch from convective mixing to overshooting happens at a distance overshoot_f0*Hp into the convection zone from the estimated location where grad_ad = grad_rad, where Hp is the pressure scale height at that location.
For exponential overshoot, D(dr) = D0*exp(-2*dr/(overshoot_f*Hp0) where D0 is the diffusion coefficient D at point r0, Hp0 is the scale height at r0.
For step overshoot: overshooting extends a distance overshoot_f*Hp0 from r0 with constant diffusion coefficient D = overshoot_D0 + overshoot_Delta0*D_ob where D_ob is the convective diffusivity at the bottom (top) of the step overshoot region for outward (inward) overshooting.
These “new” controls replace the following “old” controls:
overshoot_f_above_nonburn_core
overshoot_f0_above_nonburn_core
overshoot_f_above_nonburn_shell
overshoot_f0_above_nonburn_shell
overshoot_f_below_nonburn_shell
overshoot_f0_below_nonburn_shell
overshoot_f_above_burn_h_core
overshoot_f0_above_burn_h_core
overshoot_f_above_burn_h_shell
overshoot_f0_above_burn_h_shell
overshoot_f_below_burn_h_shell
overshoot_f0_below_burn_h_shell
overshoot_f_above_burn_he_core
overshoot_f0_above_burn_he_core
overshoot_f_above_burn_he_shell
overshoot_f0_above_burn_he_shell
overshoot_f_below_burn_he_shell
overshoot_f0_below_burn_he_shell
overshoot_f_above_burn_z_core
overshoot_f0_above_burn_z_core
overshoot_f_above_burn_z_shell
overshoot_f0_above_burn_z_shell
overshoot_f_below_burn_z_shell
overshoot_f0_below_burn_z_shell
step_overshoot_f_above_nonburn_core
step_overshoot_f_above_nonburn_shell
step_overshoot_f_below_nonburn_shell
step_overshoot_f_above_burn_h_core
step_overshoot_f_above_burn_h_shell
step_overshoot_f_below_burn_h_shell
step_overshoot_f_above_burn_he_core
step_overshoot_f_above_burn_he_shell
step_overshoot_f_below_burn_he_shell
step_overshoot_f_above_burn_z_core
step_overshoot_f_above_burn_z_shell
step_overshoot_f_below_burn_z_shell
step_overshoot_D
step_overshoot_D0_coeff
The “new” control overshoot_D_min replaces the “old” control D_mix_ov_limit.
The “new” control overshoot_brunt_B_max replaces the “old” control max_brunt_B_for_overshoot.
The “new” control overshoot_mass_full_on replaces the “old” control mass_for_overshoot_full_on.
The “new” control overshoot_mass_full_off replaces the “old” control mass_for_overshoot_full_off.
The following example will apply exponential overshoot, with f = 0.128 and f0 = 0.100, at the bottom of non-burning convective shells; and exponential overshoot, with f = 0.014 and f0 = 0.004, at all other convective boundaries.
overshoot_scheme(1) = 'exponential'
overshoot_zone_type(1) = 'nonburn'
overshoot_zone_loc(1) = 'shell'
overshoot_bdy_loc(1) = 'bottom'
overshoot_f(1) = 0.128
overshoot_f0(1) = 0.100
overshoot_scheme(2) = 'exponential'
overshoot_zone_type(2) = 'any'
overshoot_zone_loc(2) = 'any'
overshoot_bdy_loc(2) = 'any'
overshoot_f(2) = 0.014
overshoot_f0(2) = 0.004
Other examples are illustrated in the test_suite cases. Examples for exponential overshooting can be found in the following test_suite cases:
1.4M_ms_op_mono
25M_pre_ms_to_core_collapse
5M_cepheid_blue_loop/inlist_cepheid_blue_loop
7M_prems_to_AGB/inlist_7M_prems_to_AGB
accretion_with_diffusion
agb
axion_cooling
black_hole
c13_pocket
cburn_inward
envelope_inflation
example_ccsn_IIp
example_make_pre_ccsn
gyre_in_mesa_rsg
high_mass
high_z
hot_cool_wind
magnetic_braking
make_co_wd
make_metals
ppisn
pre_zahb
radiative_levitation
Examples for step overshooting can be found in the following test_suite cases:
high_rot_darkening
relax_composition_j_entropy
Version number
The MESA version_number is now represented as a string internally
and in the headers of history/profile output. User scripts that
assume this is an integer may need to be revised.
other_wind hook
The interface of the other_wind hook changed from
subroutine other_wind_interface(id, Lsurf, Msurf, Rsurf, Tsurf, w, ierr)
use const_def, only: dp
integer, intent(in) :: id
real(dp), intent(in) :: Lsurf, Msurf, Rsurf, Tsurf ! surface values (cgs)
real(dp), intent(out) :: w ! wind in units of Msun/year (value is >= 0)
integer, intent(out) :: ierr
end subroutine other_wind_interface
to
subroutine other_wind_interface(id, Lsurf, Msurf, Rsurf, Tsurf, X, Y, Z, w, ierr)
use const_def, only: dp
integer, intent(in) :: id
real(dp), intent(in) :: Lsurf, Msurf, Rsurf, Tsurf, X, Y, Z ! surface values (cgs)
real(dp), intent(out) :: w ! wind in units of Msun/year (value is >= 0)
integer, intent(out) :: ierr
end subroutine other_wind_interface
Existing user routines will need to be updated.
Removal of id_extra from run_star_extras.f
Most routines in run_star_extras.f had an argument id_extra.
This argument generally did not do anything and so has been removed.
Existing user routines will need to be updated.
A simple way to migrate from routines written for previous versions of
MESA is to find and replace the string “, id_extra” with the empty
string in run_star_extras.f.
Change of extras_startup from function to subroutine
The interface of extras_startup changed from integer function to subroutine. The current empty version of this routine is:
subroutine extras_startup(id, restart, ierr)
integer, intent(in) :: id
logical, intent(in) :: restart
integer, intent(out) :: ierr
type (star_info), pointer :: s
ierr = 0
call star_ptr(id, s, ierr)
if (ierr /= 0) return
end subroutine extras_startup
Existing user routines will need to be updated to reflect this new interface.
Hooks for extra header items
The interface of the routines
how_many_extra_history_header_itemsdata_for_extra_history_header_itemshow_many_extra_profile_header_itemsdata_for_extra_profile_header_items
has changed. If these routines are included in your
run_star_extras.f (even if they have not been customized), you
will need to update them. You should replace the old versions with:
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
! here is an example for adding an extra history header item
! also set how_many_extra_history_header_items
! names(1) = 'mixing_length_alpha'
! vals(1) = s% mixing_length_alpha
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
! here is an example for adding an extra profile header item
! also set how_many_extra_profile_header_items
! names(1) = 'mixing_length_alpha'
! vals(1) = s% mixing_length_alpha
end subroutine data_for_extra_profile_header_items
Removal of inlist_massive_defaults
The file inlist_massive_defaults has been removed from star.
Copies of the inlist can now be found in the following test cases:
25M_pre_ms_to_core_collapse
25M_z2m2_high_rotation
adjust_net
black_hole
envelope_inflation
example_ccsn_IIp
example_make_pre_ccsn
magnetic_braking
split_burn_20M_si_burn_qp
split_burn_big_net_30M
split_burn_big_net_30M_logT_9.8
Other changes
The routines
{alloc,move,store,unpack}_extra_infowere removed fromstandard_run_star_extras.inc. (These routines were used to store/retrieve information from photos.) If you have existingrun_star_extrascode that includes these routines, it will continue to function. However, in newrun_star_extrascode, the recommended way to store/retrieve data is using theother_photo_readandother_photo_writehooks. Examples can be found in the conductive_flame and brown_dwarf test suite cases.The controls
xtra_coef_os_*andxtra_dist_os_*which could be used to modifymesh_delta_coeffin overshooting regions have been removed. The same functionality is available using theother_mesh_delta_coeff_factorand an example implementation is given in theagbtest suite case.The output-related control
alpha_bdy_core_overshootingand related history optionscore_overshoot_{Hp,f,f0,hstep,r0}and{mass,radius}_bdy_core_overshootinghave been removed.The
star_datamodule was split out of thestarmodule. The source file describing the contents of thestar_infodata structure is now located atstar_data/public/star_data.inc.If not provided with an argument, the
./rescript will now restart from the most recent photo (determined by filesystem modification time).Added star_control pre_ms_relax_to_start_radiative_core to existing star_control pre_ms_relax_num_steps to provide option for creating a pre-main sequence model just after the end of the fully convective period. The relaxation steps from raw pre-ms model to end of fully convective are done using simple control setting selected for robustness. After the relaxation is complete, the actual inlist parameter settings are used.
Added a new hook other_accreting_state to allow the user to specify the specific total energy, pressure, and density of the accreting material. These properties are used by eps_mdot to compute the contribution of accretion to the energy equation. By default (when this hook is not used), these properties are all taken from the surface cell.
Changes in r12115
This section describes changes that occurred since r11554. The changes were originally described by this post to the MESA Users’ mailing list.
Backwards incompatible changes
Changes to atmospheres
There has been a major overhaul of the atmosphere controls and related
code. This improves consistency between the atmosphere and interior
calculations and offers more flexibility to users. To learn more,
please consult the user guide available here.
Changes to s% xtra variables
The MESA star pointer provides a set of extra variables that can be used in run_star_extras.f and are automatically saved and restored during retries and backups. The old variables were
s% xtra1,s% xtra2, …, etc. for floats,s% ixtra1,s% ixtra2, …, etc. for integers, ands% lxtra1,s% lxtra2, …, etc. for logicals (booleans).
These have now been collapsed into arrays (e.g., s% xtra(:)). If you use
these variables in your run_star_extras.f, you will need to enclose the
variable number in brackets. E.g., s% xtra1 becomes s% xtra(1),
s% ixtra17 becomes s% ixtra(17), etc.
The new scheme allows you to define integers with meaningful names that
can make it more obvious how an xtra variable is used. For example, if
you end up storing some integrated quantity in s% xtra(11), you could
define i_my_integral = 11 and then refer to the value as
s% xtra(i_my_integral).
The ppisn test suite case provides an example of this usage.
Other changes
Changes to WD atm tables
There are now 2 options for white dwarf atmosphere tables:
WD_tau_25: the original WD atmosphere table option for DA (H atmosphere)
WDs; also found and fixed a bug in the header of this file that was causing it to use only a small portion of the actual table
DB_WD_tau_25: new table for DB (He atmosphere) WDs
Changes to header format
The header format is now taken from the star_history_*_format and
profile_*_format variables defined in controls.defaults. This
addresses the bug caused by the compiler version string exceeding the
allowed length of a header column found by some users with the MESA
SDK and running on macOS. The default is now 40 characters but this
can be set to a larger (or smaller) value in &controls.
In analogy to the routines in run_star_extras.f,
run_binary_extras.f now has the routines
how_many_extra_binary_history_header_items
data_for_extra_binary_history_header_items
that allow the user to add custom header items to the binary history output.
New overshooting controls
We have introduced new, easier to use controls for overshooting, based on convection-zone matching criteria.
Use overshoot_new = .true. to use the new controls.
Note that in a future release, these new controls will become the default. Therefore, when you start new inlists, we recommend that you use these new controls.
In the new set of controls, for each convective boundary it is possible
to define an overshoot_zone_type, overshoot_zone_loc and an
overshoot_bdy_loc as well as values for the overshooting parameters.
The permitted values are the following:
overshoot_scheme:'exponential','double_exponential'or'step'overshoot_zone_type:'burn_H','burn_He','burn_Z','nonburn'or'any'overshoot_zone_loc:'core','shell'or'any'overshoot_bdy_loc:'bottom','top'or'any'
The following controls assign values for the diffusive or step overshooting parameters:
overshoot_fovershoot_f0overshoot_f2
The following example will apply exponential overshoot, with f = 0.128 and f0 = 0.100, at the bottom of non-burning convective shells; and exponential overshoot, with f = 0.014 and f0 = 0.004, at all other convective boundaries.
overshoot_scheme(1) = 'exponential'
overshoot_zone_type(1) = 'nonburn'
overshoot_zone_loc(1) = 'shell'
overshoot_bdy_loc(1) = 'bottom'
overshoot_f(1) = 0.128
overshoot_f0(1) = 0.100
overshoot_scheme(2) = 'exponential'
overshoot_zone_type(2) = 'any'
overshoot_zone_loc(2) = 'any'
overshoot_bdy_loc(2) = 'any'
overshoot_f(2) = 0.014
overshoot_f0(2) = 0.004
Other examples are illustrated in the gyre_in_mesa_rsg and
high_mass test_suite cases.
Changes in r11554
This section describes changes that occurred since r11532. The changes were originally described by this post to the MESA Users’ mailing list.
The release was principally made to quickly fix some memory leaks in r11532. Several users saw long-running jobs killed due to exhaustion of system memory. Thanks to Avishai Gilkis for the report.
This release also sets the star_job control
num_steps_for_garbage_collection = 1000. Periodically MESA will free some
memory from data structures that are no longer needed but have not been
deallocated yet. At present, this only targets the EOS tables.
(Implemented by Rob Farmer)
The header of MESA history/profile files now includes information about the compiler used and start date of the MESA run. (Implemented by Aaron Dotter)
1 2 3 4 5
version_number compiler build MESA_SDK_version date
11554 "gfortran" "8.3.0" "x86_64-linux-20190313" "20190314"
Changes in r11532
This section describes changes that occurred since r10398. The changes were originally described by this post to the MESA Users’ mailing list.
RSP is a new functionality in MESAstar that models the non-linear radial
stellar pulsations that characterize RR Lyrae, Cepheids, and other classes
of variable stars. See the rsp_* examples in the test suite.
We significantly enhance numerical energy conservation capabilities,
including during mass changes. For example, this enables calculations
through the He flash that conserve energy to better than 0.001%. Most test
cases now have this enabled, for instance 1.3M_ms_high_Z,
25M_pre_ms_to_core_collapse, and wd as examples.
To improve the modeling of rotating stars in MESA, we introduce a new
approach to modifying the pressure and temperature equations of stellar
structure, and a formulation of the projection effects of gravity
darkening. The latter are controlled by the grav_dark options in
history_columns.list; see high_rot_darkening for an example of its use.
A new scheme for tracking convective boundaries, called Convective Pre-Mixing (CPM), yields reliable values of the convective-core mass, and allows the natural emergence of adiabatic semiconvection regions during both core hydrogen- and helium-burning phases. Examples for this can be found in the inlists provided with the mesa 5 paper.
We have updated the equation of state and nuclear reaction physics modules.
There are an increased number of warnings for when MESA goes beyond the
validity of the input physics (for instance the nuclear reactions rates
from REACLIB are ill-defined when logT>10.0). These warnings are controlled
by the warn_* options.
The definition of eps_nuc has slightly changed (see MESA V, Section 3.2) in
order to be suitable for use with the new energy equation. If you are
running models using the dLdm form that includes eps_grav, you should
consult the controls option include_composition_in_eps_grav and its
associated documentation.
A new set of tests (gyre_in_mesa_*) demonstrate how to call GYRE on the fly
during a MESA run.
The astero module now allows users to define model parameters
(my_param[123]) that will be optimised in a similar way to the standard
options (mass, Y, FeH, alpha, f_ov). These are defined in the subroutine
set_my_params in run_star_extras.f in a similar way to how users can define
their own observables (my_var[123]).
The astero module now has controls normalize_chi2_* that allow the user to
decide whether or not to normalize each component of \(\chi^2\) by the number of
terms that contributed to that component.
The format of the OP_MONO opacity table cache has changed. If you have used these files in a previous version of MESA then you should do:
rm $MESA_OP_MONO_DATA_CACHE_FILENAME
before installing MESA. If you use multiple MESA versions, this means that
you cannot share the cache file between old and new versions. Therefore,
you should make sure to use a different cache file in each case. This may
be more easily accomplished using the controls option
op_mono_data_cache_filename rather than the environment variable.
The version of GYRE bundled with MESA has been updated to version 5.2.
Binaries can now model “twins”, where we can skip the calculation of the
companion as its assumed to be identical to the primary. This is controlled
by the binary_job parameter *_model_twins_flag.
There is a new way to treat convection in a model, via the
convective_velocity_flag. This adds an equation to solve the velocity of
convective motion, instead of using the value derived from MLT. This is
useful for models evolving on fast timescales and is a replacement for
min_T_for_acceleration_limited_conv_velocity.
Two new test cases (hydro_Ttau_solar and hydro_Ttau_evolve) demonstrate the
use of mixing length parameters and T(τ) relations calibrated to 3D
radiation-coupled hydrodynamics (RHD) simulations computed by
Trampedach et al. (2014). More details are provided in
Mosumgaard et al. (2018). MESA
also includes low-temperature opacity tables that match those used in the
3D RHD simulations, which can be used by setting kappa_lowT_prefix =
'lowT_rt14_ag89'.
There have been many bug fixes and performance enhancements to MESA. Reports of bugs or suggested improvements are welcome on the mesa-users mailing list.
A reminder to please share your inlists and run_star_extras on mesastar.org upon publication of your science papers!
Changes in r10398
This section describes changes that occurred since r11554. The changes were originally described by this post to the MESA Users’ mailing list.
Equation of State: PTEH, DT2, and ELM (Bill)
Several new options for the mesa/eos have been added, all aiming for more accurate partials for the Newton solver. All of these new eos options use bicubic spline interpolation in tables of lnPgas, lnS, and lnE as a way to get numerically accurate 1st and 2nd partial derivatives with respect to lnRho and lnT. The partials are directly calculated from the interpolating bicubic polynomials to give numerical accuracy, but this comes at a cost in thermodynamic consistency since the actual thermodynamic relations can only be approximated by bicubic splines.
The new eos options are called “PTEH”, “DT2”, and “ELM”. The PTEH tables are created using the approach of Pols, Tout, Eggleton, and Han (1995) as implemented by Paxton (2004) in a program derived from Eggleton’s stellar evolution code (1973). PTEH extends the mesa/eos coverage to lower densities than allowed by OPAL (down to 10^-18 g cm^-3) and higher metallicity than covered (OPAL stops at Z = 0.04 while PTEH covers all Z). When PTEH is enabled, it is used for low densities and for high Z in cases that for lower Z would be handled using data from OPAL/SCVH tables. In the old MESA EOS we fell back to HELM to provide approximate results for the cases now covered by PTEH.
The mesa/star default controls enable PTEH for both low densities and high Z.
use_eosPTEH_for_low_density = .true.
use_eosPTEH_for_high_Z = .true.
Z_for_all_PTEH = 0.040d0
Z_for_any_PTEH = 0.039d0
The two remaining new eos options, DT2 and ELM, provide high resolution tables in logRho and logT for values from mesa/eos for OPAL/SCVH values and for HELM respectively. These cover a subset of the standard eos domain with standard eos results for logPgas, logS, and logE in a form suitable for bicubic spline interpolation in order to give 1st and 2nd partials with high numerical accuracy. However, since use of DT2 and ELM will give decreased thermodynamic consistency that might not be compensated for by better residuals, these are both disabled by default in mesa/star.
use_eosDT2 = .false.
use_eosELM = .false.
Opacities (Josiah, Aaron)
The opacity module (kap) underwent some internal restructuring.
The kap module now exposes only a single kap_get interface
instead of separate kap_get_Type1 and kap_get_Type2
subroutines. This has two user-visible consequences.
The control
kappa_type2_logT_lower_bdywas removed. That control was no longer needed, as the existing controlkappa_blend_logT_lower_bdynow also applies to Type2 opacities. All other related opacity controls (e.g.,use_Type2_opacities) remain unchanged in name and behavior.Previously, there were separate “other” hooks for Type1 and Type2 opacities. Now, there is only one hook,
other_kap_get. It has the call signature of the previous Type2 hook, which is a super-set of the arguments to the Type1 hook (seestar/other/other_kap.f90).
In previous versions opacities where clipped to the edge values of the tables when logR=logRho-3logT+18<-8. This has been replaced for a blend to Compton opacities between logR=-7.5 and logR=-8.
Element Diffusion (Evan)
Fixed a bug in the ionization treatment for diffusion in the pressure ionization routine. This was due to a typo in the original paper that presented the ionization scheme. Restored the missing factor of rho^1/3 thanks to a later presentation of this same scheme (Dupuis et al. 1992) and a note here.
Added a user control (D_mix_ignore_diffusion) for when to ignore
element diffusion in surface or core mixing regions. Previously,
diffusion would be turned off for surface mixing regions of ANY
strength, even very weak mixing where diffusion might still be
relevant. Now this control is set to a D_mix of 10⁵ (cm²/s), so that
mixing that will obviously overwhelm diffusion (like convection) will
turn it off, but weaker mixing won’t.
Gravity Darkening (Aaron)
Added options to include gravity darkening, in the form of projected (surface-averaged) luminosities and effective temperatures of the star viewed along the equator and pole, to the history file. Assumes the star is an oblate spheroid; see here for more info.
grav_dark_L_polar !Lsun
grav_dark_Teff_polar !K
grav_dark_L_equatorial !Lsun
grav_dark_Teff_equatorial !K
Isomers (Frank, Josiah, Bill)
The isomers of ²⁶Al can now be added to a reaction network. To use them, include the isomers in your network specification file. Two examples include
add_isos_and_reactions(
neut
h 1 1 ! hydrogen
he 4 4 ! helium
mg 25 25 ! magnesium
al26-1 ! ground state
al26-2 ! meta-stable excited state
)
and
include 'mesa_45.net'
add_isos_and_reactions(
al26-1
al26-2
)
remove_iso(al26)
One may use either al26 or al26-1 and al26-2. Reaction
rates for the ²⁶Al isomers with other isotopes are picked up from the
JINA reaclib file. Reaction rates for al26-1 <-> al26-2 are
from Gupta & Meyer (2001) and located in
data/rates_data/rate_tables along with the new default
rate_list.txt file.
User-Beware: if you want a local rate_tables directory,
http://mesa.sourceforge.net/star_job_defaults.html#rate_tables_dir
<http://mesa.sourceforge.net/star_job_defaults.html#rate_tables_dir>,
and you want the ²⁶Al isomers, then the two al26-1 <-> al26-2 rate
files must be copied from their default location to your local
rate_tables directory and your local rate_list.txt modified to include
these two rates.
Installation Debugging (Rob, Josiah)
There is a new command, $MESA_DIR/help which outputs system
information we need when debugging installation issues and/or MESA
crashes. ./install will now also log its output to a file
$MESA_DIR/build.log, if you have an installation issue please include
this file when reporting an issue to mesa-users.
Miscellaneous improvements (Rob, Josiah)
You can now use the MESA_INLIST environment variable to set the
name of the main inlist file when using MESA binary.
The output cadence of MESA binary has been tweaked to that its behavior is the same as MESA star. (If you use the same options, you should get output at the same steps.)
There is now a flag b% need_to_update_binary_history_now, which if
set forces binary history output to occur at the current step.
Run_star_extras (Aaron)
Put calls to extra_header_items back into
standard_run_star_extras and provided working examples of how to
call all of them. These are useful for adding extra information to
the history and profile headers beyond what is provided by default,
such as including mixing_length_alpha in the history file header.
Building with Other Compilers
MESA currently does not compile with ifort. Other non-SDK compilers that are known to work (at the bit-for-bit level): Gfortran 7.3.1 (fedora 27)