Implemented Sunny Wong rotation brunt change

README.rst

@@ -71,6 +71,7 @@ Links
 * `MESA Users Mailing List <https://lists.mesastar.org/mailman/listinfo/mesa-users>`__ for info about new releases, news items, and requests for help/bug reports.
 * `mesa_reader <https://github.com/wmwolf/py_mesa_reader>`__ to interact and plot data from MESA in Python.
 * `MESA Test Hub <https://testhub.mesastar.org/>`__ to view results of regression testing (for Developers).
+* `MESA Jenkins <https://jenkins.flatironinstitute.org/job/mesa/job/main/>`__ to view nightly Jenkins test runs (for Developers).
 * `mesa_test <https://github.com/MESAHub/mesa_test>`__ tool to run the test suite and upload results to the MESA Test Hub (for Developers).
 * `mesa-dev yt channel <https://www.youtube.com/@mesa-dev>`__ youtube channel for recorded dev meetings (for Developers).
 

binary/defaults/binary_history_columns.list

@@ -72,6 +72,8 @@
       star_2_mass ! mass of second star in msun
       !lg_star_2_mass ! log10 mass of second star in msun
       !sum_of_masses ! star_1_mass + star_2_mass
+      !mass_ratio ! star_2_mass / star_1_mass
+      !obs_mass_ratio ! min(m2/m1, m2/m1)
       lg_mtransfer_rate ! log10 of abs(mass transfer rate) in Msun/yr
                      ! this considers the amount of mass lost from the donor due to RLOF
                      ! not the actual mass that ends up accreted

binary/defaults/pgbinary.defaults

@@ -1897,29 +1897,33 @@
       ! ::
 
    Text_Summary1_win_flag = .false.
-   Text_Summary1_win_width = 10
-   Text_Summary1_win_aspect_ratio = 0.15
+   Text_Summary1_win_width = 7
+   Text_Summary1_win_aspect_ratio = 0.6
 
       ! ::
 
    Text_Summary1_xleft = 0.02
    Text_Summary1_xright = 0.98
    Text_Summary1_ybot = 0.08
    Text_Summary1_ytop = 0.98
-   Text_Summary1_txt_scale = 4.5
+   Text_Summary1_txt_scale = 3.0
    Text_Summary1_title = ''
 
       ! setup default
 
       ! ::
 
-   Text_Summary1_num_rows = 8
-   Text_Summary1_num_cols = 4
+   Text_Summary1_num_rows = 5
+   Text_Summary1_num_cols = 1
    Text_Summary1_name(:, :) = ''
 
       ! ::
 
    Text_Summary1_name(1, 1) = 'model_number'
+   Text_Summary1_name(2, 1) = 'jdot'
+   Text_Summary1_name(3, 1) = 'mass_ratio'
+   Text_Summary1_name(4, 1) = 'period_days'
+   Text_Summary1_name(5, 1) = 'rl_relative_overflow_1'
 
       ! file output
 

binary/private/binary_history.f90

@@ -595,6 +595,10 @@ subroutine binary_history_getval(b, c, val, int_val, is_int_val, ierr)
          val = safe_log10(b% m(2) / Msun)
       case(bh_sum_of_masses)
          val = (b% m(1) + b% m(2)) / Msun
+      case(bh_mass_ratio)
+         val = b% m(2) / b% m(1)
+      case(bh_obs_mass_ratio)
+         val = min(b% m(2) / b% m(1), b% m(1) / b% m(2))
       case(bh_lg_mtransfer_rate)
          val = safe_log10(abs(b% step_mtransfer_rate) / Msun * secyer)
       case(bh_lg_mstar_dot_1)

binary/private/binary_private_def.f90

@@ -57,7 +57,9 @@ module binary_private_def
       integer, parameter :: bh_star_2_mass = bh_lg_star_1_mass + 1
       integer, parameter :: bh_lg_star_2_mass = bh_star_2_mass + 1
       integer, parameter :: bh_sum_of_masses = bh_lg_star_2_mass + 1
-      integer, parameter :: bh_lg_mtransfer_rate = bh_sum_of_masses + 1
+      integer, parameter :: bh_mass_ratio = bh_sum_of_masses + 1
+      integer, parameter :: bh_obs_mass_ratio = bh_mass_ratio + 1
+      integer, parameter :: bh_lg_mtransfer_rate = bh_obs_mass_ratio + 1
       integer, parameter :: bh_lg_mstar_dot_1 = bh_lg_mtransfer_rate + 1
       integer, parameter :: bh_lg_mstar_dot_2 = bh_lg_mstar_dot_1 + 1
       integer, parameter :: bh_lg_system_mdot_1 = bh_lg_mstar_dot_2 + 1
@@ -145,6 +147,8 @@ subroutine binary_history_column_names_init(ierr)
          binary_history_column_name(bh_star_2_mass) = 'star_2_mass'
          binary_history_column_name(bh_lg_star_2_mass) = 'lg_star_2_mass'
          binary_history_column_name(bh_sum_of_masses) = 'sum_of_masses'
+         binary_history_column_name(bh_mass_ratio) = 'mass_ratio'
+         binary_history_column_name(bh_obs_mass_ratio) = 'obs_mass_ratio'
          binary_history_column_name(bh_lg_mtransfer_rate) = 'lg_mtransfer_rate'
          binary_history_column_name(bh_lg_mstar_dot_1) = 'lg_mstar_dot_1'
          binary_history_column_name(bh_lg_mstar_dot_2) = 'lg_mstar_dot_2'

docs/source/changelog.rst

@@ -19,6 +19,8 @@ New Features
 
 ``mesa_reader`` can now be installed with ``pip``.
 
+A pseudo drag term ``v_drag`` has been reintroduced for ``u_flag`` to damp spurious shocks.
+
 .. _Bug Fixes main:
 
 Bug Fixes

docs/source/developing/infrastructure.rst

@@ -9,8 +9,8 @@ GitHub
 ------
 
 We have the `MESAHub <https://github.com/MESAHub>`__ GitHub
-organization.  The members of the MTC/MAC all have owner-level
-privileges.  MESAHub is classified as an educational organization and
+organization. The members of the MTC/MAC all have owner-level
+privileges. MESAHub is classified as an educational organization and
 this currently grants us a 100% discount, meaning this costs $0/yr.
 Unsubsidized, it would cost about $1200/yr.
 
@@ -56,7 +56,7 @@ Mailing lists
 
 The [email protected] and
 [email protected] lists are hosted by `MailmanLists
-<https://www.mailmanlists.net/>`__.  The account is controlled by
+<https://www.mailmanlists.net/>`__. The account is controlled by
 Matteo who pays the hosting fees through Flatiron.
 This costs about $100/year.
 
@@ -74,15 +74,15 @@ ReadTheDocs
 -----------
 
 The Sphinx documentation is hosted by `ReadTheDocs
-<https://readthedocs.org/>`__.  Rich controls the account (and Earl, Joey, Meridith, and Philip have access to it).  This is
+<https://readthedocs.org/>`__. Rich controls the account (and Earl, Joey, Meridith, and Philip have access to it). This is
 currently free for open source software.
 
 
 Sourceforge
 -----------
 
-The original home of MESA development was sourceforge.  Most developers
-involved c. 2015 or earlier have admin privileges.  This is a free
+The original home of MESA development was sourceforge. Most developers
+involved c. 2015 or earlier have admin privileges. This is a free
 service.
 
 Website
@@ -97,33 +97,36 @@ Slack
 -----
 
 Rich controls the Slack and pays for it (through grants at UW
-Madison).  This costs around $130 per year (about $10/user/yr).
+Madison). This costs around $130 per year (about $10/user/yr).
 
 
 TestHub
 -------
 
 The MESA TestHub runs on Heroku and the account is controlled by Bill
-Wolf.  It is funded by Frank and Bill W.  The Heroku account costs
+Wolf. It is funded by Frank and Bill W. The Heroku account costs
 around $600/yr, though its cost has been higher during the GitHub
 transition.
 
 The testing `log archive <https://logs.mesastar.org/>`__ lives on a
-server controlled by Josiah.  The marginal cost is $1/month, which he
+server controlled by Josiah. The marginal cost is $1/month, which he
 covers.
 
 Jenkins
 ^^^^^^^
 
 The Flatiron `Scientific Computing Core <https://www.simonsfoundation.org/flatiron/scientific-computing-core>`__
-provides continuous integration testing for MESA via jenkins.
-This was set up in 2021 by Dylan Simon (Flatiron) and Josiah.  The configuration lives in the ``jenkins`` directory.
-Matteo serves as the point of contact at Flatiron.
+provides continuous integration testing for MESA via Jenkins.
+This was set up in 2021 by Dylan Simon (Flatiron) and Josiah.
+The configuration lives in the ``jenkins`` directory.
+Matteo and Philip serve as the point of contact at Flatiron.
+View the `Jenkins test results <https://jenkins.flatironinstitute.org/job/mesa/job/main/>`__
+
 
 Zenodo
 ------
 
-We have multiple resources archived on Zenodo.  This is a free service.
+We have multiple resources archived on Zenodo. This is a free service.
 
 Community
 ^^^^^^^^^

docs/source/reference.rst

@@ -1,6 +1,6 @@
-*********
-Reference
-*********
+**********************
+Reference and Defaults
+**********************
 
 This page describes the options associated with MESA/star,
 MESA/binary, and MESA/astero.  

star/defaults/controls.defaults

@@ -2985,7 +2985,7 @@
     conv_premix_dump_snapshots = .false.
 
 
-   ! Rayleigh Taylor Instability
+   ! Rayleigh-Taylor Instability
    ! ____________________________
 
       ! derived from Paul Duffell's code RT1D.
@@ -4135,6 +4135,27 @@
     D_mix_rotation_min_logT_full_off = 9.5d0
 
 
+      ! D_mix_rotation_min_tau_full_off
+      ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+      ! Drop rotational components of ``D_mix`` for locations where tau <= this.
+      ! For numerical stability, turn off rotational part of ``D_mix`` at very low tau.
+
+      ! ::
+
+    D_mix_rotation_min_tau_full_off = 0d0
+
+          ! D_mix_rotation_max_tau_full_on
+      ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+      ! Use rotational components of ``D_mix`` for locations where tau >= this.
+      ! For numerical stability, turn off rotational part of ``D_mix`` at very low tau.
+
+      ! ::
+
+    D_mix_rotation_min_tau_full_on = 0d0
+
+
       ! D_omega_max_replacement_fraction
       ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       ! D_omega_growth_rate
@@ -8241,15 +8262,18 @@
       ! ::
 
     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.    
+
+
+      ! Hydrodynamic drag
+      ! =================
+
       ! drag_coefficient
       ! ~~~~~~~~~~~~~~~~
       ! min_q_for_drag
       ! ~~~~~~~~~~~~~~
 
-      ! only when v_flag.  adjusts both v and energy transfer from kinetic to thermal.
+      ! only when v_flag = .true.. Adjusts both v and energy transfer from kinetic to thermal.
       ! only for v(k) when q(k) > min_q_for_drag.
       ! kill off fraction of v = drag_coefficient (i.e. set to 1 to keep v near 0)
       ! useful for preventing the development radial pulsations during advanced
@@ -8274,13 +8298,35 @@
     use_drag_energy = .true.
     drag_coefficient = 0d0
     min_q_for_drag = 0d0
+
+
+      ! v_drag_factor
+      ! ~~~~~~~~~~~~~
+      ! v_drag
+      ! ~~~~~~
+      ! q_for_v_drag_full_off
+      ! ~~~~~~~~~~~~~~~~~~~~~
+      ! q_for_v_drag_full_on
+      ! ~~~~~~~~~~~~~~~~~~~~
 
 
-      ! for hydro comparison tests (e.g., Sedov)
+      ! Only when u_flag = .true.. Adds a pseudo drag term of the form
+      ! -v_drag_factor*(v-v_drag)^2/r, can be used damp velocities in outer layers
+      ! of a star, useful for smoothing out spurious shocks colliding in ejected layers. 
+      ! Effect is full on for q>q_for_v_drag_full_on and full off for
+      ! q < q_for_v_drag_full_off.
+
+      ! ::
+
+    v_drag_factor = 0d0
+    v_drag = 0d0
+    q_for_v_drag_full_off = 0.95d0
+    q_for_v_drag_full_on = 0.96d0
 
 
       ! Rayleigh-Taylor Instability
       ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+      ! for hydro comparison tests (e.g., Sedov)
       ! RTI_A
       ! ~~~~~
       ! RTI_B

star/dev_cases_star_to_RSP2/dev_BEP/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 

star/dev_cases_star_to_RSP2/dev_BW_Vul/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 
@@ -185,7 +185,7 @@ end subroutine extras_startup
       subroutine gyre_linear_analysis_and_set_velocities(s,restart,ierr)
          use const_def
          use math_lib
-         use gyre_lib
+         use gyre_mesa_m
          type (star_info), pointer :: s
          logical, intent(in) :: restart
          integer, intent(out) :: ierr

star/dev_cases_star_to_RSP2/dev_Cepheid/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 
@@ -514,7 +514,7 @@ end subroutine data_for_extra_profile_columns
       subroutine gyre_linear_analysis_and_set_velocities(s,restart,ierr)
          use const_def
          use math_lib
-         use gyre_lib
+         use gyre_mesa_m
          type (star_info), pointer :: s
          logical, intent(in) :: restart
          integer, intent(out) :: ierr

star/dev_cases_star_to_RSP2/dev_Cepheid_6M/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 

star/dev_cases_star_to_RSP2/dev_Cepheid_9M/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 

star/dev_cases_star_to_RSP2/dev_Delta_Scuti/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 

star/dev_cases_star_to_RSP2/dev_Mira/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 

star/dev_cases_star_to_RSP2/dev_RR_Lyrae/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 

star/dev_cases_star_to_RSP2/dev_RSG/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none
 

star/dev_cases_star_to_RSP2/dev_Type_II_Cepheid/src/run_star_extras.f90

@@ -26,7 +26,7 @@ module run_star_extras
       use star_def
       use const_def
       use math_lib
-      use gyre_lib
+      use gyre_mesa_m
 
       implicit none