merge with main (needed merge instead of rebase due to some complicat…

…ed changes)

.gitignore

@@ -32,6 +32,7 @@ vgcore.*
 
 ## Documentation
 /dox/
+docs/source/_tags
 
 
 ## Executables
@@ -44,7 +45,17 @@ vgcore.*
 **/LOGS2/
 **/photos/
 **/png/
-
+**/png1/
+**/png2/
+**/png3/
+**/pgstar_out/
+**/pgstar_out1/
+**/pgstar_out2/
+**/pgstar_out3/
+**/plt_out/
+**/plt_out1/
+**/plt_out2/
+**/plt_out3/
 
 ## Bill
 star_data/public_*

.readthedocs.yaml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.8"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

.zenodo.json

@@ -11,18 +11,21 @@
         },
         {
             "affiliation": "Center for Computational Astrophysics",
-            "name": "Bauer, Evan"
+            "name": "Bauer, Evan",
+            "orcid": "0000-0002-4791-6724"
         },
         {
-            "affiliation": "Max Planck Institute for Astrophysics",
-            "name": "Bellinger, Earl"
+            "affiliation": "Yale University",
+            "name": "Bellinger, Earl",
+            "orcid": "0000-0003-4456-4863"
         },
         {
             "affiliation": "Kavli Institute for Theoretical Physics",
-            "name": "Bildsten, Lars"
+            "name": "Bildsten, Lars",
+            "orcid": "0000-0001-8038-6836"
         },
         {
-            "affiliation": "Center for Computational Astrophysics",
+            "affiliation": "Flatiron Institute",
             "name": "Cantiello, Matteo",
             "orcid": "0000-0002-8171-8596"
         },
@@ -47,15 +50,20 @@
             "orcid": "0000-0001-5048-9973"
         },
         {
-            "affiliation": "Space Telescope Science Institute",
-            "name": "Meridith, Joyce",
+            "affiliation": "University of Wyoming",
+            "name": "Joyce, Meridith",
             "orcid": "0000-0002-8717-127X"
         },
         {
             "affiliation": "KU Leuven",
             "name": "Marchant, Pablo",
             "orcid": "0000-0002-0338-8181"
         },
+        {
+            "affiliation": "Flatiron Institute",
+            "name": "Mocz, Philip",
+            "orcid": "0000-0001-6631-2566"
+        },
         {
             "name": "Schwab, Josiah",
             "orcid": "0000-0002-4870-8855"

CODEOWNERS

@@ -56,7 +56,7 @@ star/test_suite/adjust_net
 star/test_suite/c13_pocket @fxt44
 star/test_suite/carbon_kh @evbauer
 star/test_suite/cburn_inward 
-star/test_suite/ccsn_IIp @fxt44
+star/test_suite/ccsn_IIp @fxt44 @aurimontem
 star/test_suite/check_redo @fxt44
 star/test_suite/check_pulse_atm @warrickball
 star/test_suite/conductive_flame @fxt44 
@@ -89,7 +89,7 @@ star/test_suite/make_he_wd @evbauer @fxt44
 star/test_suite/make_metals @fxt44
 star/test_suite/make_o_ne_wd @fxt44 @evbauer
 star/test_suite/make_planets @fxt44
-star/test_suite/make_pre_ccsn_13bvn @Debraheem
+star/test_suite/make_pre_ccsn_13bvn @Debraheem @aurimontem
 star/test_suite/make_sdb @evbauer
 star/test_suite/make_zams @fxt44
 star/test_suite/make_zams_low_mass @fxt44

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = "MESA"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = r24.03.04
+PROJECT_NUMBER         = r24.06.1-rc1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

README.rst

@@ -1,25 +1,44 @@
+.. image:: docs/source/mesa-logo-200.png
+  :align: center
+  :width: 200
+  :alt: MESA
+  :target: https://docs.mesastar.org/en/latest/
+
 ######################################################
 Modules for Experiments in Stellar Astrophysics (MESA)
 ######################################################
 
-.. image:: https://img.shields.io/github/license/MESAHub/mesa
-    :alt: GitHub
-    :target: https://github.com/MESAHub/mesa/blob/master/LICENSE
+.. image:: https://img.shields.io/badge/repo_status-Active-brightgreen
+    :alt: RepoStatus
+    :target: https://www.repostatus.org/#active
+.. image:: https://img.shields.io/readthedocs/mesa-doc
+    :alt: ReadTheDocs
+    :target: https://docs.mesastar.org/en/latest/
 .. image:: https://img.shields.io/github/v/release/MESAHub/mesa
     :alt: GitHub release (latest by date)
     :target: https://github.com/MESAHub/mesa/releases/latest
-.. image:: https://img.shields.io/github/issues/MESAHub/mesa
-    :alt: GitHub issues
-    :target: https://github.com/MESAHub/mesa/issues
+.. image:: https://img.shields.io/badge/zenodo-community-blue
+    :alt: Zenodo
+    :target: https://zenodo.org/communities/mesa/records?q=&l=list&p=1&s=10
+.. image:: https://img.shields.io/github/license/MESAHub/mesa
+    :alt: GitHub
+    :target: https://github.com/MESAHub/mesa/blob/master/LICENSE
+.. image:: https://github.com/MESAHub/mesa/actions/workflows/build-linux.yml/badge.svg
+    :alt: BuildLinux
+    :target: https://github.com/MESAHub/mesa/actions/workflows/build-linux.yml
+
+|
+
+   **WARNING**: The default ``main`` branch is the development version of
+   MESA and is not guaranteed to function correctly.  If you are using
+   MESA, you should use an official release version.
 
-**WARNING**: The default ``main`` branch is the development version of
-MESA and is not guaranteed to function correctly.  If you are using
-MESA, you should use an official release version.
 
 Overview
 ========
 
-MESA is built to allow users to run experiments in stellar evolution. 
+MESA is a powerful and versatile open-source software suite built to 
+allow users to run experiments in stellar evolution.
 Stellar evolution calculations (i.e., stellar evolution tracks and
 detailed information about the evolution of internal and global
 properties) are a basic tool that enable a broad range of research in
@@ -41,10 +60,14 @@ pedagogically) by accurate one-dimensional calculations, and this is
 the focus of MESA.
 
 
+Links
+=====
 
-Documentation
-=============
-
-Please visit https://docs.mesastar.org/ for up-to-date information about installing and running MESA.
+* `Code repository <https://github.com/MESAHub/mesa>`__ on GitHub (this page).
+* `Documentation <https://docs.mesastar.org/>`__ for up-to-date information about installing and running MESA.
+* `MESA Marketplace <http://cococubed.com/mesa_market/>`__ for resources for published papers using MESA. 
+* `MESA Zenodo Community <https://zenodo.org/communities/mesa/records?q=&l=list&p=1&s=10>`__ for downloading official release versions, SDKs, and MESA project inlists.
+* `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 Test Hub <https://testhub.mesastar.org/>`__ to view results of regression testing (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).
 
-The `MESA Marketplace <http://cococubed.com/mesa_market/>`__ provides resources for published papers using MESA. 

astero/private/adipls_support.f90

@@ -287,8 +287,7 @@ subroutine store_model_for_adipls (s, add_atmosphere, do_redistribute_mesh, ierr
 
          ivers = 0 ! It's not clear what this does in fgong_amdl
 
-         call fgong_amdl( &
-            cgrav, nn_in, iconst, ivar, ivers, global_data, point_data, data, aa, nn, ierr)
+         call fgong_amdl(cgrav, nn_in, iconst, ivar, ivers, global_data, point_data, data, aa, nn, ierr)
          deallocate(global_data, point_data)
 
          if (ierr /= 0) then
@@ -682,8 +681,7 @@ subroutine read_and_store(iriche, iturpr, cgrav)
             write(*,*) 'read_and_store failed in read_fgong_file'
             call mesa_error(__FILE__,__LINE__)
          end if
-         call fgong_amdl( &
-            cgrav, nn, iconst, ivar, ivers, glob, var, data, aa, nn, ierr)
+         call fgong_amdl(cgrav, nn_in, iconst, ivar, ivers, glob, var, data, aa, nn, ierr)
          if (ierr /= 0) then
             write(*,*) 'read_and_store failed in fgong_amdl'
             call mesa_error(__FILE__,__LINE__)
@@ -726,16 +724,16 @@ subroutine store_amdl(nn_in, iriche, iturpr, data, aa, x, nn, ierr)
 
          ! test for singular centre and/or surface
 
-         sincen=aa1(1,1).eq.0
-         sinsur=data(7).ge.0
+         sincen=aa1(1,1) == 0
+         sinsur=data(7) >= 0
          nsin=0
          if (sincen) nsin=nsin+1
          if (sinsur) nsin=nsin+1
 
          ! test for inclusion of g/(g tilde)
 
          idata8 = int(data(8)+0.1)
-         if (mod(idata8/10,10).eq.2) then
+         if (mod(idata8/10,10) == 2) then
             iggt = 1
             iturpr=8
          else
@@ -746,13 +744,13 @@ subroutine store_amdl(nn_in, iriche, iturpr, data, aa, x, nn, ierr)
 
          ! test for number of nonsingular points
 
-         if (iriche.ne.1.or.mod(nn-nsin,2).eq.1) then
+         if (iriche /= 1.or.mod(nn-nsin,2) == 1) then
             nshift=0
          else
             nshift=1
          end if
          nnr=nn
-         if (nshift.ne.0) then
+         if (nshift /= 0) then
             nn=nn-nshift
          end if
 
@@ -772,7 +770,7 @@ subroutine store_amdl(nn_in, iriche, iturpr, data, aa, x, nn, ierr)
             end do
          else
             do n=1,nnr
-               if (n.eq.1) then
+               if (n == 1) then
                   n1=1
                else
                   n1=n+nshift
@@ -788,16 +786,16 @@ subroutine store_amdl(nn_in, iriche, iturpr, data, aa, x, nn, ierr)
 
          ! set g/gtilde (=1 in models without turbulent pressure)
 
-         if (iturpr.eq.1) then
+         if (iturpr == 1) then
             do n=1,nn
-               if (x(n).lt.0.999) then
+               if (x(n) < 0.999) then
                   ggt=1
                else
                   ggt=1./(x(n)*x(n)*x(n)*aa(1,n))
                end if
                aa(10,n)=ggt
             end do
-         else if (iggt.eq.1) then
+         else if (iggt == 1) then
             do n=1,nn
                aa(10,n)=aa(6,n)
             end do
@@ -815,8 +813,7 @@ subroutine store_amdl(nn_in, iriche, iturpr, data, aa, x, nn, ierr)
       end subroutine store_amdl
 
 
-      subroutine fgong_amdl( &
-            cgrav, nn_in, iconst, ivar, ivers, glob, var, data, aa, nn, ierr)
+      subroutine fgong_amdl(cgrav, nn_in, iconst, ivar, ivers, glob, var, data, aa, nn, ierr)
          ! derived from fgong-amdl.d.f
          real(dp), intent(in) :: cgrav
          integer, intent(in) :: nn_in, iconst, ivar, ivers
@@ -834,7 +831,7 @@ subroutine fgong_amdl( &
          ierr = 0
          nn = nn_in
 
-         if (var(1,1).gt.var(1,nn)) then 
+         if (var(1,1) > var(1,nn)) then 
             nn1=nn+1
             do i=1,ivar
                do n=1,nn
@@ -846,7 +843,7 @@ subroutine fgong_amdl( &
             end do
          end if
 
-         if (var(1,1).gt.1.d6) then 
+         if (var(1,1) > 1.d6) then 
             do i=1,ivar
                do n=1,nn
                   var1(i,n+1)=var(i,n)
@@ -895,23 +892,23 @@ subroutine fgong_amdl( &
          aa(4,1)=var(10,1)
          aa(5,1)=0
          aa(6,1)=3.d0
-         if (aa(5,nn).le.10) then 
+         if (aa(5,nn) <= 10) then 
             nn=nn-1 
             !write(6,*) 'Chop off outermost point' 
          end if
          data(1)=glob(1)
          data(2)=glob(2)
          data(3)=var(4,1)
          data(4)=var(5,1)
-         if (glob(11).lt.0.and.glob(11).gt.-10000) then 
+         if (glob(11) < 0.and.glob(11) > -10000) then 
             data(5)=-glob(11)/var(10,1)
             data(6)=-glob(12) 
          else 
             data(5)=four_thirds_pi*cgrav*(var(5,1)*glob(2))**2/(var(4,1)*var(10,1))
             d2amax=0.d0
             do n=2,nn
                d2amax=max(d2amax,aa(5,n)/x(n)**2)
-               if (x(n).ge.0.05d0) exit
+               if (x(n) >= 0.05d0) exit
             end do
             data(6)=d2amax+data(5)
             !write(6,140) data(5), data(6)

astero/private/astero_run_support.f90

@@ -53,7 +53,6 @@ end subroutine extras_controls
 
          type (star_info), pointer :: s
          integer :: id, i, ierr
-         character (len=256) :: inlist_fname
 
          include 'formats'
 
@@ -207,7 +206,7 @@ real(dp) function eval1(id_in,ierr)
 
          type (star_info), pointer :: s
          logical :: restart
-         integer :: id, i      
+         integer :: id   
 
          include 'formats'
 
@@ -647,7 +646,7 @@ subroutine do_bobyqa_or_newuoa(newuoa_flag, ierr)
          integer, intent(out) :: ierr
          integer, parameter :: maxfun = 1000, iprint = 0
          real(dp), pointer, dimension(:) :: xl, xu, x, w
-         real(dp) :: min_chi2, rhobeg, max_value
+         real(dp) :: rhobeg, max_value
          integer :: i, npt
          include 'formats'
          ierr = 0
@@ -815,8 +814,7 @@ subroutine do_simplex(ierr)
          use num_lib
          integer, intent(out) :: ierr
 
-         real(dp) :: final_mass, final_alpha, final_Y, final_FeH, &
-              final_param(1:max_parameters)
+         real(dp) :: final_param(1:max_parameters)
          real(dp), dimension(:), pointer :: x_first, x_lower, x_upper, x_final
          real(dp), pointer :: simplex(:,:), f(:)
          real(dp) :: f_final
@@ -825,7 +823,7 @@ subroutine do_simplex(ierr)
          real(dp), pointer :: rpar(:) ! (lrpar)
          integer :: num_iters, num_fcn_calls, &
             num_fcn_calls_for_ars, num_accepted_for_ars
-         integer :: seed, i, j, k, num_samples
+         integer :: i, num_samples
          logical :: start_from_given_simplex_and_f
 
          include 'formats'
@@ -1047,7 +1045,7 @@ end subroutine save_best_for_sample
 
 
       subroutine set_sample_averages
-         integer :: ierr, jj, j, n
+         integer :: jj, j, n
          real(dp) :: avg_age_top_samples2, avg_model_number_top_samples2
 
          include 'formats'

astero/private/astero_support.f90

@@ -71,7 +71,7 @@ subroutine get_one_el_info( &
 
          real(dp) :: nu_obs, dist_j, nu, dist, min_dist, min_freq, &
             R, G, M, sig_fac, b, sum_1, sum_2, sum_3, empty(0)
-         integer :: min_dist_j, min_order, n, cnt, int_empty(0)
+         integer :: min_dist_j, min_order, n, cnt, int_empty(0), int_empty2(0)
          integer :: nsel, itrsig, nsig
          real(dp) :: els1, dels, sig1, sig2, dfsig
          integer :: num_l0_terms, k, i, j
@@ -162,7 +162,7 @@ subroutine get_one_el_info( &
             call set_to_closest(freq_target(0,:), &
                model_freq(0,:), empty, empty, &
                model_inertia(0,:), empty, empty, &
-               model_order(0,:), int_empty, int_empty, ierr)
+               model_order(0,:), int_empty, int_empty2, ierr)
 
             model_freq_alt_up(0,:) = model_freq(0,:)
             model_inertia_alt_up(0,:) = model_inertia(0,:)