Merge branch 'main' into rf/ion

Author: evbauer

.gitattributes

@@ -8,6 +8,9 @@
 *.h5 filter=lfs diff=lfs merge=lfs -text
 *.mod filter=lfs diff=lfs merge=lfs -text
 *.mp4 filter=lfs diff=lfs merge=lfs -text
+data/star_data/zams_models/zams_z2m2_y28.data filter=lfs diff=lfs merge=lfs -text
+docs/source/assets/zams_z2m2_y28_patched.data filter=lfs diff=lfs merge=lfs -text
+neu/test/test_output filter=lfs diff=lfs merge=lfs -text
 
 # Try to get github to better understand what our filetypes are
 *.inc linguist-language=Fortran

.github/workflows/build-linux.yml

@@ -12,6 +12,19 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      - name: Delete unused packages
+        run: |
+          # commands lifted from https://github.com/jlumbroso/free-disk-space
+          sudo rm -rf /usr/local/lib/android
+          sudo apt-get remove -y '^aspnetcore-.*'
+          sudo apt-get remove -y '^dotnet-.*' # 990 MB
+          sudo apt-get remove -y '^llvm-.*' # 1052 MB
+          # sudo apt-get remove -y 'php.*' # 56.6 MB
+          # sudo apt-get remove -y '^mysql-.*' # 209 MB
+          sudo apt-get remove -y azure-cli google-cloud-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri # 2274 MB
+          sudo apt-get autoremove -y # 771 MB
+          sudo apt-get clean
+
       - name: Checkout
         uses: actions/[email protected]
 
@@ -83,6 +96,9 @@ jobs:
           export "MESA_DIR=$(readlink -f ./)"
           # Everything is run as root so we need to disable the root check in the install script
           sed -i 's/\${EUID:-\$(id -u)}/1/' install
+          # Turn off caching during build to save more space
+          sed -i 's/use_cache_for_eos = .true./use_cache_for_eos = .false./g' $MESA_DIR/eos/public/eos_def.f90
+          sed -i 's/use_cache = .true./use_cache = .false./g' $MESA_DIR/star/private/star_private_def.f90
           ./install
           if [ ! -f lib/libbinary.a ]; then
             exit 1

.readthedocs.yaml

@@ -5,10 +5,17 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
 
-# Optionally set the version of Python and requirements required to build your docs
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.8
+  install:
+  - requirements: docs/requirements.txt

CODEOWNERS

@@ -8,34 +8,33 @@ astero/ @warrickball
 atm/ @rhdtownsend @warrickball
 autodiff/ 
 binary/ @orlox
-chem/ @rjfarmer @fxt44
-colors/ @rjfarmer
-const/ @rjfarmer @fxt44
-data/ @rjfarmer
+chem/ @fxt44
+colors/ 
+const/ @fxt44
+data/ 
 docs/ @rhdtownsend
 eos/ @fxt44 @evbauer
 gyre/ @rhdtownsend @warrickball
 hdfio5 @rhdtownsend
 interp_1d/ @rhdtownsend 
 interp_2d/ @rhdtownsend 
-ionization/ 
-kap/ @fxt44
-linters/ @rjfarmer
+ionization/ @fxt44
+kap/ @fxt44 @Debraheem
+linters/ 
 turb/ 
 math/ @rhdtownsend
-mtx/  @rjfarmer @mjoyceGR
-net/ @rjfarmer @fxt44
-neu/ @rjfarmer @fxt44
+mtx/  @mjoyceGR
+net/ @fxt44
+neu/ @fxt44
 num/ 
-rates/ @rjfarmer @fxt44
+rates/ @fxt44
 #star/
 #star_data/
 #stella/ 
-utils/ @rhdtownsend @warrickball @rjfarmer
+utils/ @rhdtownsend @warrickball 
 
 ### Star ###
 
-star/private/pgstar_*.f90 @rjfarmer
 star/private/rsp_*.f90 @rsmolec
 star/private/phase_separation.f90 @evbauer
 
@@ -53,20 +52,20 @@ star/test_suite/20M_z2m2_high_rotation
 star/test_suite/5M_cepheid_blue_loop @annethoul @rsmolec
 star/test_suite/7M_prems_to_AGB @annethoul
 star/test_suite/accreted_material_j @orlox
-star/test_suite/adjust_net @rjfarmer
+star/test_suite/adjust_net 
 star/test_suite/c13_pocket @fxt44
 star/test_suite/carbon_kh @evbauer
-star/test_suite/cburn_inward @rjfarmer
-star/test_suite/ccsn_IIp @rjfarmer @fxt44
+star/test_suite/cburn_inward 
+star/test_suite/ccsn_IIp @fxt44
 star/test_suite/check_redo @fxt44
 star/test_suite/check_pulse_atm @warrickball
-star/test_suite/conductive_flame @fxt44 @rjfarmer
+star/test_suite/conductive_flame @fxt44 
 star/test_suite/conserve_angular_momentum @orlox
 star/test_suite/conv_core_cpm @evbauer
-star/test_suite/custom_colors @rjfarmer
+star/test_suite/custom_colors 
 star/test_suite/custom_rates @evbauer  @fxt44
 star/test_suite/high_rot_darkening @orlox
-star/test_suite/dev_ppisn @rjfarmer
+star/test_suite/dev_ppisn 
 star/test_suite/diffusion_smoothness @fxt44
 star/test_suite/extended_convective_penetration @fxt44
 star/test_suite/gyre_in_mesa_bcep @rhdtownsend @annethoul
@@ -76,7 +75,7 @@ star/test_suite/gyre_in_mesa_rsg @rhdtownsend @annethoul
 star/test_suite/gyre_in_mesa_spb @rhdtownsend @annethoul
 star/test_suite/gyre_in_mesa_wd @rhdtownsend @annethoul
 star/test_suite/hb_2M @annethoul
-star/test_suite/high_mass @fxt44 @rjfarmer
+star/test_suite/high_mass @fxt44 
 star/test_suite/high_z @fxt44
 star/test_suite/hot_cool_wind @fxt44
 star/test_suite/hse_riemann @fxt44
@@ -85,20 +84,21 @@ star/test_suite/low_z @aarondotter
 star/test_suite/magnetic_braking 
 star/test_suite/make_brown_dwarf @fxt44
 star/test_suite/make_co_wd @wmwolf @evbauer @fxt44
-star/test_suite/make_env @rjfarmer
+star/test_suite/make_env 
 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_sdb @evbauer
 star/test_suite/make_zams @fxt44
 star/test_suite/make_zams_low_mass @fxt44
-star/test_suite/make_zams_ultra_high_mass @fxt44 @rjfarmer
-star/test_suite/ns_c @rjfarmer @fxt44
-star/test_suite/ns_h @rjfarmer @fxt44
-star/test_suite/ns_he @rjfarmer @fxt44
+star/test_suite/make_zams_ultra_high_mass @fxt44 
+star/test_suite/ns_c @fxt44
+star/test_suite/ns_h @fxt44
+star/test_suite/ns_he @fxt44
 star/test_suite/other_physics_hooks @fxt44
-star/test_suite/pisn @rjfarmer
+star/test_suite/pisn 
 star/test_suite/radiative_levitation @evbauer
 star/test_suite/R_CrB_star @fxt44
 star/test_suite/relax_composition_j_entropy @warrickball
@@ -115,8 +115,8 @@ star/test_suite/rsp_Type_II_Cepheid @rsmolec
 star/test_suite/semiconvection  @annethoul
 star/test_suite/simplex_solar_calibration @mjoyceGR
 star/test_suite/test_case_template @fxt44
-star/test_suite/test_memory @rjfarmer
-star/test_suite/timing @rjfarmer
+star/test_suite/test_memory 
+star/test_suite/timing 
 star/test_suite/T_tau_gradr @warrickball
 star/test_suite/twin_studies @fxt44
 star/test_suite/wd_acc_small_dm @wmwolf
@@ -128,21 +128,21 @@ star/test_suite/wd_he_shell_ignition @wmwolf
 star/test_suite/wd_nova_burst @wmwolf
 star/test_suite/wd_stable_h_burn @wmwolf
 
-star/test_suite/12M_pre_ms_to_core_collapse @rjfarmer
-star/test_suite/20M_pre_ms_to_core_collapse @rjfarmer
-star/test_suite/split_burn_big_net @rjfarmer
-star/test_suite/zams_to_cc_80 @rjfarmer
-star/test_suite/20M_z2m2_high_rotation @rjfarmer
+star/test_suite/12M_pre_ms_to_core_collapse @Debraheem
+star/test_suite/20M_pre_ms_to_core_collapse @Debraheem
+star/test_suite/split_burn_big_net
+star/test_suite/zams_to_cc_80 @Debraheem
+star/test_suite/20M_z2m2_high_rotation
 
 
-binary/test_suite/double_bh @orlox @rjfarmer
+binary/test_suite/double_bh @orlox 
 binary/test_suite/evolve_both_stars @orlox @mjoyceGR
 binary/test_suite/jdot_gr_check @orlox
 binary/test_suite/jdot_ls_check @orlox
 binary/test_suite/jdot_ml_check @orlox
-binary/test_suite/star_plus_point_mass @orlox @rjfarmer
+binary/test_suite/star_plus_point_mass @orlox 
 binary/test_suite/star_plus_point_mass_explicit_mdot @orlox
-binary/test_suite/wind_fed_bhhmxb @orlox @rjfarmer
+binary/test_suite/wind_fed_bhhmxb @orlox 
 
 astero/test_suite/astero_adipls @warrickball
 astero/test_suite/astero_gyre @warrickball

README.rst

@@ -45,8 +45,6 @@ the focus of MESA.
 Documentation
 =============
 
-Please visit http://mesa.sourceforge.net/ for up-to-date information about installing and running MESA.
+Please visit https://docs.mesastar.org/ for up-to-date information about installing and running MESA.
 
-Full documentation for MESA can be found at https://docs.mesastar.org/
-
-The `MESA Marketplace <http://cococubed.asu.edu/mesa_market/>`__ provides resources for published papers using MESA. 
+The `MESA Marketplace <http://cococubed.com/mesa_market/>`__ provides resources for published papers using MESA. 

adipls/make/makefile_adiajobs

@@ -14,107 +14,106 @@ include $(MESA_DIR)/utils/makefile_header
 
 ASYMP_SCALE_SRCS = \
     asymp-scale.d.o lir.d.o getcas.o rdamdl.n.d.o skpcom.o \
-    cpycom.o length.o ofiles.o blstio.o
+    cpycom.o length.o ofiles.o
 
 COMPAMOD_SRCS = \
     compamod.n.d.o ofiles.o lir.d.o vinta.d.o \
-    length.o blstio.o
+    length.o
 
 DIFF_FGONG_SRCS = \
-    diff-fgong.d.o lir.d.o blstio.o
+    diff-fgong.d.o lir.d.o
 
 DIFF_SUM_SRCS = \
-    diff-sum.d.o rdfreq.d.o wrfreq.d.o skpcom.o \
-    blstio.o
+    diff-sum.d.o rdfreq.d.o wrfreq.d.o skpcom.o
 
 FDIF_SIN_SRCS = \
     fdif.sin.d.o ofiles.o zero.d.o lir.d.o \
-    skpcom.o length.o blstio.o
+    skpcom.o length.o
 
 FGONG_AMDL_SRCS = \
-    fgong-amdl.d.o blstio.o
+    fgong-amdl.d.o
 
 FILT_GSM_SRCS = \
-    filt-gsm.d.o blstio.o
+    filt-gsm.d.o
 
 FIT_DNL_SRCS = \
-    fit-dnl.o lstsqr.o skpcom.o length.o blstio.o
+    fit-dnl.o lstsqr.o skpcom.o length.o
 
 FORM_AGSM_SRCS = \
-    form-agsm.d.o blstio.o
+    form-agsm.d.o
 
 FORM_AMDL_SRCS = \
-    form-amdl.d.o blstio.o
+    form-amdl.d.o
 
 FREQDIF_SRCS = \
     freqdif.d.o ofiles.o zero.d.o izero.o lir.d.o \
-    rdfreq.d.o rdfrqe.d.o skpcom.o length.o blstio.o
+    rdfreq.d.o rdfrqe.d.o skpcom.o length.o
 
 LSQFREQ_SRCS = \
     lsqfreq.d.o rdfrqm.d.o ofiles.o lsqpol.d.o \
-    leq.d.o skpcom.o craysub.d.o length.o blstio.o
+    leq.d.o skpcom.o craysub.d.o length.o
 
 MER_AMDE_SRCS = \
-    mer-amde.d.o blstio.o
+    mer-amde.d.o
 
 MER_SUM_SRCS = \
-    mer-sum.d.o rdfreq.d.o wrfreq.d.o skpcom.o blstio.o
+    mer-sum.d.o rdfreq.d.o wrfreq.d.o skpcom.o
 
 PRT_AMDL_SRCS = \
-    prt-amdl.d.o blstio.o
+    prt-amdl.d.o
 
 REDISTRB_SRCS = \
     redistrb.d.o ofiles.o length.o lir.d.o vinta.d.o \
-    rnmean.d.o spline.d.o blstio.o
+    rnmean.d.o spline.d.o
 
 REDISTRB_C_SRCS = \
     redistrb.c.d.o srdist.c.d.o rseta4.c.d.o ofiles.c.o \
     length.o lir.d.o lirt.d.o vinta.d.o derive.d.o \
-    rnmean.d.o blstio.o
+    rnmean.d.o
 
 RES_AMDE_SRCS = \
-    res-amde.d.o blstio.o
+    res-amde.d.o
 
 SCAN_AGSM_SRCS = \
-    scan-agsm.d.o blstio.o
+    scan-agsm.d.o
 
 SCAN_AMDE_SRCS = \
-    scan-amde.d.o blstio.o
+    scan-amde.d.o
 
 SCAN_AMDL_SRCS = \
-    scan-amdl.d.o blstio.o
+    scan-amdl.d.o
 
 SCAN_SSM_SRCS = \
-    scan-ssm.d.o blstio.o
+    scan-ssm.d.o
 
 SEL_AMDL_SRCS = \
-    sel-amdl.d.o blstio.o
+    sel-amdl.d.o
 
 SELAMDE_SRCS = \
     selamde.d.o ofiles.o length.o inrnge.o \
-    rdfreq.d.o setssm.d.o skpcom.o blstio.o
+    rdfreq.d.o setssm.d.o skpcom.o
 
 SELSUM_SRCS = \
     selsum.d.o ofiles.o length.o inrnge.o \
-    rdfreq.d.o setssm.d.o skpcom.o blstio.o
+    rdfreq.d.o setssm.d.o skpcom.o
 
 SET_ASSCAL_SRCS = \
     set-asscal.d.o rdamdl.n.d.o ofiles.o length.o \
-    squint.d.o vinta.d.o lir.d.o blstio.o
+    squint.d.o vinta.d.o lir.d.o
 
 SET_DNL_SRCS = \
-    set-dnl.d.o rdfreq.d.o skpcom.o blstio.o
+    set-dnl.d.o rdfreq.d.o skpcom.o
 
 SET_OBS_SRCS = \
-    set-obs.d.o rdfreq.d.o skpcom.o blstio.o
+    set-obs.d.o rdfreq.d.o skpcom.o
 
 SETEXEC_SRCS = \
     setexec.d.o rdfreq.d.o ofiles.o length.o \
-    skpcom.o blstio.o
+    skpcom.o
 
 SORTSUM_SRCS = \
     sortsum.d.o rdfreq.d.o rdilst.o iprsgn.d.o \
-    sort.d.o skpcom.o ofiles.o length.o blstio.o
+    sort.d.o skpcom.o ofiles.o length.o
 
 #################################################################
 #