Merge remote-tracking branch 'origin' into EbF/update_massive_star_test_suites

Author: Debraheem

astero/defaults/astero_search.defaults

@@ -49,7 +49,7 @@
    ! + ``Rcz``
 
    ! where ``M_H``, ``surface_Z_div_X``, ``surface_He`` and ``Rcz``
-   ! are now implemented in the standard ``run_star_extras.f90`.
+   ! are now implemented in the standard ``run_star_extras.f90``.
    ! The other options fall back to the history columns.
 
    ! To implement your own constraints, create the appropriate case
@@ -85,6 +85,8 @@
    ! constraint_sigma(:)
    ! ~~~~~~~~~~~~~~~~~~~
 
+   ! ::
+
       constraint_name(:) = '' ! change this to whatever you want
       constraint_target(:) = 0
       constraint_sigma(:) = 0
@@ -102,7 +104,7 @@
    ! Z_div_X_solar
    ! ~~~~~~~~~~~~~
    ! Convenience parameter leftover from the old interface that
-   ! can be used when calculating things relative to solar metallicity.
+   ! can be used when calculating things relative to solar metallicity. ::
 
       Z_div_X_solar = 0.02293d0
 
@@ -130,7 +132,7 @@
 
    ! dt_for_smaller_steps_before_age_target
    ! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   ! This should be much smaller than ``age_sigma``.
+   ! This should be much smaller than ``age_sigma``. ::
 
       dt_for_smaller_steps_before_age_target = 0.0065d8 ! 1/10 age_sigma
 
@@ -570,6 +572,7 @@
    ! parameters in the ``set_param`` subroutine in
    ! ``run_star_extras.f90``, or rely on the default
    ! implementation, which provides the legacy options
+
    ! * ``initial_mass``
    ! * ``initial_Y``
    ! * ``initial_FeH``
@@ -587,7 +590,7 @@
    ! ~~~~~~~~~~
    ! If ``.true.``, that parameter will be varied by the search.
    ! If ``.false.``, that parameter will be fixed at the first value
-   ! (see ``first_param``).
+   ! (see ``first_param``). ::
 
       vary_param(:) = .false.
 
@@ -621,7 +624,7 @@
    ! ~~~~
    ! Legacy controls from the old interface, which is available with
    ! the default ``run_star_extras.f90`` by using the parameter names
-   ! ``initial_Y`` and ``initial_FeH`.
+   ! ``initial_Y`` and ``initial_FeH``.
 
    ! If ``Y_depends_on_Z = .false.``, ``Y`` is a parameter like any other and you should set
    ! ``vary_Y``, ``first_Y``, ``min_Y`` and ``max_Y`` (and ``delta_Y`` for a grid).
@@ -941,7 +944,7 @@
    ! ~~~~~~~~~~~~~~~~~~~~~~~~~
 
    ! Formats for writing floats (reals), integers and characters
-   ! (strings) to the results file.
+   ! (strings) to the results file. ::
 
       astero_results_dbl_format = '(1pes26.16)'
       astero_results_int_format = '(i26)'
@@ -1166,16 +1169,16 @@
    ! The GYRE controls are read from the ``gyre_input_file``.
    ! Rich offers the following comments on setting them:
 
-   ! > I suggest setting freq_min to 0.9*MINVAL(l0_obs),
-   ! > and freq_max to 1.1*MAXVAL(l0_obs)
-   ! > (similarly for the other l values).
+   !  I suggest setting freq_min to 0.9*MINVAL(l0_obs),
+   !  and freq_max to 1.1*MAXVAL(l0_obs)
+   !  (similarly for the other l values).
 
-   ! > freq_units should be 'UHZ',
-   ! > and set grid_type to 'LINEAR'.
+   !  freq_units should be 'UHZ',
+   !  and set grid_type to 'LINEAR'.
 
-   ! > For n_freq, I suggest either setting it to 10*(freq_max - freq_min)/dfreq,
-   ! > where dfreq is the estimated frequency spacing; or, set it to 10*nl0.
-   ! > The factor 10 is arbitrary, but seems to be a good safety factor.
+   !  For n_freq, I suggest either setting it to 10*(freq_max - freq_min)/dfreq,
+   !  where dfreq is the estimated frequency spacing; or, set it to 10*nl0.
+   !  The factor 10 is arbitrary, but seems to be a good safety factor.
 
    ! gyre_input_file
    ! ~~~~~~~~~~~~~~~

docs/requirements.txt

@@ -2,5 +2,5 @@
 # Defining the exact version will make sure things don't break
 sphinx==5.3.0
 sphinx_rtd_theme==1.1.1
-readthedocs-sphinx-search==0.1.1
+readthedocs-sphinx-search==0.3.2
 

docs/source/changelog.rst

@@ -77,6 +77,16 @@ produced GYRE-format files that are backward-compatible with older
 GYRE releases. (If using GSM-format files, set to 110 instead for
 backward compatibility).
 
+White Dwarf O/Ne Phase Separation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Phase separation for crystallizing white dwarfs now supports options
+for either C/O or O/Ne phase diagrams. You can select the appropriate
+option with the ``phase_separation_option`` in the ``&controls`` inlist
+section (see documentation at :ref:`reference/controls:phase_separation_option`).
+The phase diagram for O/Ne separation comes from
+`Blouin & Daligault (2021b) <https://ui.adsabs.harvard.edu/abs/2021ApJ...919...87B/abstract>`_.
+
 Massive Star test_suite Updates
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 The ``12Msun_pre_ms_to_core_collapse``, ``20Msun_pre_ms_to_core_collapse``, and ``zams_to_cc_80``
@@ -99,6 +109,10 @@ starting models has been recalculated with a more stringent stopping condition,
 and now all pre-computed ZAMS models have a central hydrogen mass fraction very 
 near 0.697.
 
+The ``fixed_Teff``, ``fixed_Tsurf``, ``fixed_Psurf``,  and ``fixed_Psurf_and_Tsurf``
+atmosphere options have been reimplemented, although we caution users that their
+implementation might conflict with mlt_option = ``TDC``.
+
 Changes in r23.05.1
 ===================
 

docs/source/developing/collaboration.rst

@@ -27,7 +27,7 @@ MESA (e.g., contribute a hook/routine, make a pull request).
 
 *MESA Developers (MD)*: These are individuals committed to improving
 MESA and its infrastructure (e.g., the MESA Test Hub). Instructions on how to become
-a developer are found :doc:`here <developing/new_developers>`.
+a developer are found :doc:`here <new_developers>`.
 
 Responsibilities
 of developers include:
@@ -92,7 +92,7 @@ fulfill their responsibilities, they must inform the MD.
 Removal from MD, MTC, and MAC can be for inactivity,
 harm to the Project, or simply opting out.
 
-Onboarding to the MD is described :doc:`here <developing/new_developers>`.
+Onboarding to the MD is described :doc:`here <new_developers>`.
 
 Instrument Paper Principles
 ===========================

docs/source/installation.rst

@@ -108,6 +108,9 @@ uses export to set variables):
     export MESASDK_ROOT=/Applications/mesasdk
     source $MESASDK_ROOT/bin/mesasdk_init.sh
 
+    # add shmesa (the MESA command line tool) to your PATH 
+    export PATH=$PATH:$MESA_DIR/scripts/shmesa
+
 
 If your machine uses csh as its shell, use ``setenv`` instead of ``export``.
 

docs/source/news/2016-02-03-r8118.rst

@@ -12,7 +12,7 @@ post <https://lists.mesastar.org/pipermail/mesa-users/2016-February/006205.html>
 to learn more.
 
 -  Almost all extras routines in run_star_extras and run_binary_extras
-   are now implemented as hooks, in a similar way to all other_\*
+   are now implemented as hooks, in a similar way to all ``other_\*``
    routines. If you use a custom run_star_extras, you need to slightly
    modify it for it to be compatible with this and future versions.
 

docs/source/news/2017-09-01-three-updates.rst

@@ -8,33 +8,27 @@ This week has seen three new/updated projects announced on mesa-users.
 announces <https://lists.mesastar.org/pipermail/mesa-users/2017-August/007853.html>`__
 `MESA-Docker <https://github.com/evbauer/MESA-Docker>`__:
 
-::
-
-   It’s a Docker container with MESA already installed, and it should
+   *It’s a Docker container with MESA already installed, and it should
    work with any OS that supports Docker, including Windows 10.  This
    should serve as a useful tool for those who are ready to invest
    some extra effort to step beyond the limited options of MESA-Web,
    but not yet comfortable configuring their environment for full
-   installation.
+   installation.*
 
 `Rob Farmer
 announces <https://lists.mesastar.org/pipermail/mesa-users/2017-August/007856.html>`__
 `pyMesa <https://github.com/rjfarmer/pyMesa>`__:
 
-::
-
-   This is a set of low level python bindings for MESA to allow easy
+   *This is a set of low level python bindings for MESA to allow easy
    access to the individual MESA modules.  This is aimed for those
    people who want to quickly get a result from a MESA module and
    don’t want to worry about getting fortran code compiled and
-   working.
+   working.*
 
 `Carl Fields
 announces <https://lists.mesastar.org/pipermail/mesa-users/2017-September/007864.html>`__
 updates to `MESA-Web <http://mesa-web.asu.edu/>`__:
 
-::
-
-   1. Users can now choose to upload a custom reaction rate.
-   2. More mixing parameters available for calculations.
-   3. Jobs now run for 4hrs or until iron core collapse.
+   1. *Users can now choose to upload a custom reaction rate.*
+   2. *More mixing parameters available for calculations.*
+   3. *Jobs now run for 4hrs or until iron core collapse.*

docs/source/summer_schools.rst

@@ -1,31 +1,31 @@
 MESA Summer Schools
-=================
+===================
 
 ***
 MESA Summer School Programs -- this page under construction!
 ***
 
 History of the MESA Summer School Program
---------------------
+-----------------------------------------
 
 The MESA Summer Schools have traditionally been held in Santa Barbara, California, until 2022. The 2023 MESA Summer School program, branded as MESA@Konkoly, was held in Budapest, Hungary. As of 2023, MESA Summer Schools can be run anywhere in the world. The involvement of the MESA developers is encouraged, and we are happy to help. 
 
 
 How to run a MESA Summer School
---------------------
+-------------------------------
 
 Preparing a good program takes about a year. Historically, the program has taken place in the middle of August. Assuming this timing, preparations for next year's program should begin in September.
 
 
 1 year + out (September/October)
---------------------
+--------------------------------
 
 - Book a venue
 - Choose your organizational team
 
 
 9 months out (November)
---------------------
+-----------------------
 
 - Contact lecturers. Try to invite people with a diverse set of research areas and consider focusing on topics that have not been covered in past programs (see previous summer school pages and agendas for this information)
-- Contact TAs. 
+- Contact TAs. 

scripts/shmesa/README.md

@@ -0,0 +1,125 @@
+**shmesa**: a set of bash utilities providing convenience functions for MESA 
+
+To install, simply add `PATH=$PATH:$MESA_DIR/scripts/shmesa` to your `~/.bashrc` and start a new terminal.
+
+To use, simply call: `shmesa`
+
+```bash
+> shmesa
+      _     __  __ _____ ____    _
+  ___| |__ |  \/  | ____/ ___|  / \
+ / __| '_ \| |\/| |  _| \___ \ / _ \
+ \__ \ | | | |  | | |___ ___) / ___ \
+ |___/_| |_|_|  |_|_____|____/_/   \_\
+
+Usage: shmesa [work|change|defaults|cp|grep|extras|zip|help] [arguments]
+
+Subcommands:
+  work      copy the work directory to the current location
+  change    change a parameter in the given inlist
+  defaults  copy the history/profile defaults to the current location
+  cp        copy a MESA directory without copying LOGS, photos, etc.
+  grep      search the MESA source code for a given string
+  extras    fill in the full run_star_extras.f90 template
+  zip       prepare a MESA directory for sharing
+  help      display this helpful message
+  -h        get additional details about any of the above
+```
+
+Want more details about any of the subprograms? Just run any of them with `-h`, for example 
+```bash
+> shmesa cp -h
+Usage: shmesa cp source_dir target_dir
+Copies a MESA working directory but without copying LOGS, photos, or .mesa_temp_cache
+```
+
+### Some example usage 
+You can use this for example to make a grid of models, and e.g. include the output `delta_nu` and `nu_max` in `LOGS` with 
+```bash
+### Make a grid in M and Z in a few lines of bash
+
+# copy over a new work directory 
+shmesa work "grid_dir"
+cd grid_dir
+./mk
+
+# output asteroseismic quantities in `LOGS/history.data` 
+shmesa defaults delta_nu nu_max
+
+# loop through values of M and Z and run MESA 
+for M in 1.0 1.5 2.0; do 
+    for Z in 0.01 0.02 0.03; do 
+        shmesa change inlist_project \
+            initial_mass $M \
+            Zbase $Z \
+            initial_z $Z
+        ./star inlist_project 
+        mv LOGS "M='$M'_'Z='$Z'" 
+    done 
+done 
+
+```
+
+
+### Tests
+There is functionality for testing all the subprograms:
+
+```bash
+> shmesa test
+>> TESTING SHMESA <<
+
+>>> test: shmesa work
+SHMESA> DEBUG: Calling work with arguments: shmesa_test_work
+gfortran -Wno-uninitialized -fno-range-check -fmax-errors=7  -fprotect-parens -fno-sign-zero ...
+<<< success
+
+
+>>> test: shmesa change
+SHMESA> DEBUG: Calling change with arguments: inlist_project pgstar_flag .false.
+SHMESA> DEBUG: SHMESA> BACKING UP: inlist_project inlist_project.bak
+SHMESA> DEBUG: Calling change with arguments: inlist_project initial_mass 1.2 Z 0.01 Zbase 0.01
+SHMESA> DEBUG: SHMESA> BACKING UP: inlist_project inlist_project.bak
+<<< success
+
+...
+
+>>> test: shmesa defaults
+SHMESA> DEBUG: Calling defaults with arguments: nu_max delta_nu
+SHMESA> DEBUG: Calling defaults with arguments: logM
+SHMESA> DEBUG: SHMESA> BACKING UP: profile_columns.list
+SHMESA> DEBUG: SHMESA> BACKING UP: history_columns.list
+<<< success
+
+all done!
+```
+
+### Development
+There's instructions inside the code for adding a new bash subprogram to this driver: 
+```bash
+    ### DEVELOPMENT USE 
+    ### TEMPLATE FOR NEW SHMESA FUNCTIONS 
+    shmesa_template () {
+        if shmesa_check_h_flag "$@"; then
+            echo "Usage: mesa funcname arg [optional arg]"
+            echo "put discription here"
+            return 0
+        fi
+
+        UNTESTED # comment this out when done (crashes the program to avoid problems)
+
+        # parse required variables 
+        local example_var=5 
+        if [[ ! -z $1 ]]; then # check if it's set 
+            example_var=$1
+        #else # uncomment if you want this to be a required variable
+        #    echo "Error: "
+        #    return 1
+        fi
+        #shift # and then copy this block to parse the next one, for example 
+
+        # afterwards, update:
+        # 1. shmesa_test 
+        # 2. shmesa_help 
+        # 3. parser at the end of this file 
+    }
+```