Merge branch 'main' into restore_convective_bdy_weight

Author: evbauer

.gitignore

@@ -98,3 +98,4 @@ testhub.yml
 .mesa_temp_cache/
 TAGS
 .vscode
+.idea

CITATIONS.bib

@@ -94,19 +94,22 @@ @ARTICLE{Paxton2019
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@ARTICLE{Jermyn2022,
-       author = {{Jermyn}, Adam S. and {Bauer}, Evan B. and {Schwab}, Josiah and {Farmer}, R. and {Ball}, Warrick H. and {Bellinger}, Earl P. and {Dotter}, Aaron and {Joyce}, Meridith and {Marchant}, Pablo and {Mombarg}, Joey S.~G. and {Wolf}, William M. and {Wong}, Tin Long Sunny and {Cinquegrana}, Giulia C. and {Farrell}, Eoin and {Smolec}, R. and {Thoul}, Anne and {Cantiello}, Matteo and {Herwig}, Falk and {Toloza}, Odette and {Bildsten}, Lars and {Townsend}, Richard H.~D. and {Timmes}, F.~X.},
-        title = "{Modules for Experiments in Stellar Astrophysics (MESA): Time-Dependent Convection, Energy Conservation, Automatic Differentiation, and Infrastructure}",
-      journal = {arXiv e-prints},
-     keywords = {Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics},
-         year = 2022,
-        month = {dec},
-          eid = {arXiv:2208.03651},
-        pages = {arXiv:2208.03651},
+@ARTICLE{Jermyn2023,
+       author = {{Jermyn}, Adam S. and {Bauer}, Evan B. and {Schwab}, Josiah and {Farmer}, R. and {Ball}, Warrick H. and {Bellinger}, Earl P. and {Dotter}, Aaron and {Joyce}, Meridith and {Marchant}, Pablo and {Mombarg}, Joey S.~G. and {Wolf}, William M. and {Sunny Wong}, Tin Long and {Cinquegrana}, Giulia C. and {Farrell}, Eoin and {Smolec}, R. and {Thoul}, Anne and {Cantiello}, Matteo and {Herwig}, Falk and {Toloza}, Odette and {Bildsten}, Lars and {Townsend}, Richard H.~D. and {Timmes}, F.~X.},
+        title = "{Modules for Experiments in Stellar Astrophysics (MESA): Time-dependent Convection, Energy Conservation, Automatic Differentiation, and Infrastructure}",
+      journal = {\apjs},
+     keywords = {Stellar physics, Stellar evolution, Stellar evolutionary models, Computational methods, 1621, 1599, 2046, 1965, Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics},
+         year = 2023,
+        month = mar,
+       volume = {265},
+       number = {1},
+          eid = {15},
+        pages = {15},
+          doi = {10.3847/1538-4365/acae8d},
 archivePrefix = {arXiv},
        eprint = {2208.03651},
  primaryClass = {astro-ph.SR},
-       adsurl = {https://ui.adsabs.harvard.edu/abs/2022arXiv220803651J},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2023ApJS..265...15J},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 

chem/public/chem_def.f90

@@ -117,7 +117,7 @@ module chem_def
             'californium','einsteinium','fermium','mendelevium', &
             'nobelium','lawrencium','rutherfordium','dubnium', &
             'seaborgium','bohrium','hassium','meitnerium','darmstadtium', &
-            'roentgenium','copernicum' ]
+            'roentgenium','copernicium' ]
 
       ! aluminum isomers
       character(len=iso_name_length), dimension(2:3) :: &

docs/source/about.rst

@@ -110,6 +110,7 @@ Developers
 * `Lars Bildsten <http://www.kitp.ucsb.edu/bildsten/>`__
 * `Matteo Cantiello <http://www.matteocantiello.com/>`__
 * Aaron Dotter
+* Matthias Fabry
 * `Robert Farmer <http://rjfarmer.io/>`__
 * Eoin Farrell
 * `Meridith Joyce <http://www.meridithjoyce.com/>`__

docs/source/changelog.rst

@@ -45,6 +45,40 @@ like to see the changes without modifying the file.
 
 ``sed`` is a standard tool that is included with macOS and most Linux distributions.
 
+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.
 
 Changes in r22.11.1
 ===================

docs/source/test_suite.rst

@@ -485,6 +485,12 @@ This test checks the counter and timing routines with a 1.5 Msun, Z=0.02 metalli
 This test case exercise the capability to simultaneously evolve two model stars.
 The test vehicle is a pair of 15 Msun, Z=0.02 metallicity, models one with overshooting and one without overshooting.
 
+
+:ref:`tzo`
+^^^^^^^^^^
+
+This test case creates a Thorne-Zytkow object (TZO) and evolves until the NS has accreted a small amount of material.
+
 :ref:`wd_c_core_ignition`
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 

docs/source/test_suite/tzo.rst

@@ -0,0 +1 @@
+../../../star/test_suite/tzo/README.rst

docs/source/using_mesa/best_practices.rst

@@ -455,7 +455,7 @@ that is:
 .. code-block:: latex
 
   Modules for Experiments in Stellar Astrophysics
-  \citep[MESA][]{Paxton2011, Paxton2013, Paxton2015, Paxton2018, Paxton2019, Jermyn2022}.
+  \citep[MESA][]{Paxton2011, Paxton2013, Paxton2015, Paxton2018, Paxton2019, Jermyn2023}.
 
 
 MESA critically rests on the hard work of many researchers who have

linters/README.rst

@@ -99,3 +99,9 @@ fix_inlists.py
 --------------
 
 Fixes various controls in the test_suite inlists that should not be enabled by default.
+
+
+update_ctrls.py
+---------------
+
+This handles the replacement of ``s%`` with ``s% ctrl%`` while being smart about only doing that to controls.

linters/update_ctrls.py

@@ -0,0 +1,203 @@
+#!/usr/bin/env python
+
+# This file is designed to handle moving controls from s% xx to s% ctrl %xx
+# While this replicates alot of check_defaults.py we want this to be standalone
+# and only depend on the python stdlib. This way users can easily use it to port their
+# run_star_extras.f90 files without needing to worry about python packaging.
+
+# Usage: python update_ctrls.up file1.f90 file2.f90 ....
+
+# Note this only works for s% (or s %) it does not work if you renamed the star_type varaible 
+# to something other than s, for instance in the binary module.
+
+import os
+import re
+from collections.abc import MutableSet
+import functools
+import operator
+import sys
+
+
+MESA_DIR = os.environ["MESA_DIR"]
+
+ctrls_files = [ os.path.join("star_data","private","star_controls.inc"),
+                os.path.join("star_data","private","star_controls_dev.inc")
+            ]
+
+CRTL_NAME = 's% ctrl% '
+
+# inspiration from https://stackoverflow.com/a/27531275
+class CaseInsensitiveSet(MutableSet):
+    def __init__(self, iterable):
+        self._values = {}
+        self._fold = str.casefold
+        for v in iterable:
+            self.add(v)
+
+    def __repr__(self):
+        return repr(self._values.values())
+
+    def __contains__(self, value):
+        return self._fold(value) in self._values
+
+    def __iter__(self):
+        return iter(self._values.values())
+
+    def __len__(self):
+        return len(self._values)
+
+    def items(self):
+        return self._values.items()
+
+    def add(self, value):
+        if isinstance(value, CaseInsensitiveSet):
+            for k,v in value.items():
+                self._values[self._fold(k)] = v
+        else:
+            self._values[self._fold(value)] = value
+
+        
+    def discard(self, value):
+        v = self._fold(value)
+        if v in self._values:
+            del self._values[v]
+
+
+def get_options(filename, regexp):
+    """Return a set of MESA option names"""
+    r = re.compile(regexp)
+    with open(os.path.join(MESA_DIR, filename)) as f:
+        matches = r.finditer(f.read())
+    return CaseInsensitiveSet(m.group(1) for m in matches)
+
+
+def get_columns(filename, regexp):
+    """Return a set of MESA column names"""
+    r = re.compile(regexp)
+    with open(os.path.join(MESA_DIR, filename)) as f:
+        lines = f.readlines()
+    matches = []
+    for line in lines:
+        m = r.match(line)
+        if m is not None:
+            matches.append(m.group(1))
+    return CaseInsensitiveSet(matches)
+
+def get_defaults(filename):
+    # extract column names from defaults file
+
+    # these lines look like:
+    #  ! initial_mass = 1
+    #  ? ^^^^^^^^^
+    # that is, they may or may not be commented out
+    # and may or may not have a( )
+    # and may or may not have space before a =
+
+    regexp = "^[ \t]*[ ]?(\w+)(\(.*\))*[ ^t]*="
+
+    return get_columns(filename, regexp)
+
+def load_file(filename):
+    with open(os.path.join(MESA_DIR, filename),"r") as f:
+        lines = f.readlines()
+
+    return lines
+
+
+def get_inc(filename):
+    # extract options from a inc file
+    lines = load_file(filename)
+
+    # Remove line continutaion characters
+    lines = [i.replace("&","").strip() for i in lines if i]
+
+    # Remove type defintion (i.e real(dp) :: x) leaves just x
+    # as well as anything that starstwith a comment or has a comment embeded in it
+    for idl,line in enumerate(lines):
+        if "::" in line:
+            lines[idl] = line.split("::")[1].strip()
+
+    lines = [i.split(",") for i in lines  if i]
+
+    # Flatten list of lists
+    lines = functools.reduce(operator.iconcat, lines, [])
+
+    # Remove array sizes from variables
+    lines  = [line.split("(")[0] for line in lines if line]
+    
+    # Remove comments
+    lines = [line.split("!")[0] for line in lines if line]
+
+    # Remove = x 
+    lines  = [line.split("=")[0] for line in lines if line]
+
+    # Remove remaining empty strings
+    lines  = [line.strip() for line in lines if line]
+
+    return CaseInsensitiveSet(lines)
+
+# Load controls names
+cinc = get_inc(ctrls_files[0])
+
+for f in ctrls_files[1:]:
+    cinc.add(get_inc(f))
+
+
+def update(filename):
+    try:
+        lines = load_file(filename)
+    except (UnicodeDecodeError, IsADirectoryError):
+        return
+        
+    " s[0 or more space] % [0 or more space] [1 or more character or number or _]"
+    # This wont match when s has been renamed 
+    regex_all = "(s[ \t]?[a-zA-Z0-9_]?%[ \t]?[a-zA-Z0-9_]*)"
+
+    " s [0 or more space] % [0 or more space] "
+    regex_s = 's[ \ta-zA-Z0-9_]?%[ \t]?'
+
+    r_all = re.compile(regex_all)
+    r_s = re.compile(regex_s)
+
+    for idl,line in enumerate(lines):
+        # Split on s% something
+        line_split = re.split(regex_all,line)
+        for idm,match in enumerate(line_split):
+            # Remove the s% so we can check if the variable is a control
+            var = match.replace('s%','').strip()
+            if var in cinc:
+                # If it is a control then replace s% with CRTL_NAME
+                line_split[idm] = re.sub(regex_s,CRTL_NAME,match)
+        lines[idl] = ''.join(line_split)
+
+    with open(filename,'w') as f:
+        f.writelines(lines)
+
+if __name__ == "__main__":
+    for i in sys.argv[1:]:
+        update(i)
+
+# Run over MESA_DIR
+
+# python3 linters/update_ctrls.py star/test/src/*
+# python3 linters/update_ctrls.py star/work/src/*
+# python3 linters/update_ctrls.py star/job/*
+# python3 linters/update_ctrls.py star/p*/*.f90 
+# python3 linters/update_ctrls.py star/test_suite/*/src/*.f90
+# python3 linters/update_ctrls.py star/other/*.f90
+# python3 linters/update_ctrls.py */test_suite/*/src/*.inc
+# python3 linters/update_ctrls.py */test_suite/*/src/*/*.inc
+
+# python3 linters/update_ctrls.py binary/test/src/*
+# python3 linters/update_ctrls.py binary/work/src/*
+# python3 linters/update_ctrls.py binary/job/*
+# python3 linters/update_ctrls.py binary/p*/*.f90 
+# python3 linters/update_ctrls.py binary/test_suite/*/src/*.f90
+# python3 linters/update_ctrls.py binary/other/*.f90
+
+# python3 linters/update_ctrls.py astero/test/src/*
+# python3 linters/update_ctrls.py astero/work/src/*
+# python3 linters/update_ctrls.py astero/job/*
+# python3 linters/update_ctrls.py astero/p*/*.f90 
+# python3 linters/update_ctrls.py astero/test_suite/*/src/*.f90
+# python3 linters/update_ctrls.py astero/other/*.f90