While experimenting with MESA and developing setups, I often compare
inlists (for single and/or binary stars) with each other. A simple
diff is often not informative because of the comments, non-matching
order of the entries, or missing entries in one file that are present
in the other file, but have no effect because they are set to the
defaults. For this reason, I’ve written the (executable) script compare_inlists.py
which can print an option-by-option diff of two inlists, ignoring
comments and empty lines, and checking the defaults from the
documentation when entries are missing. It assumes you use the same
MESA version for both inlists for this last task.
This can be used inside of scripts or notebooks, or from command line (which is the usual way I do it), thanks to click.
Install the latest version from this repository:
$ pip install git+https://github.com/mathren/compare_workdir_MESA/This script is in src/compare_workdir/ and does a one-to-one
comparison of two inlists (without considering nested inlist that
might overwrite settings in the inlists considered).
# if installed with pip
compare_inlists --help
# if just cloned the repository
python /path/to/repo/compare_inlists.py --help
Usage: compare_inlists.py [OPTIONS] INLIST1 INLIST2
Options:
--pgstar TEXT Show also diff of pgstar namelists.
--mesa_dir TEXT use customized location of $MESA_DIR. Will use environment
variable if empty.
--vb TEXT Show also matching lines using green.
--help Show this message and exit.
It uses termcolor to print in red entries that differ between
two inlists, and, if invoked adding --vb=True (for verbose) from the command
line it will also print in green entries that are equal. If one entry
is in one inlist but not the other, but the inlist that contains it
has the default value, it is considered as a “green” entry.
This has been tested with MESA version 12778 or later, and works for inlists
for single stars and binaries (but will refuse to compare an
inlist_binary with an inlist for a single star). It can take a
customized $MESA_DIR with the optional argument --mesa_dir. If not
provided it will use the $MESA_DIR environment variable currently
set.
By default the comparison between pgstar namelist is disabled because
I need it less, but it can be enabled using --pgstar=True.
A screenshot of an example with --vb=True and $MESA_DIR set as
environment variable:
Note that if you installed this package with pip you can call this
script with compare_inlists from anywhere (without typing python, the
path to the script, and the extension).
This script is in src/compare_workdir/ and does a one-to-one
comparison of two inlists (following down the rabbit hole of nesting).
MESA allows to nest namelists (i.e., star_job, controls, and/or
pgstar, and their binary counterparts) using read_extra_star_job_inlist* and
extra_star_job_inlist*_name (and similar). The script compare_all_work_dir_inlists.py uses
the functions defined in compare_inlists.py to compare the entire MESA
setup of two work directories, taking care of nested inlist that might
over-write each others.
It will not work to compare a work directory for a single star with a
work directory for a binary. However, the functions in the
compare_inlists.py and compare_all_work_dir_inlists.py could be
used to create a comparison (e.g., of a single star with the donor of
a binary).
As compare_inlists.py, it can be used inside of scripts or notebooks, or from command line.
# if installed with pip
compare_all_workdir_inlists --help
# if just cloned the repository
python /path/to/repo/src/compare_workdir/compare_all_work_dir_inlists.py --help
Usage: compare_all_workdir_inlists.py [OPTIONS] WORK_DIR1 WORK_DIR2
Options:
--pgstar TEXT Show also diff of pgstar namelists.
--mesa_dir TEXT use customized location of $MESA_DIR. Will use environment
variable if empty and return an error if empty.
--vb TEXT Show also matching lines using green.
--help Show this message and exit.
If called on a pair of folders both for single stars (or both for
binaries), it first builds a “main” dictionary with of all the
options MESA reads for each namelist, starting from inlist and
checking if it contains nested namelists. It then performs the
comparison of the “main” dictionaries of the two folders. If the
same read_extra_star_job_inlist* (i.e. same number instead of the
*) appears in multiple nested inlists the last read will over-write
the previous, which is the same behavior as in MESA. Same for controls
and pgstar and the corresponding binary namelists. In the case of
binary folders, it will also compare all the namelists for each of the
stars in the binary. The comparison between the pgstar namelists is
also disabled by default and can be done using --pgstar=True from
command line.
The output is similar to the example above for individual inlists.
Sometimes I need to merge the profiles_columns.list,
history_columns.list, or binary_history_columns.list between two or
more runs. This script does that, once again removing all the comments
(so the merged file won’t be very nice), and not caring about order of
the options. It will check that the lists you want to merge are
compatible and refuse to merge, e.g., a profiles_columns.list with a
history_columns.list. The merged list is printed to a file OUTLIST
specified by the user.
As of now it does not check if the merged list is compatible with the MESA version.
# if installed with pip
merge_column_lists --help
# if just cloned the repository
python /path/to/repo/src/compare_workdir/merge_column_lists.py --help
Usage: merge_column_lists.py [OPTIONS] LIST1 LIST2 OUTLIST
Options:
--mesa_dir TEXT use customized location of $MESA_DIR. Will use environment
variable if empty and return an error if empty.
--help Show this message and exit.
Thanks to brethil for help transforming this into a python package.