Cite:
MESA2HYDRO is now written in Python3. The most up-to-date documentation is here on GitHub.
The cython package is no longer a dependency!
Read the paper
Refereed: https://iopscience.iop.org/article/10.3847/1538-4357/ab3405/meta
Free: https://arxiv.org/abs/1907.09062
Read the User's Guide (WARNING: updated less frequently):
https://github.com/mjoyceGR/MESA2HYDRO/blob/master/DOCUMENTATION/MESA2HYDRO_users_guide.pdf
From discrete stellar structure data in the style of MESA (http://mesa.sourceforge.net/) density profiles, this package creates initial conditions (IC) files readable by smoothed-particle hydrodynamics (SPH) codes such as Phantom (https://phantomsph.bitbucket.io/).
The primary purpose of this software is to generate "NR" files, which contain coordinates parameterizing the mass distribution of an arbitrary model star to arbitrary depth.
An NR file is a basic text file containing 4 columns of numerical data: (1) integer N (dimensionless), (2) radii (cm), (3) masses M (grams), and (4) internal energy (ergs).
The first column contains the integer used by HEALPix to determine the number of particles (np) distributed over a spherical shell--see the HEALPix papers for more information.
The radii represent midpoint values rmid = (ru + rl) / 2 , in physical units (cm), corresponding to the radius at which a given shell must be placed in order to recast the mass contained in a region ru - rl as a shellular distribution of particles. The third column contains the mass contained in the computed interval. The fourth contains the internal energy (cgs units) at the midpoint radius. The length of the file corresponds to the number of shells needed to reconstruct the sampled 1D density profile as a 3D particle distribution built of concentric shells.
Cloning this git repository (or downloading the tarball) is the safest way to collect all software and dependencies:
git clone https://github.com/mjoyceGR/MESA2HYDRO.git
Download and upack the .zip file via
unzip MESA2HYDRO-master.zip
Download and upack a .tar file via
tar -xvf MESA2HYDRO-master.tar
After cloning or unpacking, move to the head directory via
cd MESA2HYDRO/
Issue the following command in the top level directory
python3 local_setup.py
to install the package locally.
To compile the Fortran components separately before installation, run
./setup.py build_ext
followed by
./setup.py install --user
MESA2HYDRO is also theoretically available via pip, but this will not be updated as frequently as the git repo. WARNING: some issues may occur if you have multiple versions of pip installed.
Using pip3, run
pip3 install MESA2HYDRO
In some cases, "pip" and "python" can/should replace "pip3" and "python3", respectively (i.e. if your default version is Python3)
To upgrade, run
pip install --upgrade MESA2HYDRO==1.1.XXXX
where 0.1.XXXX is the lastest version number on https://pypi.org/manage/project/MESA2HYDRO/releases/
Sometimes the error
ERROR: Cannot uninstall 'MESA2HYDRO'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
is triggered by an attempt to use pip install --upgrade. As a workaround, remove any current installation of MESA2HYDRO, followed by
pip install MESA2HYDRO==0.1.XXXX
or
pip install MESA2HYDRO
for the most recent version.
If you've failed to specify pip3 and have other versions of Python installed, the package may end up somewhere unexpected. You can locate the package by typing
pip show MESA2HYDRO
You may want to copy or move the entire MESA2HYDRO root directory somewhere where it is easier to work out of directly
mv MESA2HYDRO/ /home/your_name/
From there, you should set the $MESA2HYDRO_ROOT environment variable in your .bashrc to point to the root directory:
export MESA2HYDRO_ROOT=/home/your_name/MESA2HYDRO
Then
cd MESA2HYDRO/work/
and follow the instructions for Running a Test Case. No additional setup or compilation should be required if installed via pip.
For a complete list of Python and external software dependencies, see the Prerequisites section of the user's guide. This project was developed with MESA version 10398 and uses example inlists and input models (e.g. wd.mod) included in mesa-r10398. Neither Phantom nor MESA is required for operation, but we recommend these two packages.
To run a basic MESA2HYDRO calculation, move to the work directory via
cd MESA2HYDRO/work/
Basic operation proceeds via
python3 run_conversion.py mainsequence.cfg
where mainsequence.cfg is a configuration file. These are the files that the user should modify to suit their problem.
Failure may be caused by missing packages. The user must have, at minimum, the following Python3 and external packages installed on their machine:
healpy
matplotlib
numpy
python-tk
scipy.interpolate
scipy.optimize
If they were not automatically installed via pip or the setup procedure, these can be installed from the command line via, e.g.,
sudo apt-get install python3-numpy
or similarly via, e.g.,
pip3 install numpy
The authors have had better results installing these additional libraries via command line rather than through pip.
In particular, one must have numerical and other libraries required by healpy/HEALPix (https://healpy.readthedocs.io/en/latest/) installed on their machine. More information on dealing with healpy can be found at https://healpy.readthedocs.io/en/latest/install.html
Some failures to install can be rectified by installing python3-dev via
sudo apt-get install python3-dev
In your Python3 environment is out of date, the following set of commands may solve this:
sudo apt update
sudo apt upgrade
sudo apt-get install --reinstall python3-apt
sudo apt install python3.7 python3.7-dev python3.7-venv
You can then install the required dependencies via
sudo apt-get install python3-matplotlib
sudo apt-get install python3-scipy
sudo apt-get install python3-h5py
sudo apt-get install python3-healpy
or equivalent. See "requirements.txt" in the top MESA2HYDRO directory for all dependencies