NuGridPy is a Python package containing tools to access and analyse (e.g. plot) various output formats (including the hdf5-based se format) from NuGrid codes (mppnp and ppn) and from the MESA stellar evolution code. In principle the NuGridPy package can be used on any stellar evolution code output if the tools to write se hdf5 files available on the NuGrid web page are used. The mesa.py module will work with MESA ASCII output in the 'LOGS' directory.
MOST RECENT SVN REVISION STILL CONTAINING NUGRIDPY: r6619
NuGridPy has been migrated to this github repository from the svn <<<<<<< HEAD:README.md repository. All components present here have now been removed from the svn. Please checkout r6619 if you would like access to the most recent version in the svn prior to NuGridPy's removal.
======= repository. All components present here have now been removed from the svn. Please checkout r6619 if you would like access to the most recent version in the svn prior to NuGridPy's removal.
NuGridPy is a Python package containing tools to access and analyse (e.g. plot) various output formats (including the hdf5-based se format) from NuGrid codes (mppnp and ppn) and from the MESA stellar evolution code. In principle the NuGridPy package can be used on any stellar evolution code output if the tools to write se hdf5 files available on the NuGrid web page are used. The mesa.py module will work with MESA ASCII output in the 'LOGS' directory. These modules were written with an interactive work mode in mind, in particular taking advantage of the interactive ipython session that we usually start with 'ipython --pylab' or inside an ipython notebook.
NuGrid/master:README
These modules were written with an interactive work mode in mind, in
particular taking advantage of the interactive ipython session that we usually
start with ipython --pylab and work inside an ipython or jupyter notebook.
You may also "install" NuGridPy by copying the directory to the site-packages directory wherever your primary python installation lives.
Either way, you should be able to import the mesa (or nugridse or ppn)
module (depending on which type of data you are working with):
from NuGridPy import mesa as ms
and read the docstring:
help(ms)
There are reasonable doc strings in the modules. If you have made tested and debugged improvements we are happy to know about them and we may add them to the release available on the web page. The tools provided here are useful to us, but of course there are still many things that need attention and improvement. We have a good list of scheduled improvements, let us know if you want to help with these. Pull requests and new issues are most welcome!
-
standard:
- xlrd
- numpy
- matplotlib
- h5py
- unittest
-
python2/3 compatibility
- future (provides 'past' and 'builtin' modules)
Most of these are standard. If necessary, you can install them with pip, e.g.
pip install future
To install several required packages at once
sudo pip(3) install -U xlrd future h5py
or, if you want to install in the user home directory,
pip(3) install --user -U xlrd future h5py
- on Fedora python2:
dnf install -y h5py python2-future
If h5py complains about missing hdf5.h or hdf5_hl.h:
sudo apt-get install libhdf5-dev
NuGrid/master:README
- Install ipython and pip:
- port install py34-ipython py34-pip
- port select --set ipython py34-ipython
- port select --set pip py34-pip
- Install standard prerequisites with pip: <<<<<<< HEAD:README.md
- pip install -U --user numpy scipy xlrd matplotlib future
=======
pip install -U --user numpy scipy xlrd matplotlib future unittest
NuGrid/master:README
- Install h5py:
- port install openmpi-gcc5
- port install hdf5 +hl +openmpi +cxx +fortran +gcc5
- HDF5_DIR=~/macports CFLAGS="-I$HOME/macports/include/openmpi-gcc5" pip install -U --user h5py
Errors about failure to rebuild netcdf package can be ignored.
- Set up PYTHONPATH environment variable to point to the parent directory of NuGridPy, e.g.:
export PYTHONPATH="$HOME/NuGrid"
The following command runs a suite of test cases for the NuGridPy package:
python -m NuGridPy.selftest