Description:
ytree 3.2.1
ytree
This is ytree, a yt extension for
working with merger tree data.
Structure formation in cosmology proceeds in a hierarchical fashion,
where dark matter halos grow via mergers with other halos. This type
of evolution can be conceptualized as a tree, with small branches
connecting to successively larger ones, and finally to the trunk. A
merger tree describes the growth of halos in a cosmological
simulation by linking a halo appearing in a given snapshot to its
direct ancestors in a previous snapshot and its descendent in the next
snapshot.
Merger trees are computationally expensive to generate and a great
number of codes exist for computing them. However, each of these codes
saves the resulting data to a different format. ytree is Python
package for reading and working with merger tree data from multiple
formats. If you are already familiar with using
yt to analyze snapshots from
cosmological simulations, then think of ytree as the yt of merger
trees.
To load a merger tree data set with ytree and print the masses of
all the halos in a single tree, one could do:
>>> import ytree
>>> a = ytree.load('tree_0_0_0.dat')
>>> my_tree = a[0]
>>> print(my_tree['tree', 'mass'].to('Msun'))
[6.57410072e+14 6.57410072e+14 6.53956835e+14 6.50071942e+14 ...
2.60575540e+12 2.17122302e+12 2.17122302e+12] Msun
A list of all currently supported formats can be found in the online
documentation. If
you would like to see support added for another format, we would be
happy to work with you to make it happen. In principle, any type of
tree-like data where an object has one or more ancestors and a single
descendent can be supported.
Installation
ytree can be installed with pip or conda:
pip installation
pip install ytree
conda installation
conda install -c conda-forge ytree
source installation
To get the development version, clone this repository and install like this:
git clone https://github.com/ytree-project/ytree
cd ytree
pip install -e .
Getting Started
The ytree documentation will walk you
through installation, get you started analyzing merger trees, and help
you become a contributor to the project. Have a look!
Sample Data
Sample data for all merger tree formats supported by ytree is available on the
yt Hub in the
ytree data collection.
Contributing
ytree would be much better with your contribution! As an extension of
the yt Project, we follow the yt
guidelines for contributing.
Citing ytree
If you use ytree in your work, please cite the following:
Smith et al., (2019). ytree: A Python package for analyzing merger trees.
Journal of Open Source Software, 4(44), 1881,
https://doi.org/10.21105/joss.01881
For BibTeX users:
@article{ytree,
doi = {10.21105/joss.01881},
url = {https://doi.org/10.21105/joss.01881},
year = {2019},
month = {dec},
publisher = {The Open Journal},
volume = {4},
number = {44},
pages = {1881},
author = {Britton D. Smith and Meagan Lang},
title = {ytree: A Python package for analyzing merger trees},
journal = {Journal of Open Source Software}
}
If you would like to also cite the specific version of ytree used in
your work, include the following reference:
@software{britton_smith_2022_7335683,
author = {Britton Smith and
Meagan Lang and
Juanjo Bazán},
title = {ytree-project/ytree: ytree 3.2.0 Release},
month = nov,
year = 2022,
publisher = {Zenodo},
version = {ytree-3.2.0},
doi = {10.5281/zenodo.7335683},
url = {https://doi.org/10.5281/zenodo.7335683}
}
Resources
The latest documentation can be found at
https://ytree.readthedocs.io.
The ytree
paper in the
Journal of Open Source Software.
ytree is an extension of the yt
Project. The yt-project community
resources can be used
for ytree-related communication. The ytree developers can usually
be found on the yt project Slack channel.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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