ytree 2.3

An extension of yt for working with merger-tree data.

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:

pip install ytree

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

Below is a notebook that demonstrates how to use ytree with merger tree data. For more information, see the full ytree documentation.

• Introduction

Sample Data

Sampled 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:

Britton Smith, & Meagan Lang. (2018, February 16). ytree: merger-tree toolkit. Zenodo.
https://doi.org/10.5281/zenodo.1174374

For BibTeX users:

  @misc{britton_smith_2018_1174374,
    author       = {Britton Smith and
                    Meagan Lang},
    title        = {ytree: merger-tree toolkit},
    month        = feb,
    year         = 2018,
    doi          = {10.5281/zenodo.1174374},
    url          = {https://doi.org/10.5281/zenodo.1174374}
  }

If possible, please also add a footnote pointing to https://ytree.readthedocs.io.

Resources

• The latest documentation can be found at https://ytree.readthedocs.io

• 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.