Make a resampling tree visual after running a WE simulation.
This tutorial contains the code necessary to generate a resampling tree with a Wepy simulation hdf5 file. A small, example hdf5 file is provided. This file has a 25 cycle, 12 trajectory dataset and an observable used for coloring of nodes. This tree can be visualized in Gephi.
Adapted from: https://gitlab.com/nmroussey/resampling_tree_tutorial Converted from compatibility with wepy h5 to westpa h5 files (in progress).
If you have generated a Wepy hdf5 file, your environment should already contain all necessary packages.
Wepy: pip install wepy[all]
NumPy, NetworkX, and sys are also required.
- run_restree_gen.py
The script to run to generate the tree. Arguments are: input h5 file and output file name.
- restree/
The codes required to make the tree.
- example_input.wepy.h5
A sample wepy output file.
In your enviornment that contains Wepy do:
python run_restree_gen.py example_input.wepy.h5 test_outfile.gexf
This will generate a .gexf file for use in 'Gephi'. Data included is nodes and edges, weights/probabilities (for node size), and an extra piece of information named COM, for coloring the tree.
NOTE: No merging and cloning is visible in this tree due to the short length of the simulation. This is not a mistake in the tree generation code.
'Wepy'
'NumPy'
'Gephi'
'Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling' Lotz, S., & Dickson, A., ACS Omega, 2020
ENV: conda install -c condo-forge mdtraj pip install wepy[all] Downgrade numpy to 1.23.* (pip install numpy=1.23)