zoo

Peridynamics data visualization tool

Installation

Conda:

The full set of dependencies for Zoo is quite complex. It's recommended that you create a new environment for Zoo to avoid any conflicts. This can be done with

conda create -n zooenv -c conda-forge -c hallrc zoo

Note: The name of the environment can be anything, and is zooenv in this example.

You can install the Zoo package in the standard way with

conda install -c conda-forge -c hallrc zoo

(conda-forge must be included for dependencies.)

The Zoo package can be updated with

conda update -c conda-forge -c hallrc zoo

Zoo is not currently available through PIP.

Usage

After activating the relevant environment (e.g. conda activate zooenv), open Zoo from the command line with

zoo

At which point, a file can be opened through the usual File > Open, with ctrl+O, or by dragging a file into the window.

A file can be opened immediately by including it as an argument when opening Zoo.

zoo path/to/file.h5

If you want to, Zoo can be opened from within Python with

import zoo
zoo.run()

Zoo currently accepts two types of files:

1. An hdf5 file that has been written using the Pandas "table" format under the field "data". i.e. A file created with

   dataframe.to_hdf(target_file, "data", "w", format="table")

   The first set of indeces must be the timestep, and six columns are expected: x1, x2, x3, and u1, u2, u3.

2. An Emu grid file that is either comma-separated (CSV) or whitespace-separated. The first row of the file is ignored, and the first four columns are expected to be the x-y-z coordinates and the material number. Any extra columns are ignored.

Note: The file type is inferred from the extension. The compatible file extensions are currently .hdf5 and .h5 for an hdf5 file, and .grid and .csv for a grid file.

Warning: Currently, not all memory is released when a tab is closed. Zoo may need to be restarted to recover memory after opening and closing many files.