Setting up the python tools

Introduction

This document describes the use of Python for processing MPI-AMRVAC simulation data. Both the reading of native .dat- and vtk-filetypes (.vtu, .pvtu, .vti) are supported. The goal of these Python tools is to provide additional data-analysis support with main focus on 1D and 2D simulation data, although there is functionality to read in and process 3D datasets.

All Python tools are located in the directory $AMRVAC_DIR/tools/python. This folder contains a setup script to install the package, a small readme with some instructions and finally the subdirectory amrvac_pytools itself, containing the Python tools for both the .dat files and .vtk files.

These tools were originally initiated by Oliver Porth (in particular the vtk readers), and have recently been refactored and extended to include datfile support by Niels Claes and Clément Robert.

Installation

Prerequisites

The Python tools depend on a few standard packages:

• SciPy which bundles essential numerical tools
• matplotlib as a plotting backend
• IPython which provides a command-line interface for interactive use
• vtk for image processing and visualisation

Setting up

The tools are packed into a handy Python package, which is continuously further developed and improved. We recommend installing it with develop arguments, so that it does not need to be reinstalled with each update. This can be done in three distinct ways:

1. Using conda (recommended)

    cd $AMRVAC_DIR/tools/python
    conda install conda-build
    conda develop .
   

2. Using pip

    cd $AMRVAC_DIR/tools/python
    pip install -e .
   

3. Simply vanilla python

    cd $AMRVAC_DIR/tools/python
    python setup.py develop
   

   Alternative method

Ofcourse, adding the folder directly to your PYTHONPATH works as well but is not recommended.

1. Expanding the PYTHONPATH environment variable
   • [Mac, Linux] Simply type the following in your bash shell:

     export PYTHONPATH=$AMRVAC_DIR/tools/python:$PYTHONPATH
     

   • [Windows] Windows users can modify the environment variables using the control panel:

     Start > Control panel > Edit the system environment variables >
     tab 'advanced' > environment variables
     

     Create or edit the variable PYTHONPATH in the system variables list, where you add the full path to .../amrvac/tools/python. Multiple paths for a single environment variable are separated by a semicolon ';'.