pyoculus

A Python version of Oculus - The eye into the chaos: a comprehensive magnetic field diagnostic package for non-integrable, toroidal magnetic fields (and more general 1 1/2-D or 2D Hamiltonian system). Oculus is the Latin word for 'eye'.

Installation

You can obtain the package from PYPI by

pip3 install pyoculus

pyoculus

Definition __init__.py:1

or

pip3 install --user pyoculus

Alternatively, you can clone this repository. In this case, additional steps are needed to compile the FORTRAN interfaces for SPEC magnetic field and PJH. See below.

Usage

To use the package, simply import it in Python:

import pyoculus

Examples can be found in the examples subfolder.

Documentation

The documentation of pyoculus is managed by Doxygen.

You can find the documentation on Github Page: https://zhisong.github.io/pyoculus/

This documentation will be updated regularly but may not be most up-to-date. To generate the documentation from source, please run

make doxygen

The documentation will appear in the subfolder doc/html. Please open doc/html/index.html in your browser.

SPEC magnetic field and Pressure Jump Hamiltonian (PJH)

Some additional steps are needed to run pyoculus on outputs generated by the Stepped Pressure Equilibrium Code or SPEC.

Pre-requisite

You will need the py_spec package to read a SPEC output file and give it to pyoculus. However, py_spec is not a requirement for pyoculus. Link to py_spec

Compilation

If you are not obtaining the package via PYPI, to use the pyoculus on SPEC magnetic field and PJH, please compile the Fortran modules for SPEC by

pip3 install -e .

Alternatively, you can manually compile *.f90 in pyoculus/problems/SPECfortran using f2py to generate a module pyoculus_spec_fortran_module. This is not recommended.

Documentation for f2py can be found here.

Developers

Zhisong Qu (zhiso.nosp@m.ng.q.nosp@m.u@anu.nosp@m..edu.nosp@m..au)
Arunav Kumar (aruna.nosp@m.v.ku.nosp@m.mar@a.nosp@m.nu.e.nosp@m.du.au)
Stuart Hudson (shuds.nosp@m.on@p.nosp@m.ppl.g.nosp@m.ov)

Link to the original Oculus package:

Github: https://github.com/SRHudson/Oculus

Documentation: https://w3.pppl.gov/~shudson/Oculus/oculus.pdf