oommfpy 1.3

Minimal Python lib to process OOMMF format output files

   .+------+-------+-------+-------+-------+-------+-------+
 .'      .'      .'      .'      .'      .'      .'      .'|
+---+--+'------+'------+'------+'------+'------+'------+'  -
|      |       |       |       |       |       |       |   |
|   O  +   O   +   M   +   M   +   F   +   P   +   Y   +   +
|      |       |       |       |       |       |       | .'
+------+'------+'------+'------+-------+-------+-------+'

OOMMFPy

A very minimal and simple Python library to read and extract data from OOMMF magnetisation files omf, which are also used in MuMax3. In addition to this library we provide tools to plot omf files and convert them to vtk files.

Highlights:

• Read omf files in any format
• Can also read ovf files and MuMax3 files
• Painless conversion of the data in an omf file into Numpy arrays for data analysis
• Fast calculation (using Numpy) of the skyrmion number in a slice of the system in any plane orientation (xy, xz, yz)
• Fast reading of omf files in binary format (using Numpy's fromfile)
• Minimal and super fast tool to convert omf files to VTK format
• Plot functions
• Early support for Paraview plugin: read omf files directly!

Install

The easiest is to use pip or poetry to install the package from PyPI

pip install oommfpy

The Github address can also be directly used to install the package via pip

pip install git+https://github.com/davidcortesortuno/oommfpy

Alternatively, a setup.py file is provided to install this library

git clone https://github.com/davidcortesortuno/oommfpy
cd oommfpy
pip install ./

If successful, the plot_omf and omf2vtk tools are installed in the corresponding bin directory and can be called from the command line.

A C library is built with the installation process, thus the setup file tries to install Cython if is not present in the system.

Paraview plugin

A first version of a reader for Paraview is added in this last version. For now the installation is a bit of a hack:

• After installing the oommfpy library, locate the oommfpy folder from thesite-packages directory

• Download the latest version of Paraview with Python > 3.8 support

• Copy the oommfpy directory into the Paraview Python site-packages folder. For example, for Paraview 5.9.0 installed in the home folder:

  cp -r oommfpy $HOME/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/lib/python3.8/site-packages/
  

• Open Paraview and go to Tools -> Manage Plugins -> Load New and select the Python file in the tools/ folder of oommfpy (you can clone the repository)

• Now you can open any omf file without converting to VTK!

Documentation

For now check the doc/ipynb folder which contains a tutorial with basic functionality. To load a file with a magnetisation field, which is found more commonly in simulations, use the MagnetisationData class. To load any field, such as the dipolar field, use the FieldData class.

Scripts to convert omf to VTK can be called directly as, for example,

omf2vtk -i omfs/my_oommf_output.omf -o test.vtk

The input path can also be a directory or a path with a wildcard, e.g. omfs/*.omf. This method assumes the files in the path come from the same simulation as the tool loads the mesh from the first file in the path and then only updates the magnetisation fields.

Similar options are provided for the plot_omf function. Use the --help for details.

TODO

• More tests
• Add pyproject.toml file to avoid manual installation of Cython in setup.py
• More options to plotting library
• Print z coordinate when computing sk number
• Allow Periodic boundaries for the skyrmion number calculation
• Add typing check
• Support for multiple OS

Citation

If you find this library useful, please cite this repository as:

@Misc{Cortes2019,
  author       = {David Cort{\'e}s-Ortu{\~n}o},
  title        = {OOMMFPy},
  howpublished = {Zenodo doi:10.5281/zenodo.2611194. Github: https://github.com/davidcortesortuno/oommfpy},
  year         = {2019},
  doi          = {10.5281/zenodo.2611194},
  url          = {https://doi.org/10.5281/zenodo.2611194},
}