Some Software developed by the group

Tools

• nbval VALidation of jupyter NoteBooks. Allows to treat documentation or tutorial Notebooks as system tests.

  http://nbval.readthedocs.io

  https://github.com/computationalmodelling/nbval

Data Analysis

• Tools for data analysis at European XFEL (such as extra-data, extra-geom, extra-foam)

  http://https://rtd.xfel.eu/docs/data-analysis-user-documentation/en/latest/

  http://github.com/european-XFEL

COVID data analysis

• Open Science COVID Analysis

  https://oscovida.github.io

  https://github.com/oscovida/oscovida

Micromagnetics

• Ubermag - A Python based domain specific language to express micromagnetic problems, combined with the ability to solve those using OOMMF.

  https://ubermag.github.io

  https://github.com/ubermag/

• OOMMF Docker images

  https://github.com/fangohr/oommf/tree/master/docker

  https://hub.docker.com/r/oommf/oommf

• OOMMF in conda

  Conda-forge: https://anaconda.org/conda-forge/oommf

• OOMMF in Spack

  https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/oommf/package.py

  https://github.com/fangohr/oommf-in-spack

• OOMMF source in get repository

  https://github.com/fangohr/oommf

• ovf2vtk - converts OOMMF's OVF (and OMF) files into VTK files. Useful for (3d) visualisations of fields computed with OOMMF.

  http://www.southampton.ac.uk/~fangohr/software/ovf2vtk/

  http://www.southampton.ac.uk/~fangohr/software/ovf2vtk/dist/

• ngtoucd converts NetGen mesh files to the UCD format that is read by Magpar.

  http://www.magpar.net/static/magpar/doc/html/tools.html

  http://www.magpar.net/static/magpar/doc/html/files.html (part of magpar)

• Oxs_UniaxialAnisotropy4 is an extension of the OOMMF package that provides a fourth order uniaxial anisotropy energy term.

  http://www.southampton.ac.uk/~fangohr/software/oxs_uniaxial4.html

  http://math.nist.gov/oommf/contrib/oxsext/ced_soton/ced_uniaxialanisotropy.html

• Oxs_CubicAnisotropy8 is an extension of the OOMMF package that provides a sixth and eighth order cubic anisotropy term.

  http://www.southampton.ac.uk/~fangohr/software/oxs_cubic8.html

  http://math.nist.gov/oommf/contrib/oxsext/ced_soton/ced_cubic8.html

• nmag is a micromagnetic simulation package.

  https://nmag-project.github.io/index.html

  https://nmag-project.github.io/download.html

  https://github.com/nmag-project and https://github.com/nmag-project/nmag-src

  https://nmag.readthedocs.io/en/latest/

  https://nmag-project.github.io/current/manual/manual.pdf

• ovf2mfm - converts OOMMF's OVF (and OMF) files into VTK files that show the signal from Magnetic Force Microscopy experiments.

  http://www.southampton.ac.uk/~fangohr/software/ovf2mfm

  https://bitbucket.org/fangohr/ovf2mfm

• Virtual micromagnetics environments

  Scripts to create a virtualmachine tailored to provide ready-installed (public domain) micromagnetic simulation packages.

  https://github.com/fangohr/virtualmicromagnetics

  for Azure: https://vmdepot.msopentech.com/Vhd/Show?vhdId=50171

• Mifmaker - create OOMMF MIF configurations files automatically

  https://bitbucket.org/fangohr/mifmaker

  https://bitbucket.org/fangohr/mifmaker

• fidimag - a finite difference micromagnetic tool with Python interface

  https://github.com/fangohr/fidimag

  

• Jupyter OOMMF - embedding OOMMF in the Jupyter Notebook

  (various subprojects at https://github.com/joommf)

Multiphysics simulations

• nsim is a multiphysics simulation library.

  This is part of the Nmag distribution and source code.

  http://nmag-project.github.io

  https://github.com/nmag-project/nmag-src

  http://arxiv.org/abs/0907.1587

• dolfin5tools Tools that allow saving and reading multiple timesteps and FEniCS fields (i.e. dolfin function) to a hdf5 file only the dolfin hdf5 commands, thus working in (MPI) parallel runs

  https://github.com/fangohr/dolfinh5tools

  https://github.com/fangohr/dolfinh5tools/blob/master/doc/tutorial.ipynb

Python

• Delny is a Python package which can be used to make a Delaunay triangulation from a set of n-dimensional points (based on qhull, libqhull).

  <https://bitbucket.org/flub/delny>`__

• nbval - plugin for py.test to validate Jupyter Notebooks

  Re-executes a stored Jupyter notebook, and compares the computed output with the stored output. Deviations result to failed tests. Regular expressions and customised code to sanitise output before comparison can be provided.

  https://github.com/computationalmodelling/nbval

  https://github.com/computationalmodelling/nbval/blob/master/documentation.ipynb

  

• plot_vtk_matplotlib - a library to produce high quality 2d vector field representations from 3d vtk files

  https://github.com/fangohr/plot_vtk_matplotlib

  https://github.com/fangohr/plot_vtk_matplotlib/blob/master/tutorial/plot_vtk_matplotlib_tutorial.ipynb

• Polygon-finite-difference-mesh-tools - given a 2d polygon, fill it with rectangles as well as possible. Useful for cell selection in finite difference simulations.

  https://github.com/fangohr/polygon-finite-difference-mesh-tools

  https://github.com/fangohr/polygon-finite-difference-mesh-tools/blob/master/notebooks/MeshArea.ipynb

  

• Fenics-anisotropic-magneto-resistance - tool that computers the AMR value for a given magnetisation field and applied voltage using FEniCS}. Useful for multi-physics simulations.

  https://github.com/fangohr/fenics-anisotropic-magneto-resistance

  

Utilities

• Aeon is a Python package to help the routine profiling of whole functions and blocks of code within a simulation software.

  https://github.com/logicabrity/aeon

Objective Caml (Ocaml)

• Tutorial on OCaml

• A modified Python interface PyCaml [1]. This has been taken forward in https://github.com/chemoelectric/pycaml (as of 2014)

  https://bitbucket.org/chemoelectric/pycaml

• The Mersenne Twister Random Number Generator for OCaml (mt19937) [1]

• nlog. Logging as with the Python logging module for OCaml [1]

  https://bitbucket.org/fangohr/nmag-src/src/tip/src/nlog.ml, https://bitbucket.org/fangohr/nmag-src/src/tip/src/nlog.mli

• Plotting for NEB method

  https://github.com/davidcortesortuno/nebm_plot_functions

  https://github.com/davidcortesortuno/nebm_plot_functions/blob/master/tutorial/tutorial_fidimag.ipynb

Vortex state (superconductors)

• vdsim - is the Vortex Dynamics SIMulation package. It can simulate the dynamics of pancake vortices in a superconducting layer, or of stiff (rigid) vortices in a film. Provides arbitrary pinning, thermal fluctations, post processing of data.

  http://www.southampton.ac.uk/~fangohr/software/vdsimsoft.html