You will find on this page computer software and documentation, including slides from computer-related seminars.

Scientific software

RMPCDMD

The software for my nanomotor and chemically active colloids simulations. Open-source and available at https://github.com/pdebuyl-lab/RMPCDMD

H5MD

H5MD is not a software in itself, but a specification based on HDF5 to store simulation data. The development of the specification is made at Savannah, where we have a project page.

The specification is found here and has been presented in P. de Buyl, P. Colberg and F. Höfling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. (2014) - [arXiv:1308.6382].

pyMPCD

pyMPCD is a hydrodynamical simulation module in Python/Fortran. The code is available on GitHub https://github.com/pdebuyl/pyMPCD

vmf90

vmf90 is a software for the numerical resolution of the Vlasov equation. The code is available on GitHub https://github.com/pdebuyl/vmf90 and has been presented in P. de Buyl, The vmf90 program for the numerical resolution of the Vlasov equation for mean-field systems , Comp. Phys. Comm. (2014) - [arXiv.org:1310.0805].

ParseText

ParseText is a small Fortran 95 library that allows to parse simple text files. If your files looks like

  alpha = 1.41d0
  N = 128

you can use the following in your Fortran code

  alpha = PTread_d(CF,'alpha')
  N = PTread_i(CF,'N')

where CF is the data structure of ParseText, PTread_d allows to read double precision variable, PTread_i is for integer. Other kinds are provided.