Improve analysis (rerun, on the fly output)

[rc83]

Faunus do – beside running MC simulations – also analysis of data. It would be beneficial to perform the same analysis on an existing trajectory without actually running the simulation. It shall be considered that several properties may change during the simulation, e.g., an atomic charge, and not all formats can handle them, e.g., xtc format stores only atomic coordinates, pqr format stores coordinates, charges and radii.

The analysis is performed in parallel to the simulation. However only summary values are usually written at the end. It can be reasonable to write out the analysis result progressively. Either values for every (n-th) step if desirable or as an average over a block of n steps. The output can be written to separate files or in various formats, e.g., csv, hdf5, depending on the nature of data.

[mlund]

mdtraj uses an HDF5 trajectory format that I suspect could be expanded with charges:

• http://mdtraj.org/1.9.3/hdf5_format.html.
• c++ library: https://github.com/BlueBrain/HighFive
• c++17 library: https://github.com/DavidAce/h5pp