About lionanalysis

Author:

Matti Hellström

lionanalysis is a command-line program that analyses frames with atomic coordinates. It is particularly good at extracting atoms with some special environment. When the frames are trajectories from molecular dynamics simulations, various time correlation functions can be calculated.

It reads a text input file and produces text output files.

It is possible to read/plot the results files in gnuplot or using Python with numpy and pandas. See the Examples.

Quickstart

Features

Extract atoms with given atomic environments, and do the below analysis only for the atoms that fulfill your criteria:

  • Visualize interesting atomic environments

  • Radial distribution functions

  • Angular distribution functions

  • Number density along axis

  • Histograms of coordination numbers

  • Bond life time (hydrogen bonds, metal-ligand bonds, …)

  • Species life time (hydroxide ion lifetime, …)

    • Stable states picture

    • Intermittent time correlation function

    • Continuous time correlation function

  • Proton transfer free energy landscape

  • Mean squared displacement, diffusion coefficient

    • Follow multiple Grotthuss-diffusing hydroxide/hydronium ions!

  • Velocity autocorrelation function, power spectrum

  • Determine coordination polyhedra

Who should use lionanalysis?

If you run simulations that are more “atomistic” than “molecular”, and the system size is no more than a few thousand atoms or so, then lionanalysis is for you!

Lionanalysis is designed around atomic environments. It is easy to detect that a C atom is bonded to 1 H and 2 C, and that those carbons are themselves also bonded to 1 H and 2 C, but it’s very difficult to set up lionanalysis to determine if a C atom is part of a benzene molecule.

If you already know which atoms are part of benzene molecules, you can set up lionanalysis to do analysis on those. But they will be treated as atoms, not as molecules. For example, when calculating mean squared displacement, you do so on the atomic positions and not on the center of mass of each molecule.

Current limitations

  • Only orthorhombic simulation boxes are supported

  • Mean squared displacement of atoms, not center-of-mass-of-molecule

Compilation

You need a C++11 compiler. Compilation should be as easy as:

cd src && make

See the Makefile for details.

lionanalysis has only been tested on Linux, but should in principle also work on other platforms.

Running the program

Copy the lionanalysis.exe executable created by the compilation to somewhere on your PATH.

Check your installation:

lionanalysis.exe --help

To run an input file:

lionanalysis.exe name-of-input-file

There are various flags, run lionanalysis.exe --help to see them. Options specified on the command line will typically override any options given in the input file. The default name of the input file is “ionanalysis.config”. See also the standalone olblock.sh utility.

References