Implementation of a cylindrical distribution function for the analysis of anisotropic molecular dynamics simulations
Richard J. Mandle
Abstract
The cylindrical distribution function (CDF) is a convenient anisotropic analogue of the radial distribution function, the difference being the use of cylindrical shells for binning. As such, CDF analysis can be a powerful tool for the analysis of positional correlations within anisotropic systems, such as liquid crystals. Here we describe a lightweight Python tool, cylindr, for the calculation of cylindrical distribution function, which is compatible with the output of a number of popular MD engines. We demonstrate the use of cylindr in computing the CDF of a number of exemplar materials: classical and ferroelectric nematics; lamellar and columnar liquid crystals.
Topics & Concepts
Molecular dynamicsDynamics (music)Function (biology)Statistical physicsPhysicsDistribution (mathematics)AnisotropyBiologyMathematicsMathematical analysisEvolutionary biologyOpticsQuantum mechanicsAcousticsAdvanced Chemical Physics StudiesSpectroscopy and Quantum Chemical StudiesAdvanced Physical and Chemical Molecular Interactions