UMMAP: a statistical analysis software package for molecular modelling

摘要

Universal Molecular Modelling Analysis Package (UMMAP) is a software package designed to provide a command line driven analysis suite for particle-based simulation codes. It is developed to work closely alongside the mesoscale dissipative particle dynamics software embedded in DL_MESO, and the molecular dynamics codes NAMD and LAMMPS. UMMAP is designed to be extendable to other modelling software. UMMAP is targeted at users working in the computational soft matter field and those looking for an 'all-in-one' analytical software package. It offers a unique mix of analytical tools, from widely used geometrical analyses (e.g. bond and angles distributions, structure factor, radial distributions and density profiles), to specific solutions for the soft matter community (e.g. polymer statistics, critical micelle concentration and cluster/micelle shape analyses). It provides the possibility, for a more expert user, to build in additional bespoke analyses, whilst benefiting from UMMAP's core functionality. It is very flexible in the way it reads and analyses the trajectory, allowing for several tools to be used at the same time via a single command line input. A rational set of software flags and detailed error messages render UMMAP ergonomic and user friendly while output integrity is ensured by storing manifest files to prevent the storage of unrelated material.