nMoldyn: a program package for the calculation and analysis of neutron scattering spectra from MD simulations
nMoldyn is a software package designed to perform various calculations on the basis of MD simulation trajectories. The first and being still independently developed version of a similar program was written in Fortran 77 in early 90's by Gerald Kneller and coworkers. Implementation of nMoldyn in Python was started in 1999 by Tomasz Róg and was later continued by Krzysztof Murzyn. Konrad Hinsen has contributed at various stages of developing this package.
The Python version of nMoldyn makes use of advanced algorithms implemented in the Fortran version; however, in many aspects it's different from its great predecessor:
- it's coded in Python - a modern object oriented language,
- it uses MMTK, Numerical and Scientific Python modules,
- it has a user-friendly graphical interface,
- it enables parallel computations,
- it has an extended set of calculated functions.
Amongst the steadily growing number of properties which can be be calculated with nMoldyn, one can particularly acknowledge rapid computation of:
- neutron-scattering related properties (coherent and incoherent scattering functions, structure factors),
- dynamic properties (mean square displacement and diffusion constants, velocity autocorrelation function and its power spectrum, angular velocity autocorrelation function and reorientational correlation function, etc.)
In addition to this, a very basic analysis of the calculated data can be performed. A trajectory can be digitally filtered in the frequency domain, allowing to visualise selected atomic motions of interest. Why nMoldyn is unique? That's simple. We put an enormous effort to make using this program extremely easy but at the same time it's possible to perform highly sophisticated analysis with it. In fact, its applications are only limited by a user creativity. This is because nMoldyn takes in an input file which is a Python program and it's as limited as a computer program can be...