Standards for molecular dynamics modelling and simulation of relaxation

Abstract

An attempt is made to formulate a set of requirements for simulation and modelling of relaxation in dense media. Each requirement is illustrated by examples of numerical simulation of particles with different types of interaction given by softsphere, Lennard -Jones, embedded atom method or Coulomb potential. The approaches developed are expected to be universal for some classes of relaxation processes in liquids, fluids, crystals and plasmas.

Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs

“…LAMMPS has a long history and it was successfully used for similar problems of the nonequilibrium condensed matter simulations (see e.g. [1,2]). It provides good parallelizing efficiency especially at large computing clusters.…”

“…The method of molecular dynamics (MD) is widely used to study static and dynamic properties of the condensed matter [1,2]. In particular this method is indispensable for studying the relaxation of nonequilibrium and metastable states which play essential role in the impulse loading processes such as shock compression, laser ablation, etc.…”

“…These simulations are computationally intensive due to the large MD cell size (many particles), long relaxation period (many time steps) or large number of statistical averages. The general approach for studying the relaxation of metastable states is presented in [2]. Its basic idea is to consider a small system volume but average the results over an ensemble of initial states.…”

Direct simulations of homogeneous bubble nucleation: Agreement with classical nucleation theory and no local hot spots

“…One main conclusion of most of the MD simulations was that CNT generally underestimates bubble nucleation rates by very large factors. However, most of the existing simulations use only around 10 000 or fewer atoms and could be affected by their small simulation volumes [30,31,34] and by errors from * diemand@physik.uzh.ch; http://www.physik.uzh.ch/diemand/ applying methods like forward flux sampling (FFS) to the bubble nucleation process (see Ref. [35] for a discussion of possible problems).…”

Distributed Applications from Scratch: Using GridMD Workflow Patterns

“…Available MD/MC packages (such as NAMD [2] or LAMMPS [1]) provide efficient serial and parallel algorithms for simple execution scenarios, such as to take the system of particles at some initial state and to propagate it through the chain of other states. At higher level the numerical experiment includes statistical averaging [3], parameter sweep, optimal parameter search, etc. While distributed environment looks very promising for these tasks, the researchers face the problem of constructing complicated scenarios and workflows.…”