DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism

Abstract

DL_POLY_3 is a general-purpose massively parallel molecular dynamics simulation package embedding a highly efficient set of methods and algorithms such as: Domain Decomposition (DD), Linked Cells (LC), Daresbury Advanced Fourier Transform (DAFT), Trotter derived Velocity Verlet (VV) integration and RATTLE. Written to support academic research, it has a wide range of applications and can run on a wide range of computers; from single processor workstations to multi-processor computers. The code development has placed particular emphasis on the efficient utilization of multi-processor power by optimised memory workload and distribution, which makes it possible to simulate systems of the order of tens of millions of particles and beyond. In this paper we discuss the new DL_POLY_3 design, and report on the performance, capability and scalability. We also discuss new features implemented to simulate highly non-equilibrium processes of radiation damage and analyse the structural damage during such processes. have introduced the Domain Decomposition (DD) 10 version, DL_POLY_3, to permit simulation of systems of the order of tens of millions of atoms and beyond. As we shall see in the Performance and discussion section, DL_POLY_3's inherent parallelism allows close to perfect parallelisation up to impressively high processor counts.

Novel high-temperature ferroelectric domain morphology in PbTiO3 ultrathin films

“…We studied (001) properties of strained PbTiO 3 ultrathin films under open circuit conditions using molecular dynamics as implemented in the DL POLY code [24]. We used the adiabatic core-shell forcefield derived in Gindele et al, that reproduces the structural parameters of the cubic and tetragonal phases, the Born effective charge tensors, the elastic properties and soft phonon modes of PbTiO 3 in excellent agreement with density functional theory (DFT) calculations [25].…”

Ion migration in crystalline and amorphous HfOX

“…The molecular-dynamics (MD) simulations employed the velocity Verlet algorithm 29 to propagate the system through phase space and the thermostat and barostat by Martyna et al 30 to establish a NpT ensemble (constant particle number N, pressure p, and temperature T ). The DL POLY code 31 was used for all MD simulations. A 10a × 10a × 10a supercell (=12 000 ions) was generated, and 50 oxygen ions were removed from randomly chosen lattice sites.…”

Understanding the Initial Stages of Reversible Mg Deposition and Stripping in Inorganic Nonaqueous Electrolytes

“…All the geometries employed in the AIMD simulations were created by inserting a number of THF molecules at the experimental density (0.889 g/cm 3 ) in the vacuum space between slabs to simulate liquid, resulting in unit cells with ∼ 550 atoms. To accelerate computationally costly AIMD simulations, we performed an intermediate 1 ns pre-equilibration NVT classical molecular dynamics simulation using the CHARMM potential as implemented in DL POLY 26,27 while keeping the coordinates of the surface and adsorbate atoms fixed as obtained from preliminary adsorption calculations. The concentration of the MgCl + salt in the AIMD is 0.30 M and falls in the range of the experimental concentrations 0.25 -0.40 M explored by Aurbach and collaborators.…”