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.

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Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.