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The MOLDY short-range molecular dynamics package

Research output: Contribution to journalArticle

Original languageEnglish
Pages (from-to)2587-2604
Number of pages18
JournalComputer Physics Communications
Volume182
Issue number12
DOIs
StatePublished - Dec 2011

Abstract

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelisecl using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy.

Program summary

Program title: MOLDY

Catalogue identifier: AEJU_v1_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: GNU General Public License version 2

No. of lines in distributed program, including test data, etc.: 382 881

No. of bytes in distributed program, including test data, etc.: 6 705 242

Distribution format: tar.gz

Programming language: Fortran 95/OpenMP

Computer: Any

Operating system: Any

Has the code been vectorised or parattelized?: Yes. OpenMP is required for parallel execution

RAM: 100 MB or more

Classification: 7.7

Nature of problem: Moldy addresses the problem of many atoms (of order 106) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture. twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces.

Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals.

Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order-N scaling will fail. Different interatomic potential forms require recompilation of the code.

Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects.

Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop. (C) 2011 Elsevier B.V. All rights reserved.

    Research areas

  • Molecular dynamics, Embedded atom method, OpenMP, ALPHA-IRON, INTERATOMIC POTENTIALS, POSITRON-ANNIHILATION, THERMAL-EQUILIBRIUM, TRANSITION-METALS, IMPURITIES, SIMULATION, MODEL, SYSTEMS, COPPER

ID: 1187731