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Manuscript Title: The MOLDY short-range molecular dynamics package
Authors: G.J. Ackland, K. D'Mellow, S.L. Daraszewicz, D.J. Hepburn, M. Uhrin, K. Stratford
Program title: MOLDY
Catalogue identifier: AEJU_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 182(2011)2587
Programming language: Fortran 95 / OpenMP.
Computer: Any.
Operating system: Any.
Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution.
RAM: 100 MB or more
Keywords: Molecular dynamics, Embedded atom method, OpenMP.
PACS: 71.15.Pd, 71.20.Be.
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.