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Moldy: a portable molecular dynamics simulation program for serial and parallel computers. (English) Zbl 1040.81501
Summary: Moldy is a highly portable C program for performing molecular-dynamics simulations of solids and liquids using periodic boundary conditions. It runs in serial mode on a conventional workstation or on a parallel system using an interface to a parallel communications library such as MPI or BSP. The “replicated data” parallelization strategy is used to achieve reasonable performance with a minimal difference between serial and parallel code. The code has been optimized for high performance in both serial and parallel cases.
The model system is completely specified in a run-time input file and may contain atoms, molecules or ions in any mixture. Molecules or molecular ions are treated in the rigid-molecule approximation and their rotational motion is modeled using quaternion methods. The equations of motion are integrated using a modified form of the Beeman algorithm. Simulations may be performed in the usual NVE ensemble or in isobaric and/or isothermal ensembles.
Potential functions of the Lennard-Jones, 6-exp and MCY forms are supported and the code is structured to give an straightforward interface to add a new functional form. The Ewald method is used to calculate long-ranged electrostatic forces.

MSC:
81-08 Computational methods for problems pertaining to quantum theory
81V35 Nuclear physics
Software:
Moldy
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