PROGRAM SUMMARY
Title of program:
Moldy
Catalogue identifier:
ADLT
Ref. in CPC:
126(2000)310
Distribution format: tar gzip file
Operating system: Unix, VAX/VMS, OpenVMS, DOS, Windows 95
High speed store required:
128K words
Number of bits in a word:
64
Number of lines in distributed program, including test data, etc:
63313
Keywords:
Molecular dynamics, Condensed matter, Simulation, Parallel, Coulombic,
Solid state physics, Other.
Programming language used: C
Computer:
Cray PVP ,
Cray T3D, T3E ,
IBM SP2 ,
SGI Origin 2000 ,
Convex Exemplar .
Nature of physical problem:
Statistical thermodynamics of liquids and solids.
Method of solution
Molecular dynamics simulation. The model system consists of atoms and
molecules interacting via pairwise potentials of various forms.
Arbitrary admixtures of different atomic or molecular species are
allowed. Electrostatic contributions to the interaction are modelled
as point-charges and the Ewald sum is used to calculate the long-range
part of the interaction. Periodic boundary conditions are applied and
simulations may be performed in the usual NVE ensemble or in NVT,
NsigmaH or NsigmaT ensembles.
Restrictions on the complexity of the problem
Polyatomic molecules are modelled in the rigid-molecule approximation.
Only pairwise central force models and point-charge electrostatics are
allowed. Many-body forces, polarizable atoms, point dipoles or higher
multipoles are not supported.
Typical running time
0.71s/timestep on DEC Alpha 5/266 for a system of 256 TIP4P water
molecules. Scales linearly with N, the number of particles for
non-coulombic systems, as N3/2 for coulombic systems.
Unusual features of the program
(a) The minimum-image convention, usual in periodic simulations is not
applied. Instead, all images of a particle within the cut-off radius
are considered.
(b) A rigid surface or cage can be treated as a special type of molecule
known as a "framework" which periodically repeats to fill space.
(c) There is a new "skew start" method for generating initial
configurations for liquid simulations.
(Programming language: The program conforms to the ISO/IEC standard
[1] and uses only the standard libraries with very minor exceptions.
Function prototypes are not used for compatibility with compilers for
Kernighan and Ritchie C [2] and it should be possible to compile on
these systems too.
The code vectorizes with the aid of options instructing the compiler to
ignore apparent vector dependencies. The SPMD model of parallelism is
supported with interfaces to a variety of communications libraries.
The program uses 1-512 processors.)
References
[1] International Standard for the C programming language, 1990.
ISO/IEC 9899:1990.
[2] B.W. Kernighan and D. Ritchie, The C Programming language, (Prentice
Hall, Cambridge, 1st edn., 1978).