Massively parallel molecular-dynamics simulation of ice crystallisation and melting: The roles of system size, ensemble, and electrostatics

2014 ◽  
Vol 141 (23) ◽  
pp. 234501 ◽  
Author(s):  
Niall J. English
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
System Size ◽  
Dynamics Simulation ◽  
Massively Parallel ◽  
Parallel Molecular Dynamics

PARALLELIZATION OF A MOLECULAR DYNAMICS SIMULATION OF AN ION-SURFACE COLLISION SYSTEM: Ar–Ni(100)

2005 ◽  
Vol 16 (06) ◽  
pp. 969-990 ◽  
Author(s):  
MURAT ATİŞ ◽  
CEM ÖZDOĞAN ◽  
ZİYA B. GÜVENÇ
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
System Size ◽  
Dynamics Simulation ◽  
Collision System ◽  
Surface Collision ◽  
Speed Up ◽  
Parallel Molecular Dynamics ◽  
Physical Quantities ◽  
Full Simulation

Parallel molecular dynamics simulation study of the ion-surface collision system is reported. A sequential molecular dynamics simulation program is converted into a parallel code utilizing the concept of parallel virtual machine (PVM). An effective and favorable algorithm is developed. Our parallelization of the algorithm shows that it is more efficient because of the optimal pair listing, linear scaling, and constant behavior of the internode communications. The code is tested in a distributed memory system consisting of a cluster of eight PCs that run under Linux (Debian 2.4.20 kernel). Our results on the collision system are discussed based on the speed up, efficiency and the system size. Furthermore, the code is used for a full simulation of the Ar–Ni (100) collision system and calculated physical quantities are presented.

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