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236
Large-scale molecular-dynamics study of the nucleation process of martensite in Fe-Ni alloys
"... Abstrac t. High-performance large-scale molecular-dynamics (MD) simulations provide an atom-istic insight of the nucleation process in FesoNi2o- With the MD code SPaSM (Scalable Parallel Short-range Molecular Dynamics [1]) it is possible to follow the nucleation and further growth of the martensite ..."
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Abstrac t. High-performance large-scale molecular-dynamics (MD) simulations provide an atom-istic insight of the nucleation process in FesoNi2o- With the MD code SPaSM (Scalable Parallel Short-range Molecular Dynamics [1]) it is possible to follow the nucleation and further growth of the martensite
Fast Parallel Algorithms for Short-Range Molecular Dynamics
- JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 653 (7 self)
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dynamics models which can be difficult to parallelize efficiently -- those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed--memory parallel machine which allows for message--passing of data between independently executing processors
Feeding a Large-scale Physics Application to Python
- In 6th International Python Conference
, 1997
"... We describe our experiences using Python with the SPaSM molecular dynamics code at Los Alamos National Laboratory. Originally developed as a large monolithic application for massively parallel processing systems, we have used Python to transform our application into a flexible, highly modular, and e ..."
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Cited by 12 (1 self)
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developing a largescale physics code for performing molecular-dynamics simulations of materials. This code, SPaSM (Scalable Parallel Short-range Molecular-dynamics), was originally developed for the Connection Machine 5 massively parallel supercomputing system and later moved to a number of other machines
Scalable molecular dynamics with NAMD.
- J Comput Chem
, 2005
"... Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and la ..."
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Cited by 849 (63 self)
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Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop
NAMD2: Greater Scalability for Parallel Molecular Dynamics
- JOURNAL OF COMPUTATIONAL PHYSICS
, 1998
"... Molecular dynamics programs simulate the behavior of biomolecular systems, leading to insights and understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this ..."
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Cited by 322 (45 self)
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Molecular dynamics programs simulate the behavior of biomolecular systems, leading to insights and understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness
A Parallel Scalable Approach to Short-Range Molecular Dynamics on the CM-5
- In Proc. Scalable High Performance Computing Conference--92
, 1992
"... We present an scalable algorithm for short-range Molecular Dynamics which minimizes interprocessor communications at the expense of a modest computational redundancy. The method combines Verlet neighbor lists with coarse-grained cells. Each processing node is associated with a cubic volume of space ..."
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Cited by 3 (0 self)
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We present an scalable algorithm for short-range Molecular Dynamics which minimizes interprocessor communications at the expense of a modest computational redundancy. The method combines Verlet neighbor lists with coarse-grained cells. Each processing node is associated with a cubic volume of space
Modeling Dynamic Load Balancing in MolecularDynamics to Achieve Scalable Parallel Execution
"... ..."
Comparison of PVM and MPI performance in short-range molecular dynamics simulation
"... In this paper we compare timing results for short-range 12/6 Lennard-Jones parallel molecular dynamics 3D simulation using two programming environments PVM and MPI on HP Exemplar SPP computers. The results obtained on Intel Paragon XP/S are also reported. ..."
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In this paper we compare timing results for short-range 12/6 Lennard-Jones parallel molecular dynamics 3D simulation using two programming environments PVM and MPI on HP Exemplar SPP computers. The results obtained on Intel Paragon XP/S are also reported.
Molecular Dynamics for 400 Million Particles with Short-Range Interactions
- IEEE Comp. Sot
, 1996
"... We report the design and performance of a computational molecular dynamics (MD) code for 400 million particles interacting through the standard pairwise 6--12 Lennard-Jones potential on a 1024-node Intel Paragon, a distributed-memory MIMD parallel computer. The initially recorded "particle-step ..."
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Cited by 1 (0 self)
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We report the design and performance of a computational molecular dynamics (MD) code for 400 million particles interacting through the standard pairwise 6--12 Lennard-Jones potential on a 1024-node Intel Paragon, a distributed-memory MIMD parallel computer. The initially recorded "
Large-Scale Molecular-Dynamics Simulation of 19 Billion Particles
- Int. J. Modern Phys. C
, 2004
"... We have performed parallel large-scale molecular-dynamics simulations on the QSCmachine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a ..."
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Cited by 10 (1 self)
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We have performed parallel large-scale molecular-dynamics simulations on the QSCmachine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a
Results 1 - 10
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236
