Design and Implementation of the Delft Molecular-Dynamics Processor

Bakker, A.; Bruin, C.

doi:10.1016/b978-0-12-049260-2.50010-6

Cited by 17 publications

(12 citation statements)

References 20 publications

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“…We are planning to search for this kind of symmetry breaking in realistic systems. When preparing the final version of the present paper, we became aware that Berim and Ruckenstein 32 found that the SSB effect also occurs in the case of the quantum fluid 4 He confined between identical walls of Cs.…”

Section: Discussionmentioning

confidence: 99%

“…About 20 years ago, van Leeuwen and co-workers carried out calculations for simple fluids confined in such a slit geometry on the Delf molecular dynamics ͑MD͒ processor, which was designed ad hoc for MD simulations of this kind of system. 3,4 It was assumed that the atoms of the fluid interact via standard Lennard-Jones ͑LJ͒ potentials with strength f f and size f f parameters. The width of the slit was L = 29.1 f f , which is sufficiently large to avoid any capillary effect and support solid-liquid ͑s-l͒, solid-vapor ͑s-v͒, and liquid-vapor ͑l-v͒ interfaces.…”

Section: Introductionmentioning

confidence: 99%

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Confinement of Ar between two identical parallel semi-infinite walls

Sartarelli

Szybisz

2010

The Journal of Chemical Physics

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The confinement of Ar in planar slits of two identical parallel semi-infinite walls of alkali metals, alkaline-earth metal Mg, and CO 2 is investigated within the framework of the density functional theory. It is assumed that ͑1͒ the fluid atoms interact via a recently proposed effective attractive pair potential with strength, f f , which reproduces the experimental data of the surface tension of the liquid-vapor interface at the bulk coexistence curve, and ͑2͒ the adsorption on the walls is described by ab initio potentials characterized by a well depth, W sf . In this way the systems were studied in the framework of a realistic approach. We found that for small coverages, the slit is always filled by forming two symmetric vapor films, one at each wall. For increasing coverage the behavior depends on the ratio W sf / f f and the temperature T. In the case of alkali metals, we found at the triple point, T t , of the adsorbate a regime of average density av ‫ء‬ in which the ground state exhibits asymmetric density profiles, leading to the so-called spontaneous symmetry breaking ͑SSB͒ effect. The SSB appears at an average density sb1 ‫ء‬ and disappears at a higher average density sb2‫ء‬ . When T is increased, the range of densities sb1 ‫ء‬ Յ av ‫ء‬ Յ sb2 ‫ء‬ diminishes and eventually the SSB disappears at a critical temperature, T sb , which coincides with the critical prewetting temperature T cpw observed in the adsorption on a single wall. For T Ͼ T cpw the slit is filled symmetrically up to the phase transition to capillary condensation. All these features are examined as a function of the strength of the substrate and the width of the slit. Furthermore, no SSB effect was found for Mg and CO 2 .

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Confinement of Ar between two identical parallel semi-infinite walls

Sartarelli

Szybisz

2010

The Journal of Chemical Physics

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“…Specialized hardware for MD has a surprisingly long history: the Delft machine [2], operational in 1982, implemented a 4 MHz arithmetic pipeline similar to one of our PPIPs. Other specialized hardware projects, e.g., FASTRUN [9], MD Engine [26], and MDGRAPE [16], have also accelerated the inner loop of MD calculations using the technology available at the time.…”

Section: Related Workmentioning

confidence: 99%

High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation

Larson

Salmon

Dror

et al. 2008

2008 IEEE 14th International Symposium on High Performance Computer Architecture

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Anton is a massively parallel special-purpose supercomputer designed to accelerate molecular dynamics (MD) simulations by several orders of magnitude, making possible for the first time the atomic-level simulation of many biologically important phenomena that take place over microsecond to millisecond time scales. The majority of the computation required for MD simulations involves the calculation of pairwise interactions between particles and/or gridpoints separated by no more than some specified cutoff radius. In Anton, such range-limited interactions are handled by a high-throughput interaction subsystem (HTIS). The HTIS on each of Anton's 512 ASICs includes 32 computational pipelines running at 800 MHz, each producing a result on every cycle that would require approximately 50 arithmetic operations to compute on a general-purpose processor. In order to feed these pipelines and collect their results at a speed sufficient to take advantage of this computational power, Anton uses two novel techniques to limit inter-and intra-chip communication. The first is a recently developed parallelization algorithm for the range-limited N-body problem that offers major advantages in both asymptotic and absolute terms by comparison with traditional methods. The second is an architectural feature that processes pairs of points chosen from two point sets in time proportional to the product of the sizes of those sets, but with input and output volume proportional only to their sum. Together, these features allow Anton to perform pairwise interactions with very high throughput and unusually low latency, enabling MD simulations on time scales inaccessible to other general-and special-purpose parallel systems. * * Correspondence to shaw@deshaw.com. David E. Shaw is also with the

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“…In fact, there were a number of attempts to develop special-purpose computers for molecular dynamics, and some of them used the pipeline architecture rather similar to GRAPE pipeline (Bakker & Bruin 1988;Fine, Dimmler & Levinthal 1991). We also applied the GRAPE architecture to molecular dynamics, starting with GRAPE-2A (Ito et al 1994).…”

Section: Project Historymentioning

confidence: 99%

Current Status of GRAPE Project

Makino¹

2007

Proc. IAU

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Abstract. I'll summarize the current status of GRAPE project. GRAPE-6, completed in 2002, has been used by a number of people, for a wide variety of problems such as planet formation, star cluster dynamics, galactic nuclei, and cosmology. In 2004, we started the development of the next-generation machine, GRAPE-DR. GRAPE-DR has a architecture radically different from that of previous GRAPEs. It does not have hardwired pipeline for gravitational force calculation but a large number of small and simple programmable processors. This change made it possible to apply GRAPE-DR to a wide range of problems to which GRAPE was not efficient, and at the same time it helps us to explore new algorithms for N-body simulations. The GRAPE-DR chip was completed in 2006, and second prototype board was completed in May 2007. We hope to have full production-level board commercially available by the end of year 2007. A single board will offer the theoretical peak speed of 2 Tflops, about 20 times as that of a single PCI card version of GRAPE-6.

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Design and Implementation of the Delft Molecular-Dynamics Processor

Cited by 17 publications

References 20 publications

Confinement of Ar between two identical parallel semi-infinite walls

Confinement of Ar between two identical parallel semi-infinite walls

High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation

Current Status of GRAPE Project

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